Starting phenix.real_space_refine on Fri Mar 6 04:37:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbd_27280/03_2026/8dbd_27280.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.280 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 204 5.16 5 C 17784 2.51 5 N 4980 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28464 Number of models: 1 Model: "" Number of chains: 24 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 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: 6.06, per 1000 atoms: 0.21 Number of scatterers: 28464 At special positions: 0 Unit cell: (128.24, 138.545, 140.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 24 15.00 O 5472 8.00 N 4980 7.00 C 17784 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: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 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 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 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 284 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 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 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 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 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 284 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 314 removed outlier: 3.633A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 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 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 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 284 removed outlier: 3.667A 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 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 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 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 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 284 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 314 removed outlier: 3.632A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 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 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 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 284 removed outlier: 3.665A 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 314 removed outlier: 3.631A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 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 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 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 284 removed outlier: 3.666A 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 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 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 Processing helix chain 'G' and resid 147 through 159 Processing helix chain 'G' and resid 161 through 164 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 284 removed outlier: 3.666A 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 314 removed outlier: 3.632A pdb=" N SER G 314 " --> pdb=" O TYR G 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 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 Processing helix chain 'H' and resid 147 through 159 Processing helix chain 'H' and resid 161 through 164 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 284 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 314 removed outlier: 3.632A pdb=" N SER H 314 " --> pdb=" O TYR H 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 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 Processing helix chain 'I' and resid 147 through 159 Processing helix chain 'I' and resid 161 through 164 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 284 removed outlier: 3.667A 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 314 removed outlier: 3.631A pdb=" N SER I 314 " --> pdb=" O TYR I 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 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 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 161 through 164 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 284 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 314 removed outlier: 3.631A pdb=" N SER J 314 " --> pdb=" O TYR J 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 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 Processing helix chain 'K' and resid 147 through 159 Processing helix chain 'K' and resid 161 through 164 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 284 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 314 removed outlier: 3.632A pdb=" N SER K 314 " --> pdb=" O TYR K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 24 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 Processing helix chain 'L' and resid 147 through 159 Processing helix chain 'L' and resid 161 through 164 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 284 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 314 removed outlier: 3.632A pdb=" N SER L 314 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.698A 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: 6.745A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.698A 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: 6.745A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.745A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.217A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.745A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.745A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.746A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS G 5 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL G 56 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE G 7 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 53 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL G 88 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE G 55 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS G 123 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET G 127 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE G 124 " --> pdb=" O ASP G 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 145 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.745A pdb=" N MET G 222 " --> pdb=" O THR G 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY G 251 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS G 250 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS H 5 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL H 56 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE H 7 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 53 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL H 88 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE H 55 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS H 123 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET H 127 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU H 145 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.746A pdb=" N MET H 222 " --> pdb=" O THR H 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY H 251 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS H 250 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS I 5 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL I 56 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE I 7 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 53 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 88 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE I 55 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS I 123 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET I 127 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE I 124 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU I 145 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.746A pdb=" N MET I 222 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY I 251 " --> pdb=" O MET I 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS I 250 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS J 5 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL J 56 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE J 7 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL J 53 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 88 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE J 55 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS J 123 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET J 127 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE J 124 " --> pdb=" O ASP J 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU J 145 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.745A pdb=" N MET J 222 " --> pdb=" O THR J 249 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLY J 251 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS J 250 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS K 5 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL K 56 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE K 7 " --> pdb=" O VAL K 56 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL K 53 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 88 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE K 55 " --> pdb=" O VAL K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS K 123 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET K 127 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE K 124 " --> pdb=" O ASP K 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU K 145 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.744A pdb=" N MET K 222 " --> pdb=" O THR K 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY K 251 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS K 250 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS L 5 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL L 56 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE L 7 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL L 53 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL L 88 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE L 55 " --> pdb=" O VAL L 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS L 123 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET L 127 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 124 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU L 145 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 6.699A 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: 6.746A pdb=" N MET L 222 " --> pdb=" O THR L 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY L 251 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS L 250 " --> pdb=" O THR L 272 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9014 1.33 - 1.45: 3429 1.45 - 1.57: 16117 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 28860 Sorted by residual: bond pdb=" O4 PO4 I 402 " pdb=" P PO4 I 402 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O4 PO4 K 402 " pdb=" P PO4 K 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 28855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 35459 1.17 - 2.33: 2827 2.33 - 3.50: 475 3.50 - 4.66: 218 4.66 - 5.83: 69 Bond angle restraints: 39048 Sorted by residual: angle pdb=" C LEU H 27 " pdb=" N GLY H 28 " pdb=" CA GLY H 28 " ideal model delta sigma weight residual 120.10 115.70 4.40 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta sigma weight residual 120.10 115.71 4.39 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU E 27 " pdb=" N GLY E 28 " pdb=" CA GLY E 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 ... (remaining 39043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 15588 15.96 - 31.92: 1428 31.92 - 47.88: 432 47.88 - 63.84: 144 63.84 - 79.80: 48 Dihedral angle restraints: 17640 sinusoidal: 6888 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER I 8 " pdb=" C SER I 8 " pdb=" N GLY I 9 " pdb=" CA GLY I 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 17637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2891 0.047 - 0.095: 1294 0.095 - 0.142: 326 0.142 - 0.189: 73 0.189 - 0.236: 36 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU L 27 " pdb=" N LEU L 27 " pdb=" C LEU L 27 " pdb=" CB LEU L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU J 27 " pdb=" N LEU J 27 " pdb=" C LEU J 27 " pdb=" CB LEU J 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4617 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 26 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C GLU I 26 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU I 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU I 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU G 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU G 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU G 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU D 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU D 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU D 27 " 0.021 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 496 2.68 - 3.23: 27371 3.23 - 3.79: 47180 3.79 - 4.34: 64031 4.34 - 4.90: 104172 Nonbonded interactions: 243250 Sorted by model distance: nonbonded pdb=" NZ LYS K 176 " pdb=" OD2 ASP L 101 " model vdw 2.119 3.120 nonbonded pdb=" NZ LYS E 176 " pdb=" OD2 ASP F 101 " model vdw 2.120 3.120 nonbonded pdb=" O ILE G 6 " pdb=" N GLY G 28 " model vdw 2.217 3.120 nonbonded pdb=" O ILE A 6 " pdb=" N GLY A 28 " model vdw 2.218 3.120 nonbonded pdb=" O ILE H 6 " pdb=" N GLY H 28 " model vdw 2.218 3.120 ... (remaining 243245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.90 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.007 0.071 28860 Z= 0.374 Angle : 0.768 5.827 39048 Z= 0.485 Chirality : 0.059 0.236 4620 Planarity : 0.004 0.036 4992 Dihedral : 15.086 79.805 10632 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 13.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3660 helix: 1.21 (0.15), residues: 1488 sheet: 0.04 (0.18), residues: 948 loop : -0.47 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 177 TYR 0.023 0.004 TYR B 146 PHE 0.011 0.002 PHE I 189 TRP 0.013 0.003 TRP I 162 HIS 0.006 0.002 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00713 (28860) covalent geometry : angle 0.76847 (39048) hydrogen bonds : bond 0.13390 ( 1428) hydrogen bonds : angle 6.14279 ( 3996) *********************** 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 869 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 783 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 8 SER cc_start: 0.8101 (t) cc_final: 0.7762 (p) REVERT: A 66 ASN cc_start: 0.9156 (m-40) cc_final: 0.8731 (m-40) REVERT: A 79 ILE cc_start: 0.8977 (pt) cc_final: 0.8645 (mm) REVERT: A 291 ASP cc_start: 0.7994 (t70) cc_final: 0.7635 (t70) REVERT: A 307 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 73 MET cc_start: 0.8569 (mtp) cc_final: 0.8157 (mtp) REVERT: B 273 ASN cc_start: 0.8857 (p0) cc_final: 0.8470 (p0) REVERT: C 5 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8095 (mmtp) REVERT: C 65 ASP cc_start: 0.7693 (m-30) cc_final: 0.7462 (m-30) REVERT: C 79 ILE cc_start: 0.9051 (pt) cc_final: 0.8655 (mm) REVERT: C 114 ASN cc_start: 0.8412 (m-40) cc_final: 0.8177 (m-40) REVERT: C 220 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7615 (t0) REVERT: C 263 ASN cc_start: 0.8210 (m-40) cc_final: 0.7910 (m-40) REVERT: C 291 ASP cc_start: 0.7999 (t70) cc_final: 0.7631 (t70) REVERT: D 37 ASN cc_start: 0.7751 (p0) cc_final: 0.7454 (p0) REVERT: D 57 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7926 (tp40) REVERT: E 5 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8284 (mmtp) REVERT: E 79 ILE cc_start: 0.9003 (pt) cc_final: 0.8587 (mm) REVERT: E 143 ASP cc_start: 0.8068 (m-30) cc_final: 0.7820 (m-30) REVERT: F 57 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7827 (tp-100) REVERT: G 46 GLU cc_start: 0.7623 (pt0) cc_final: 0.7395 (pt0) REVERT: G 68 MET cc_start: 0.7818 (tpp) cc_final: 0.7577 (tpt) REVERT: G 294 MET cc_start: 0.7992 (pmm) cc_final: 0.7702 (pmm) REVERT: H 5 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8210 (mmtp) REVERT: H 68 MET cc_start: 0.8213 (tpp) cc_final: 0.8010 (tpt) REVERT: H 79 ILE cc_start: 0.8964 (pt) cc_final: 0.8547 (mm) REVERT: H 99 LYS cc_start: 0.7386 (pttp) cc_final: 0.7161 (pttp) REVERT: H 143 ASP cc_start: 0.7878 (m-30) cc_final: 0.7572 (m-30) REVERT: I 21 ASP cc_start: 0.5804 (m-30) cc_final: 0.5579 (m-30) REVERT: J 5 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7795 (mmmm) REVERT: J 65 ASP cc_start: 0.7719 (m-30) cc_final: 0.7494 (m-30) REVERT: J 78 LYS cc_start: 0.8370 (tptm) cc_final: 0.8169 (tmtm) REVERT: J 79 ILE cc_start: 0.9008 (pt) cc_final: 0.8683 (mm) REVERT: J 114 ASN cc_start: 0.8490 (m-40) cc_final: 0.8235 (m-40) REVERT: J 220 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7541 (t0) REVERT: J 263 ASN cc_start: 0.8338 (m-40) cc_final: 0.8022 (m-40) REVERT: J 291 ASP cc_start: 0.8052 (t70) cc_final: 0.7348 (t0) REVERT: K 73 MET cc_start: 0.8575 (mtp) cc_final: 0.8185 (mtp) REVERT: L 291 ASP cc_start: 0.8043 (t70) cc_final: 0.7767 (t70) outliers start: 86 outliers final: 29 residues processed: 851 average time/residue: 0.2073 time to fit residues: 268.9470 Evaluate side-chains 642 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 611 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 220 ASP Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 305 ASN C 66 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 HIS F 305 ASN G 37 ASN G 305 ASN H 193 HIS I 123 HIS I 305 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS L 38 GLN L 123 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.179930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135437 restraints weight = 29353.886| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.66 r_work: 0.3169 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28860 Z= 0.167 Angle : 0.537 13.158 39048 Z= 0.295 Chirality : 0.048 0.165 4620 Planarity : 0.003 0.033 4992 Dihedral : 5.338 46.671 3975 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.20 % Allowed : 13.26 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3660 helix: 1.40 (0.14), residues: 1512 sheet: -0.10 (0.17), residues: 948 loop : -0.51 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 22 TYR 0.012 0.001 TYR A 146 PHE 0.011 0.002 PHE C 253 TRP 0.010 0.002 TRP H 162 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00376 (28860) covalent geometry : angle 0.53715 (39048) hydrogen bonds : bond 0.04178 ( 1428) hydrogen bonds : angle 5.01517 ( 3996) *********************** 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 823 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 691 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9130 (pt) cc_final: 0.8896 (mm) REVERT: A 98 ASP cc_start: 0.8367 (p0) cc_final: 0.8013 (p0) REVERT: A 99 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7507 (pttt) REVERT: A 158 ASN cc_start: 0.8149 (m110) cc_final: 0.7853 (m110) REVERT: A 291 ASP cc_start: 0.8650 (t70) cc_final: 0.8151 (t70) REVERT: A 307 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 260 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7056 (mtt180) REVERT: C 5 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8600 (mmtp) REVERT: C 39 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 263 ASN cc_start: 0.8303 (m-40) cc_final: 0.7884 (m-40) REVERT: D 17 GLN cc_start: 0.8055 (tp40) cc_final: 0.7644 (tp40) REVERT: D 37 ASN cc_start: 0.8753 (p0) cc_final: 0.8435 (p0) REVERT: D 96 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7626 (mtp85) REVERT: D 281 MET cc_start: 0.7726 (mtp) cc_final: 0.7507 (mtp) REVERT: D 305 ASN cc_start: 0.8884 (m-40) cc_final: 0.8454 (m-40) REVERT: E 139 ASP cc_start: 0.6947 (m-30) cc_final: 0.6722 (m-30) REVERT: E 143 ASP cc_start: 0.8512 (m-30) cc_final: 0.8270 (m-30) REVERT: E 220 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7571 (t70) REVERT: E 291 ASP cc_start: 0.8575 (t70) cc_final: 0.8367 (t0) REVERT: F 157 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7312 (mt-10) REVERT: G 17 GLN cc_start: 0.7706 (tp40) cc_final: 0.6960 (tp40) REVERT: G 21 ASP cc_start: 0.7585 (m-30) cc_final: 0.7020 (m-30) REVERT: G 38 GLN cc_start: 0.8400 (mt0) cc_final: 0.8161 (mt0) REVERT: G 62 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: G 263 ASN cc_start: 0.8789 (m-40) cc_final: 0.8499 (m110) REVERT: G 286 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8625 (ptpt) REVERT: H 79 ILE cc_start: 0.9153 (pt) cc_final: 0.8950 (mm) REVERT: H 143 ASP cc_start: 0.8463 (m-30) cc_final: 0.8176 (m-30) REVERT: H 220 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7550 (t0) REVERT: I 17 GLN cc_start: 0.7668 (tp40) cc_final: 0.7294 (tp-100) REVERT: I 267 GLU cc_start: 0.8907 (tp30) cc_final: 0.8665 (tp30) REVERT: J 5 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8393 (mmmm) REVERT: J 39 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7750 (mt-10) REVERT: J 78 LYS cc_start: 0.8816 (tptm) cc_final: 0.8482 (tmtm) REVERT: J 263 ASN cc_start: 0.8366 (m-40) cc_final: 0.7936 (m-40) REVERT: K 156 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7990 (mtt90) REVERT: L 68 MET cc_start: 0.8954 (tpt) cc_final: 0.8699 (tpt) REVERT: L 79 ILE cc_start: 0.9006 (pt) cc_final: 0.8786 (mm) REVERT: L 96 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7782 (mtp85) REVERT: L 98 ASP cc_start: 0.8352 (p0) cc_final: 0.7992 (p0) REVERT: L 156 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8062 (mtt90) REVERT: L 279 ASP cc_start: 0.6863 (t70) cc_final: 0.6557 (t0) outliers start: 132 outliers final: 69 residues processed: 776 average time/residue: 0.1948 time to fit residues: 235.9549 Evaluate side-chains 715 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 641 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 286 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 0.5980 chunk 333 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS B 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN G 37 ASN G 123 HIS G 305 ASN H 158 ASN I 37 ASN J 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.163384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115794 restraints weight = 29085.557| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.88 r_work: 0.2877 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28860 Z= 0.168 Angle : 0.507 9.954 39048 Z= 0.278 Chirality : 0.048 0.168 4620 Planarity : 0.003 0.028 4992 Dihedral : 4.811 47.014 3954 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.02 % Allowed : 16.19 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3660 helix: 1.65 (0.14), residues: 1512 sheet: -0.38 (0.16), residues: 936 loop : -0.59 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 156 TYR 0.010 0.001 TYR L 146 PHE 0.016 0.001 PHE F 35 TRP 0.008 0.001 TRP E 162 HIS 0.005 0.001 HIS L 123 Details of bonding type rmsd covalent geometry : bond 0.00388 (28860) covalent geometry : angle 0.50690 (39048) hydrogen bonds : bond 0.03967 ( 1428) hydrogen bonds : angle 4.81288 ( 3996) *********************** 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 829 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 734 time to evaluate : 1.094 Fit side-chains REVERT: A 5 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8624 (mmtp) REVERT: A 12 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8328 (t-90) REVERT: A 34 LYS cc_start: 0.7731 (mttt) cc_final: 0.7428 (mttt) REVERT: A 51 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 65 ASP cc_start: 0.8236 (m-30) cc_final: 0.7984 (m-30) REVERT: A 79 ILE cc_start: 0.9162 (pt) cc_final: 0.8827 (mm) REVERT: A 98 ASP cc_start: 0.8498 (p0) cc_final: 0.8187 (p0) REVERT: A 158 ASN cc_start: 0.8121 (m110) cc_final: 0.7716 (m110) REVERT: A 291 ASP cc_start: 0.8708 (t70) cc_final: 0.8274 (t70) REVERT: A 307 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8434 (mt-10) REVERT: B 52 ASP cc_start: 0.8748 (t0) cc_final: 0.8447 (t0) REVERT: B 96 ARG cc_start: 0.8266 (mtp85) cc_final: 0.8025 (mtp85) REVERT: C 263 ASN cc_start: 0.8259 (m-40) cc_final: 0.7765 (m-40) REVERT: D 22 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7929 (tpp80) REVERT: D 37 ASN cc_start: 0.8962 (p0) cc_final: 0.8557 (p0) REVERT: D 286 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8541 (mtmm) REVERT: D 298 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8103 (mm-30) REVERT: E 13 GLN cc_start: 0.8283 (tp40) cc_final: 0.8081 (tp40) REVERT: E 143 ASP cc_start: 0.8510 (m-30) cc_final: 0.8220 (m-30) REVERT: E 148 GLU cc_start: 0.7992 (tt0) cc_final: 0.7730 (tt0) REVERT: E 220 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7523 (t70) REVERT: F 3 ASN cc_start: 0.7905 (m-40) cc_final: 0.7685 (m-40) REVERT: F 17 GLN cc_start: 0.7701 (tp40) cc_final: 0.6925 (tp40) REVERT: F 21 ASP cc_start: 0.7529 (m-30) cc_final: 0.6761 (m-30) REVERT: F 51 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8030 (mm-30) REVERT: F 157 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7135 (mt-10) REVERT: F 260 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6973 (mtt180) REVERT: F 263 ASN cc_start: 0.8794 (m-40) cc_final: 0.8585 (m110) REVERT: G 17 GLN cc_start: 0.7790 (tp40) cc_final: 0.7189 (tp40) REVERT: G 21 ASP cc_start: 0.7724 (m-30) cc_final: 0.7143 (m-30) REVERT: G 22 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7942 (tpp80) REVERT: G 62 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: G 68 MET cc_start: 0.8371 (tpp) cc_final: 0.8057 (tpt) REVERT: G 96 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7967 (mtp85) REVERT: G 263 ASN cc_start: 0.8722 (m-40) cc_final: 0.8451 (m-40) REVERT: G 286 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8561 (ptpt) REVERT: H 5 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8586 (mmtp) REVERT: H 46 GLU cc_start: 0.8606 (pt0) cc_final: 0.8347 (pt0) REVERT: H 79 ILE cc_start: 0.9091 (pt) cc_final: 0.8848 (mm) REVERT: H 143 ASP cc_start: 0.8566 (m-30) cc_final: 0.8271 (m-30) REVERT: H 148 GLU cc_start: 0.8032 (tt0) cc_final: 0.7783 (tt0) REVERT: H 220 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7539 (t70) REVERT: I 17 GLN cc_start: 0.7673 (tp40) cc_final: 0.7288 (tp-100) REVERT: I 267 GLU cc_start: 0.8907 (tp30) cc_final: 0.8699 (tp30) REVERT: I 298 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8068 (mm-30) REVERT: I 305 ASN cc_start: 0.8814 (m110) cc_final: 0.8393 (m-40) REVERT: J 5 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8380 (mmmm) REVERT: J 13 GLN cc_start: 0.8565 (tp40) cc_final: 0.8303 (tp40) REVERT: J 78 LYS cc_start: 0.8740 (tptm) cc_final: 0.8480 (ttpt) REVERT: J 96 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8014 (mtp85) REVERT: J 158 ASN cc_start: 0.8243 (m-40) cc_final: 0.7774 (m110) REVERT: J 263 ASN cc_start: 0.8241 (m-40) cc_final: 0.7747 (m-40) REVERT: J 291 ASP cc_start: 0.8694 (t70) cc_final: 0.8296 (t70) REVERT: K 260 ARG cc_start: 0.7314 (ttm170) cc_final: 0.7033 (mtm180) REVERT: L 5 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8741 (mmtp) REVERT: L 79 ILE cc_start: 0.9150 (pt) cc_final: 0.8839 (mm) REVERT: L 96 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8224 (mtp85) REVERT: L 98 ASP cc_start: 0.8562 (p0) cc_final: 0.8191 (p0) REVERT: L 267 GLU cc_start: 0.8174 (tp30) cc_final: 0.7930 (tp30) REVERT: L 291 ASP cc_start: 0.8784 (t70) cc_final: 0.8048 (t0) REVERT: L 307 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8433 (mt-10) outliers start: 95 outliers final: 57 residues processed: 788 average time/residue: 0.1932 time to fit residues: 237.3241 Evaluate side-chains 758 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 696 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 220 ASP Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 243 optimal weight: 0.0970 chunk 207 optimal weight: 5.9990 chunk 305 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 246 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 305 ASN G 305 ASN H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.162827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.105751 restraints weight = 28925.664| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.01 r_work: 0.2819 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28860 Z= 0.132 Angle : 0.467 9.634 39048 Z= 0.255 Chirality : 0.047 0.197 4620 Planarity : 0.003 0.031 4992 Dihedral : 4.490 46.182 3944 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.61 % Allowed : 17.56 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3660 helix: 1.84 (0.14), residues: 1512 sheet: -0.69 (0.16), residues: 972 loop : -0.50 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 22 TYR 0.007 0.001 TYR H 146 PHE 0.010 0.001 PHE E 266 TRP 0.007 0.001 TRP A 162 HIS 0.006 0.001 HIS L 12 Details of bonding type rmsd covalent geometry : bond 0.00304 (28860) covalent geometry : angle 0.46668 (39048) hydrogen bonds : bond 0.03462 ( 1428) hydrogen bonds : angle 4.64476 ( 3996) *********************** 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 789 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 707 time to evaluate : 0.966 Fit side-chains REVERT: A 5 LYS cc_start: 0.8893 (mmtp) cc_final: 0.8651 (mmtp) REVERT: A 34 LYS cc_start: 0.7799 (mttt) cc_final: 0.7476 (mmtt) REVERT: A 65 ASP cc_start: 0.8236 (m-30) cc_final: 0.7884 (m-30) REVERT: A 79 ILE cc_start: 0.9048 (pt) cc_final: 0.8813 (mm) REVERT: A 98 ASP cc_start: 0.8629 (p0) cc_final: 0.8285 (p0) REVERT: A 99 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7596 (pttt) REVERT: A 158 ASN cc_start: 0.8256 (m110) cc_final: 0.7839 (m110) REVERT: A 272 THR cc_start: 0.8871 (p) cc_final: 0.8655 (t) REVERT: A 291 ASP cc_start: 0.8744 (t70) cc_final: 0.8310 (t70) REVERT: A 292 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 307 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 260 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6785 (mtm180) REVERT: C 13 GLN cc_start: 0.8416 (tp40) cc_final: 0.8168 (tp40) REVERT: C 263 ASN cc_start: 0.8114 (m-40) cc_final: 0.7845 (m-40) REVERT: C 292 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (pp) REVERT: C 294 MET cc_start: 0.8625 (pmm) cc_final: 0.8048 (pmm) REVERT: D 22 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7917 (tpp80) REVERT: D 37 ASN cc_start: 0.8908 (p0) cc_final: 0.8492 (p0) REVERT: D 286 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8379 (mtmm) REVERT: D 298 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8017 (mm-30) REVERT: E 13 GLN cc_start: 0.8324 (tp40) cc_final: 0.8069 (tp40) REVERT: E 65 ASP cc_start: 0.8418 (m-30) cc_final: 0.8208 (m-30) REVERT: E 115 MET cc_start: 0.9370 (mtm) cc_final: 0.9166 (mtm) REVERT: E 143 ASP cc_start: 0.8474 (m-30) cc_final: 0.8235 (m-30) REVERT: E 148 GLU cc_start: 0.8008 (tt0) cc_final: 0.7720 (tt0) REVERT: F 17 GLN cc_start: 0.7747 (tp40) cc_final: 0.7216 (tp-100) REVERT: F 21 ASP cc_start: 0.7617 (m-30) cc_final: 0.7034 (m-30) REVERT: F 38 GLN cc_start: 0.8721 (mt0) cc_final: 0.8357 (mm-40) REVERT: F 51 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8079 (mm-30) REVERT: F 114 ASN cc_start: 0.9188 (m-40) cc_final: 0.8852 (m-40) REVERT: F 157 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7080 (mt-10) REVERT: G 17 GLN cc_start: 0.7752 (tp40) cc_final: 0.6802 (tp40) REVERT: G 21 ASP cc_start: 0.7770 (m-30) cc_final: 0.6895 (m-30) REVERT: G 22 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7867 (tpp80) REVERT: G 62 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: G 68 MET cc_start: 0.8441 (tpp) cc_final: 0.8069 (tpt) REVERT: G 96 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7980 (mtp85) REVERT: G 118 VAL cc_start: 0.9191 (p) cc_final: 0.8988 (p) REVERT: G 212 LYS cc_start: 0.8794 (mptt) cc_final: 0.8573 (mptt) REVERT: H 5 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8653 (mmtp) REVERT: H 13 GLN cc_start: 0.8293 (tp40) cc_final: 0.8026 (tp40) REVERT: H 34 LYS cc_start: 0.7849 (mttt) cc_final: 0.7370 (mmtt) REVERT: H 65 ASP cc_start: 0.8382 (m-30) cc_final: 0.7927 (m-30) REVERT: H 143 ASP cc_start: 0.8390 (m-30) cc_final: 0.8152 (m-30) REVERT: H 148 GLU cc_start: 0.8043 (tt0) cc_final: 0.7774 (tt0) REVERT: I 37 ASN cc_start: 0.8535 (p0) cc_final: 0.8089 (p0) REVERT: I 267 GLU cc_start: 0.8908 (tp30) cc_final: 0.8619 (tp30) REVERT: I 305 ASN cc_start: 0.8811 (m110) cc_final: 0.8366 (m-40) REVERT: J 5 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8396 (mmmm) REVERT: J 13 GLN cc_start: 0.8433 (tp40) cc_final: 0.8109 (mm-40) REVERT: J 78 LYS cc_start: 0.8759 (tptm) cc_final: 0.8441 (ttpt) REVERT: J 158 ASN cc_start: 0.8265 (m-40) cc_final: 0.7861 (m-40) REVERT: J 263 ASN cc_start: 0.8232 (m-40) cc_final: 0.7949 (m-40) REVERT: J 292 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8618 (pp) REVERT: K 260 ARG cc_start: 0.7292 (ttm170) cc_final: 0.6993 (mtm180) REVERT: L 96 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8240 (mtp85) REVERT: L 98 ASP cc_start: 0.8683 (p0) cc_final: 0.8324 (p0) REVERT: L 267 GLU cc_start: 0.8266 (tp30) cc_final: 0.8037 (tp30) REVERT: L 286 LYS cc_start: 0.8047 (ptpt) cc_final: 0.7814 (mtmt) REVERT: L 291 ASP cc_start: 0.8788 (t70) cc_final: 0.7995 (t0) REVERT: L 292 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8508 (pp) REVERT: L 307 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8376 (mt-10) outliers start: 82 outliers final: 49 residues processed: 749 average time/residue: 0.1953 time to fit residues: 226.2388 Evaluate side-chains 728 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 672 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 17 GLN C 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN L 158 ASN ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.160585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.106847 restraints weight = 28982.393| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.07 r_work: 0.2782 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28860 Z= 0.213 Angle : 0.516 8.974 39048 Z= 0.281 Chirality : 0.048 0.198 4620 Planarity : 0.003 0.033 4992 Dihedral : 4.540 47.123 3938 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.99 % Allowed : 17.59 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3660 helix: 1.77 (0.14), residues: 1512 sheet: -0.82 (0.15), residues: 1044 loop : -0.98 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.010 0.002 TYR H 146 PHE 0.017 0.001 PHE F 35 TRP 0.006 0.001 TRP C 162 HIS 0.010 0.001 HIS L 12 Details of bonding type rmsd covalent geometry : bond 0.00502 (28860) covalent geometry : angle 0.51623 (39048) hydrogen bonds : bond 0.03982 ( 1428) hydrogen bonds : angle 4.65844 ( 3996) *********************** 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 805 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 711 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8610 (mmtp) REVERT: A 96 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8216 (mtp85) REVERT: A 98 ASP cc_start: 0.8606 (p0) cc_final: 0.8243 (p0) REVERT: A 99 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7922 (pttm) REVERT: A 158 ASN cc_start: 0.8266 (m110) cc_final: 0.7972 (m110) REVERT: A 291 ASP cc_start: 0.8779 (t70) cc_final: 0.8237 (t0) REVERT: A 292 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8546 (pp) REVERT: A 305 ASN cc_start: 0.9124 (m110) cc_final: 0.8294 (m110) REVERT: A 307 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8330 (mt-10) REVERT: B 260 ARG cc_start: 0.7374 (ttm170) cc_final: 0.6933 (mtm180) REVERT: B 267 GLU cc_start: 0.8632 (tt0) cc_final: 0.8378 (tt0) REVERT: C 13 GLN cc_start: 0.8389 (tp40) cc_final: 0.8187 (tp40) REVERT: C 158 ASN cc_start: 0.8020 (m110) cc_final: 0.7776 (m110) REVERT: C 263 ASN cc_start: 0.8095 (m-40) cc_final: 0.7828 (m-40) REVERT: D 17 GLN cc_start: 0.8010 (tp40) cc_final: 0.7794 (tp40) REVERT: D 37 ASN cc_start: 0.8805 (p0) cc_final: 0.8384 (p0) REVERT: D 158 ASN cc_start: 0.7809 (m-40) cc_final: 0.7522 (m-40) REVERT: D 286 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: D 298 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8014 (mm-30) REVERT: E 13 GLN cc_start: 0.8286 (tp40) cc_final: 0.8072 (tp40) REVERT: E 143 ASP cc_start: 0.8550 (m-30) cc_final: 0.8228 (m-30) REVERT: F 17 GLN cc_start: 0.7789 (tp40) cc_final: 0.7576 (tp-100) REVERT: F 21 ASP cc_start: 0.7683 (m-30) cc_final: 0.7406 (m-30) REVERT: F 38 GLN cc_start: 0.8743 (mt0) cc_final: 0.8304 (mm-40) REVERT: F 51 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8118 (mm-30) REVERT: F 157 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6974 (mt-10) REVERT: G 17 GLN cc_start: 0.7791 (tp40) cc_final: 0.7491 (tp-100) REVERT: G 21 ASP cc_start: 0.7762 (m-30) cc_final: 0.7349 (m-30) REVERT: G 22 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7886 (tpp80) REVERT: G 62 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: G 68 MET cc_start: 0.8480 (tpp) cc_final: 0.8092 (tpt) REVERT: G 212 LYS cc_start: 0.8838 (mptt) cc_final: 0.8565 (mptt) REVERT: H 5 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8522 (mmtp) REVERT: H 46 GLU cc_start: 0.8651 (pt0) cc_final: 0.8301 (pt0) REVERT: H 65 ASP cc_start: 0.8439 (m-30) cc_final: 0.8129 (m-30) REVERT: H 143 ASP cc_start: 0.8548 (m-30) cc_final: 0.8230 (m-30) REVERT: H 148 GLU cc_start: 0.8118 (tt0) cc_final: 0.7850 (tt0) REVERT: I 99 LYS cc_start: 0.8184 (pttp) cc_final: 0.7873 (pttp) REVERT: I 158 ASN cc_start: 0.7852 (m-40) cc_final: 0.7553 (m-40) REVERT: I 267 GLU cc_start: 0.8904 (tp30) cc_final: 0.8558 (tp30) REVERT: I 298 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7941 (mm-30) REVERT: I 305 ASN cc_start: 0.8766 (m110) cc_final: 0.8314 (m-40) REVERT: J 5 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8395 (mmmt) REVERT: J 13 GLN cc_start: 0.8390 (tp40) cc_final: 0.8146 (tp40) REVERT: J 25 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8470 (mt) REVERT: J 34 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7497 (mttt) REVERT: J 78 LYS cc_start: 0.8738 (tptm) cc_final: 0.8344 (ttpt) REVERT: J 158 ASN cc_start: 0.8291 (m-40) cc_final: 0.7861 (m-40) REVERT: J 263 ASN cc_start: 0.8130 (m-40) cc_final: 0.7843 (m-40) REVERT: K 260 ARG cc_start: 0.7279 (ttm170) cc_final: 0.6962 (mtm180) REVERT: L 98 ASP cc_start: 0.8724 (p0) cc_final: 0.8395 (p0) REVERT: L 292 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8592 (pp) REVERT: L 307 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8299 (mt-10) outliers start: 94 outliers final: 70 residues processed: 766 average time/residue: 0.1978 time to fit residues: 233.2896 Evaluate side-chains 763 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 687 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 222 MET Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 286 optimal weight: 0.0970 chunk 346 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN G 193 HIS I 193 HIS ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 ASN L 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.163264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.105621 restraints weight = 29008.701| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.98 r_work: 0.2827 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28860 Z= 0.115 Angle : 0.455 8.808 39048 Z= 0.248 Chirality : 0.046 0.162 4620 Planarity : 0.003 0.031 4992 Dihedral : 4.377 46.913 3936 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.93 % Allowed : 18.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3660 helix: 1.98 (0.14), residues: 1512 sheet: -0.84 (0.16), residues: 1044 loop : -0.90 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 177 TYR 0.009 0.001 TYR H 146 PHE 0.010 0.001 PHE E 266 TRP 0.006 0.001 TRP C 162 HIS 0.010 0.001 HIS L 12 Details of bonding type rmsd covalent geometry : bond 0.00262 (28860) covalent geometry : angle 0.45459 (39048) hydrogen bonds : bond 0.03212 ( 1428) hydrogen bonds : angle 4.50088 ( 3996) *********************** 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 796 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 704 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9000 (pt) cc_final: 0.8789 (mm) REVERT: A 98 ASP cc_start: 0.8573 (p0) cc_final: 0.8242 (p0) REVERT: A 99 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7822 (pttm) REVERT: A 158 ASN cc_start: 0.8200 (m110) cc_final: 0.7889 (m110) REVERT: A 291 ASP cc_start: 0.8737 (t70) cc_final: 0.7988 (t0) REVERT: A 292 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8479 (pp) REVERT: A 305 ASN cc_start: 0.9111 (m110) cc_final: 0.8317 (m-40) REVERT: A 307 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 260 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6814 (mtm180) REVERT: B 267 GLU cc_start: 0.8572 (tt0) cc_final: 0.8304 (tt0) REVERT: C 13 GLN cc_start: 0.8378 (tp40) cc_final: 0.8122 (tp40) REVERT: C 33 LYS cc_start: 0.7187 (pttt) cc_final: 0.6909 (ptpp) REVERT: C 263 ASN cc_start: 0.8035 (m-40) cc_final: 0.7748 (m-40) REVERT: C 294 MET cc_start: 0.8566 (pmm) cc_final: 0.7960 (pmm) REVERT: D 17 GLN cc_start: 0.7948 (tp40) cc_final: 0.7364 (tp40) REVERT: D 37 ASN cc_start: 0.8798 (p0) cc_final: 0.8370 (p0) REVERT: D 158 ASN cc_start: 0.7800 (m-40) cc_final: 0.7527 (m-40) REVERT: D 286 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: E 13 GLN cc_start: 0.8266 (tp40) cc_final: 0.8019 (tp40) REVERT: E 35 PHE cc_start: 0.7719 (m-10) cc_final: 0.7503 (m-10) REVERT: E 143 ASP cc_start: 0.8457 (m-30) cc_final: 0.8237 (m-30) REVERT: E 148 GLU cc_start: 0.8014 (tt0) cc_final: 0.7759 (tt0) REVERT: E 286 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7790 (mtmt) REVERT: F 17 GLN cc_start: 0.7842 (tp40) cc_final: 0.7244 (tp-100) REVERT: F 21 ASP cc_start: 0.7719 (m-30) cc_final: 0.7053 (m-30) REVERT: F 38 GLN cc_start: 0.8621 (mt0) cc_final: 0.8348 (mm-40) REVERT: F 51 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8024 (mm-30) REVERT: F 68 MET cc_start: 0.8431 (tpp) cc_final: 0.7950 (tpt) REVERT: F 114 ASN cc_start: 0.9164 (m-40) cc_final: 0.8789 (m-40) REVERT: F 118 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.9015 (p) REVERT: F 157 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6937 (mt-10) REVERT: F 260 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6938 (mtm180) REVERT: G 17 GLN cc_start: 0.7771 (tp40) cc_final: 0.6813 (tp40) REVERT: G 21 ASP cc_start: 0.7755 (m-30) cc_final: 0.6934 (m-30) REVERT: G 38 GLN cc_start: 0.8536 (mt0) cc_final: 0.8214 (mm-40) REVERT: G 62 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: G 68 MET cc_start: 0.8481 (tpp) cc_final: 0.8109 (tpt) REVERT: G 114 ASN cc_start: 0.9150 (m-40) cc_final: 0.8770 (m-40) REVERT: G 212 LYS cc_start: 0.8871 (mptt) cc_final: 0.8595 (mptt) REVERT: H 5 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8514 (mmtp) REVERT: H 13 GLN cc_start: 0.8266 (tp40) cc_final: 0.7918 (tp40) REVERT: H 34 LYS cc_start: 0.7923 (mttt) cc_final: 0.7483 (mttt) REVERT: H 65 ASP cc_start: 0.8325 (m-30) cc_final: 0.8060 (m-30) REVERT: H 143 ASP cc_start: 0.8422 (m-30) cc_final: 0.8215 (m-30) REVERT: H 148 GLU cc_start: 0.8019 (tt0) cc_final: 0.7700 (tt0) REVERT: H 286 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7805 (mtmt) REVERT: I 37 ASN cc_start: 0.8405 (p0) cc_final: 0.7966 (p0) REVERT: I 51 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7713 (mm-30) REVERT: I 64 ASN cc_start: 0.8991 (m-40) cc_final: 0.8723 (m-40) REVERT: I 102 LYS cc_start: 0.8570 (mttp) cc_final: 0.8280 (mptt) REVERT: I 158 ASN cc_start: 0.7768 (m-40) cc_final: 0.7467 (m110) REVERT: I 267 GLU cc_start: 0.8872 (tp30) cc_final: 0.8571 (tp30) REVERT: I 305 ASN cc_start: 0.8795 (m110) cc_final: 0.8333 (m-40) REVERT: J 5 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8302 (mmmm) REVERT: J 13 GLN cc_start: 0.8376 (tp40) cc_final: 0.7983 (mm-40) REVERT: J 78 LYS cc_start: 0.8699 (tptm) cc_final: 0.8398 (ttpt) REVERT: J 158 ASN cc_start: 0.8207 (m-40) cc_final: 0.7775 (m-40) REVERT: J 263 ASN cc_start: 0.8097 (m-40) cc_final: 0.7810 (m-40) REVERT: K 260 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6900 (mtm180) REVERT: L 98 ASP cc_start: 0.8682 (p0) cc_final: 0.8325 (p0) REVERT: L 162 TRP cc_start: 0.8461 (p-90) cc_final: 0.7993 (p-90) REVERT: L 291 ASP cc_start: 0.8757 (t70) cc_final: 0.8111 (t0) REVERT: L 292 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8443 (pp) REVERT: L 307 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8383 (mt-10) outliers start: 92 outliers final: 65 residues processed: 759 average time/residue: 0.1918 time to fit residues: 226.6940 Evaluate side-chains 739 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 666 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 194 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 281 optimal weight: 0.1980 chunk 329 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.163335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105903 restraints weight = 28969.106| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.97 r_work: 0.2812 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28860 Z= 0.141 Angle : 0.468 8.982 39048 Z= 0.254 Chirality : 0.047 0.206 4620 Planarity : 0.003 0.027 4992 Dihedral : 4.339 47.613 3936 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.28 % Allowed : 18.03 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3660 helix: 2.00 (0.14), residues: 1512 sheet: -0.75 (0.17), residues: 900 loop : -1.00 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 177 TYR 0.009 0.001 TYR H 146 PHE 0.014 0.001 PHE F 35 TRP 0.005 0.001 TRP A 162 HIS 0.008 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00326 (28860) covalent geometry : angle 0.46812 (39048) hydrogen bonds : bond 0.03365 ( 1428) hydrogen bonds : angle 4.44916 ( 3996) *********************** 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 780 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 677 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9080 (pt) cc_final: 0.8783 (mm) REVERT: A 98 ASP cc_start: 0.8648 (p0) cc_final: 0.8304 (p0) REVERT: A 99 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7829 (pttt) REVERT: A 158 ASN cc_start: 0.8194 (m110) cc_final: 0.7883 (m110) REVERT: A 291 ASP cc_start: 0.8717 (t70) cc_final: 0.8239 (t0) REVERT: A 292 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8497 (pp) REVERT: A 305 ASN cc_start: 0.9093 (m110) cc_final: 0.8323 (m-40) REVERT: A 307 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8398 (mt-10) REVERT: B 260 ARG cc_start: 0.7221 (ttm170) cc_final: 0.6822 (mtm180) REVERT: B 267 GLU cc_start: 0.8600 (tt0) cc_final: 0.8323 (tt0) REVERT: C 13 GLN cc_start: 0.8380 (tp40) cc_final: 0.8107 (tp40) REVERT: C 263 ASN cc_start: 0.7672 (m-40) cc_final: 0.7359 (m-40) REVERT: C 291 ASP cc_start: 0.8779 (t70) cc_final: 0.8510 (t70) REVERT: C 294 MET cc_start: 0.8569 (pmm) cc_final: 0.7824 (pmm) REVERT: D 37 ASN cc_start: 0.8785 (p0) cc_final: 0.8373 (p0) REVERT: D 158 ASN cc_start: 0.7779 (m-40) cc_final: 0.7483 (m-40) REVERT: D 286 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8331 (mtmm) REVERT: E 13 GLN cc_start: 0.8210 (tp40) cc_final: 0.7971 (tp40) REVERT: E 35 PHE cc_start: 0.7672 (m-10) cc_final: 0.7448 (m-10) REVERT: E 143 ASP cc_start: 0.8479 (m-30) cc_final: 0.8258 (m-30) REVERT: E 237 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7326 (mt) REVERT: E 286 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: F 17 GLN cc_start: 0.7793 (tp40) cc_final: 0.7526 (tp-100) REVERT: F 21 ASP cc_start: 0.7710 (m-30) cc_final: 0.7404 (m-30) REVERT: F 38 GLN cc_start: 0.8608 (mt0) cc_final: 0.8371 (mm-40) REVERT: F 51 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8059 (mm-30) REVERT: F 62 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: F 68 MET cc_start: 0.8396 (tpp) cc_final: 0.7942 (tpt) REVERT: F 118 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8992 (p) REVERT: F 157 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6956 (mt-10) REVERT: F 260 ARG cc_start: 0.7272 (mtt180) cc_final: 0.7006 (mtm180) REVERT: G 17 GLN cc_start: 0.7819 (tp40) cc_final: 0.7123 (tp40) REVERT: G 21 ASP cc_start: 0.7792 (m-30) cc_final: 0.7080 (m-30) REVERT: G 62 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: G 68 MET cc_start: 0.8451 (tpp) cc_final: 0.8045 (tpt) REVERT: G 212 LYS cc_start: 0.8883 (mptt) cc_final: 0.8661 (mmtm) REVERT: H 13 GLN cc_start: 0.8280 (tp40) cc_final: 0.7910 (tp40) REVERT: H 143 ASP cc_start: 0.8486 (m-30) cc_final: 0.8270 (m-30) REVERT: H 286 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7826 (mtmt) REVERT: I 37 ASN cc_start: 0.8414 (p0) cc_final: 0.7988 (p0) REVERT: I 51 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7639 (mm-30) REVERT: I 64 ASN cc_start: 0.8985 (m-40) cc_final: 0.8706 (m-40) REVERT: I 102 LYS cc_start: 0.8579 (mttp) cc_final: 0.8318 (mptt) REVERT: I 158 ASN cc_start: 0.7800 (m-40) cc_final: 0.7473 (m110) REVERT: I 267 GLU cc_start: 0.8840 (tp30) cc_final: 0.8525 (tp30) REVERT: I 286 LYS cc_start: 0.8764 (ptpp) cc_final: 0.8429 (mtmt) REVERT: I 305 ASN cc_start: 0.8812 (m110) cc_final: 0.8329 (m-40) REVERT: J 5 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8376 (mmmt) REVERT: J 13 GLN cc_start: 0.8395 (tp40) cc_final: 0.7985 (mm-40) REVERT: J 33 LYS cc_start: 0.7112 (pttm) cc_final: 0.6657 (ptmm) REVERT: J 38 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7749 (mp10) REVERT: J 78 LYS cc_start: 0.8737 (tptm) cc_final: 0.8416 (ttpt) REVERT: J 158 ASN cc_start: 0.8184 (m-40) cc_final: 0.7822 (m-40) REVERT: J 263 ASN cc_start: 0.8012 (m-40) cc_final: 0.7717 (m-40) REVERT: K 114 ASN cc_start: 0.9304 (m-40) cc_final: 0.9068 (m-40) REVERT: K 260 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6925 (mtm180) REVERT: L 98 ASP cc_start: 0.8723 (p0) cc_final: 0.8363 (p0) REVERT: L 307 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8332 (mt-10) outliers start: 103 outliers final: 82 residues processed: 741 average time/residue: 0.1920 time to fit residues: 222.2123 Evaluate side-chains 751 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 660 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 222 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 282 LYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 0.0030 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 359 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 17 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN I 263 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN K 263 ASN L 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.165273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112158 restraints weight = 28957.667| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.18 r_work: 0.2835 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28860 Z= 0.113 Angle : 0.451 8.647 39048 Z= 0.244 Chirality : 0.046 0.178 4620 Planarity : 0.003 0.029 4992 Dihedral : 4.239 47.730 3936 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.12 % Allowed : 18.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3660 helix: 2.11 (0.14), residues: 1512 sheet: -0.73 (0.17), residues: 900 loop : -0.94 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 177 TYR 0.007 0.001 TYR H 146 PHE 0.010 0.001 PHE E 266 TRP 0.006 0.001 TRP G 162 HIS 0.007 0.001 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00260 (28860) covalent geometry : angle 0.45093 (39048) hydrogen bonds : bond 0.03090 ( 1428) hydrogen bonds : angle 4.35583 ( 3996) *********************** 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 781 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 683 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8648 (p0) cc_final: 0.8313 (p0) REVERT: A 99 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7832 (pttt) REVERT: A 158 ASN cc_start: 0.8156 (m110) cc_final: 0.7720 (m110) REVERT: A 222 MET cc_start: 0.8107 (ptm) cc_final: 0.7783 (ttm) REVERT: A 291 ASP cc_start: 0.8793 (t70) cc_final: 0.8268 (t0) REVERT: A 292 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8639 (pp) REVERT: A 305 ASN cc_start: 0.9098 (m110) cc_final: 0.8330 (m-40) REVERT: A 307 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 96 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7851 (mmm-85) REVERT: B 260 ARG cc_start: 0.7207 (ttm170) cc_final: 0.6801 (mtm180) REVERT: B 267 GLU cc_start: 0.8657 (tt0) cc_final: 0.8432 (tt0) REVERT: C 39 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7989 (mt-10) REVERT: C 78 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8776 (tttm) REVERT: C 263 ASN cc_start: 0.7686 (m-40) cc_final: 0.7370 (m-40) REVERT: C 294 MET cc_start: 0.8591 (pmm) cc_final: 0.7978 (pmm) REVERT: D 22 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7746 (ttm-80) REVERT: D 37 ASN cc_start: 0.8767 (p0) cc_final: 0.8357 (p0) REVERT: D 96 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7928 (mtp85) REVERT: D 158 ASN cc_start: 0.7780 (m-40) cc_final: 0.7454 (m110) REVERT: D 286 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8320 (mtmm) REVERT: E 13 GLN cc_start: 0.8222 (tp40) cc_final: 0.8009 (tp40) REVERT: E 237 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7269 (mt) REVERT: E 286 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7818 (mtmt) REVERT: F 17 GLN cc_start: 0.7863 (tp40) cc_final: 0.7163 (tp-100) REVERT: F 21 ASP cc_start: 0.7754 (m-30) cc_final: 0.7068 (m-30) REVERT: F 38 GLN cc_start: 0.8675 (mt0) cc_final: 0.8277 (mm-40) REVERT: F 51 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8076 (mm-30) REVERT: F 62 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: F 68 MET cc_start: 0.8481 (tpp) cc_final: 0.8069 (tpt) REVERT: F 118 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8966 (p) REVERT: F 157 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6960 (mt-10) REVERT: F 260 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6989 (mtm180) REVERT: G 17 GLN cc_start: 0.7843 (tp40) cc_final: 0.6864 (tp40) REVERT: G 21 ASP cc_start: 0.7805 (m-30) cc_final: 0.6964 (m-30) REVERT: G 62 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: G 68 MET cc_start: 0.8487 (tpp) cc_final: 0.8097 (tpt) REVERT: G 114 ASN cc_start: 0.9166 (m-40) cc_final: 0.8829 (m-40) REVERT: G 212 LYS cc_start: 0.8913 (mptt) cc_final: 0.8694 (mmtm) REVERT: H 5 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8550 (mmtp) REVERT: H 13 GLN cc_start: 0.8299 (tp40) cc_final: 0.7924 (tp40) REVERT: H 69 GLU cc_start: 0.8589 (tt0) cc_final: 0.8382 (tt0) REVERT: H 237 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7315 (mt) REVERT: H 286 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7837 (mtmt) REVERT: I 17 GLN cc_start: 0.8136 (tp40) cc_final: 0.7866 (tp-100) REVERT: I 51 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7659 (mm-30) REVERT: I 64 ASN cc_start: 0.8903 (m-40) cc_final: 0.8625 (m-40) REVERT: I 267 GLU cc_start: 0.8812 (tp30) cc_final: 0.8508 (tp30) REVERT: J 5 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8380 (mmmt) REVERT: J 13 GLN cc_start: 0.8404 (tp40) cc_final: 0.8014 (mm-40) REVERT: J 33 LYS cc_start: 0.7303 (pttm) cc_final: 0.6817 (ptmm) REVERT: J 39 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7965 (mt-10) REVERT: J 78 LYS cc_start: 0.8742 (tptm) cc_final: 0.8413 (ttpt) REVERT: J 158 ASN cc_start: 0.8064 (m-40) cc_final: 0.7717 (m-40) REVERT: J 263 ASN cc_start: 0.8025 (m-40) cc_final: 0.7742 (m-40) REVERT: J 286 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7910 (mtpt) REVERT: K 157 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7410 (mt-10) REVERT: K 260 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6820 (mtm180) REVERT: K 267 GLU cc_start: 0.8558 (tt0) cc_final: 0.8339 (tt0) REVERT: L 33 LYS cc_start: 0.7345 (pttm) cc_final: 0.7058 (ptpt) REVERT: L 78 LYS cc_start: 0.8739 (tppt) cc_final: 0.8180 (tmtm) REVERT: L 98 ASP cc_start: 0.8803 (p0) cc_final: 0.8451 (p0) REVERT: L 292 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8653 (pp) outliers start: 98 outliers final: 76 residues processed: 740 average time/residue: 0.1933 time to fit residues: 222.4897 Evaluate side-chains 739 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 652 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 282 LYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 222 MET Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 207 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 GLN A 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN J 123 HIS ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 158 ASN K 263 ASN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN L 158 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.162955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.108264 restraints weight = 29110.938| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.14 r_work: 0.2816 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28860 Z= 0.171 Angle : 0.490 8.562 39048 Z= 0.265 Chirality : 0.047 0.181 4620 Planarity : 0.003 0.050 4992 Dihedral : 4.386 48.506 3936 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.99 % Allowed : 18.48 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3660 helix: 2.00 (0.14), residues: 1512 sheet: -0.80 (0.16), residues: 1044 loop : -0.82 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.014 0.001 TYR H 54 PHE 0.017 0.001 PHE F 35 TRP 0.005 0.001 TRP A 162 HIS 0.011 0.001 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00402 (28860) covalent geometry : angle 0.49041 (39048) hydrogen bonds : bond 0.03516 ( 1428) hydrogen bonds : angle 4.38764 ( 3996) *********************** 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 756 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 662 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8699 (p0) cc_final: 0.8261 (p0) REVERT: A 99 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (pttt) REVERT: A 158 ASN cc_start: 0.8178 (m110) cc_final: 0.7897 (m110) REVERT: A 305 ASN cc_start: 0.9096 (m110) cc_final: 0.8274 (m110) REVERT: A 307 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8379 (mt-10) REVERT: B 114 ASN cc_start: 0.9315 (m-40) cc_final: 0.9066 (m-40) REVERT: B 133 GLN cc_start: 0.8853 (mp10) cc_final: 0.8531 (mp10) REVERT: B 157 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 267 GLU cc_start: 0.8577 (tt0) cc_final: 0.8318 (tt0) REVERT: C 39 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 263 ASN cc_start: 0.7683 (m-40) cc_final: 0.7377 (m-40) REVERT: C 294 MET cc_start: 0.8565 (pmm) cc_final: 0.7953 (pmm) REVERT: D 37 ASN cc_start: 0.8784 (p0) cc_final: 0.8336 (p0) REVERT: D 96 ARG cc_start: 0.8264 (mtp85) cc_final: 0.8002 (mtp85) REVERT: D 158 ASN cc_start: 0.7783 (m-40) cc_final: 0.7449 (m110) REVERT: D 286 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8278 (mtmm) REVERT: E 13 GLN cc_start: 0.8252 (tp40) cc_final: 0.8050 (tp40) REVERT: E 234 ASP cc_start: 0.7403 (m-30) cc_final: 0.7178 (m-30) REVERT: E 237 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7244 (mt) REVERT: E 286 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7838 (mtmt) REVERT: F 17 GLN cc_start: 0.7842 (tp40) cc_final: 0.7560 (tp-100) REVERT: F 21 ASP cc_start: 0.7705 (m-30) cc_final: 0.7401 (m-30) REVERT: F 38 GLN cc_start: 0.8680 (mt0) cc_final: 0.8256 (mm-40) REVERT: F 51 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8089 (mm-30) REVERT: F 62 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: F 68 MET cc_start: 0.8456 (tpp) cc_final: 0.8045 (tpt) REVERT: F 118 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.9020 (p) REVERT: F 157 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6970 (mt-10) REVERT: F 260 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7041 (mtm180) REVERT: G 17 GLN cc_start: 0.7863 (tp40) cc_final: 0.7142 (tp40) REVERT: G 21 ASP cc_start: 0.7832 (m-30) cc_final: 0.7199 (m-30) REVERT: G 62 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: G 68 MET cc_start: 0.8489 (tpp) cc_final: 0.8080 (tpt) REVERT: G 212 LYS cc_start: 0.8898 (mptt) cc_final: 0.8673 (mmtm) REVERT: H 35 PHE cc_start: 0.7713 (m-10) cc_final: 0.7351 (m-10) REVERT: H 237 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7256 (mt) REVERT: H 286 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (mtmt) REVERT: I 51 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7608 (mm-30) REVERT: I 158 ASN cc_start: 0.7800 (m-40) cc_final: 0.7444 (m-40) REVERT: I 267 GLU cc_start: 0.8767 (tp30) cc_final: 0.8459 (tp30) REVERT: I 298 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8114 (mm-30) REVERT: I 305 ASN cc_start: 0.8799 (m110) cc_final: 0.8315 (m-40) REVERT: J 5 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8382 (mmmt) REVERT: J 13 GLN cc_start: 0.8425 (tp40) cc_final: 0.7970 (mm-40) REVERT: J 39 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7973 (mt-10) REVERT: J 78 LYS cc_start: 0.8722 (tptm) cc_final: 0.8395 (ttpt) REVERT: J 158 ASN cc_start: 0.8088 (m-40) cc_final: 0.7834 (m-40) REVERT: J 263 ASN cc_start: 0.8023 (m-40) cc_final: 0.7732 (m-40) REVERT: K 157 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7451 (mt-10) REVERT: K 260 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6848 (mtm180) REVERT: L 98 ASP cc_start: 0.8872 (p0) cc_final: 0.8532 (p0) REVERT: L 158 ASN cc_start: 0.7591 (m110) cc_final: 0.7387 (m-40) outliers start: 94 outliers final: 81 residues processed: 717 average time/residue: 0.1815 time to fit residues: 206.9997 Evaluate side-chains 742 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 652 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 222 MET Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 238 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 218 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 161 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 214 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 149 optimal weight: 0.0980 chunk 127 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 263 ASN B 17 GLN B 158 ASN E 158 ASN F 57 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN I 263 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN K 263 ASN L 13 GLN 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 = 0.165885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.113214 restraints weight = 28813.201| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.01 r_work: 0.2890 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28860 Z= 0.101 Angle : 0.448 8.437 39048 Z= 0.243 Chirality : 0.046 0.168 4620 Planarity : 0.003 0.049 4992 Dihedral : 4.198 48.575 3936 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.83 % Allowed : 18.99 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3660 helix: 2.17 (0.14), residues: 1512 sheet: -0.75 (0.16), residues: 1044 loop : -0.76 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 177 TYR 0.011 0.001 TYR H 54 PHE 0.022 0.001 PHE L 266 TRP 0.006 0.001 TRP H 162 HIS 0.012 0.001 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00228 (28860) covalent geometry : angle 0.44837 (39048) hydrogen bonds : bond 0.02959 ( 1428) hydrogen bonds : angle 4.28424 ( 3996) ********************** 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 762 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 673 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8642 (p0) cc_final: 0.8294 (p0) REVERT: A 99 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7771 (pttt) REVERT: A 158 ASN cc_start: 0.8163 (m110) cc_final: 0.7731 (m110) REVERT: A 291 ASP cc_start: 0.8698 (t70) cc_final: 0.8170 (t0) REVERT: A 305 ASN cc_start: 0.9073 (m110) cc_final: 0.8305 (m-40) REVERT: B 3 ASN cc_start: 0.8144 (m-40) cc_final: 0.7926 (m-40) REVERT: B 157 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 267 GLU cc_start: 0.8549 (tt0) cc_final: 0.8335 (tt0) REVERT: B 291 ASP cc_start: 0.8444 (t0) cc_final: 0.8177 (t0) REVERT: C 39 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 263 ASN cc_start: 0.7652 (m-40) cc_final: 0.7338 (m-40) REVERT: C 294 MET cc_start: 0.8561 (pmm) cc_final: 0.7940 (pmm) REVERT: D 22 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7725 (ttm-80) REVERT: D 37 ASN cc_start: 0.8721 (p0) cc_final: 0.8301 (p0) REVERT: D 38 GLN cc_start: 0.8655 (mt0) cc_final: 0.8434 (mm-40) REVERT: D 96 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7849 (mtp85) REVERT: D 158 ASN cc_start: 0.7712 (m-40) cc_final: 0.7367 (m110) REVERT: D 286 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8276 (mtmm) REVERT: E 234 ASP cc_start: 0.7299 (m-30) cc_final: 0.7088 (m-30) REVERT: E 237 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7412 (mt) REVERT: E 286 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7809 (mtmt) REVERT: E 291 ASP cc_start: 0.8652 (t70) cc_final: 0.8295 (t0) REVERT: F 3 ASN cc_start: 0.8128 (m-40) cc_final: 0.7925 (m-40) REVERT: F 17 GLN cc_start: 0.7850 (tp40) cc_final: 0.7153 (tp-100) REVERT: F 21 ASP cc_start: 0.7717 (m-30) cc_final: 0.7017 (m-30) REVERT: F 38 GLN cc_start: 0.8539 (mt0) cc_final: 0.8249 (mm-40) REVERT: F 51 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7993 (mm-30) REVERT: F 62 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: F 68 MET cc_start: 0.8417 (tpp) cc_final: 0.7997 (tpt) REVERT: F 118 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8940 (p) REVERT: F 157 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6937 (mt-10) REVERT: F 158 ASN cc_start: 0.7871 (m-40) cc_final: 0.7642 (m-40) REVERT: F 260 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6988 (mtm180) REVERT: G 17 GLN cc_start: 0.7814 (tp40) cc_final: 0.6851 (tp40) REVERT: G 21 ASP cc_start: 0.7788 (m-30) cc_final: 0.6954 (m-30) REVERT: G 35 PHE cc_start: 0.7691 (m-80) cc_final: 0.7480 (m-80) REVERT: G 62 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: G 68 MET cc_start: 0.8524 (tpp) cc_final: 0.8113 (tpt) REVERT: G 212 LYS cc_start: 0.8934 (mptt) cc_final: 0.8714 (mmtm) REVERT: H 13 GLN cc_start: 0.8427 (tp40) cc_final: 0.8140 (tp40) REVERT: H 35 PHE cc_start: 0.7646 (m-10) cc_final: 0.7181 (m-10) REVERT: H 237 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7433 (mt) REVERT: H 286 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: H 291 ASP cc_start: 0.8616 (t70) cc_final: 0.8209 (t0) REVERT: I 17 GLN cc_start: 0.8127 (tp40) cc_final: 0.7866 (tp-100) REVERT: I 51 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7577 (mm-30) REVERT: I 52 ASP cc_start: 0.8589 (t0) cc_final: 0.8160 (t0) REVERT: I 158 ASN cc_start: 0.7730 (m-40) cc_final: 0.7358 (m110) REVERT: I 267 GLU cc_start: 0.8691 (tp30) cc_final: 0.8378 (tp30) REVERT: J 5 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8290 (mmmm) REVERT: J 13 GLN cc_start: 0.8375 (tp40) cc_final: 0.7992 (mm-40) REVERT: J 33 LYS cc_start: 0.7159 (pttm) cc_final: 0.6735 (ptmm) REVERT: J 78 LYS cc_start: 0.8699 (tptm) cc_final: 0.8379 (ttpt) REVERT: J 263 ASN cc_start: 0.7723 (m-40) cc_final: 0.7414 (m-40) REVERT: K 157 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7363 (mt-10) REVERT: K 260 ARG cc_start: 0.7079 (ttm170) cc_final: 0.6807 (mtm180) REVERT: L 98 ASP cc_start: 0.8825 (p0) cc_final: 0.8471 (p0) REVERT: L 292 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (pp) outliers start: 89 outliers final: 78 residues processed: 727 average time/residue: 0.1812 time to fit residues: 209.5135 Evaluate side-chains 736 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 649 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 222 MET Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 294 MET Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 79 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 57 GLN A 263 ASN B 158 ASN B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 263 ASN L 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105893 restraints weight = 29075.544| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.99 r_work: 0.2824 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28860 Z= 0.135 Angle : 0.467 8.413 39048 Z= 0.253 Chirality : 0.046 0.168 4620 Planarity : 0.003 0.053 4992 Dihedral : 4.273 49.468 3936 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.86 % Allowed : 19.31 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3660 helix: 2.16 (0.14), residues: 1512 sheet: -0.75 (0.16), residues: 1044 loop : -0.76 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 184 TYR 0.011 0.001 TYR H 54 PHE 0.020 0.001 PHE L 266 TRP 0.005 0.001 TRP H 162 HIS 0.011 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00314 (28860) covalent geometry : angle 0.46709 (39048) hydrogen bonds : bond 0.03248 ( 1428) hydrogen bonds : angle 4.29140 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8331.20 seconds wall clock time: 142 minutes 54.09 seconds (8574.09 seconds total)