Starting phenix.real_space_refine on Mon May 26 11:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_27280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_27280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_27280.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_27280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbd_27280/05_2025/8dbd_27280.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.280 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.25, per 1000 atoms: 0.57 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: 7.09 Conformation dependent library (CDL) restraints added in 3.8 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: 3.75 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: 10.59 Time building geometry restraints manager: 8.18 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: 0.25 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.90 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.170 Set scattering table: 0.310 Process input model: 62.540 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (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 TRP 0.013 0.003 TRP I 162 HIS 0.006 0.002 HIS C 130 PHE 0.011 0.002 PHE I 189 TYR 0.023 0.004 TYR B 146 ARG 0.004 0.001 ARG H 177 Details of bonding type rmsd hydrogen bonds : bond 0.13390 ( 1428) hydrogen bonds : angle 6.14279 ( 3996) covalent geometry : bond 0.00713 (28860) covalent geometry : angle 0.76847 (39048) *********************** 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 : 2.888 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: 0.7634 (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: 0.8158 (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: 0.9052 (pt) cc_final: 0.8655 (mm) REVERT: C 114 ASN cc_start: 0.8412 (m-40) cc_final: 0.8176 (m-40) REVERT: C 220 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7617 (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: 0.7632 (t70) REVERT: D 37 ASN cc_start: 0.7751 (p0) cc_final: 0.7453 (p0) REVERT: D 57 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7928 (tp40) REVERT: E 5 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8288 (mmtp) REVERT: E 68 MET cc_start: 0.8211 (tpp) cc_final: 0.8009 (tpt) 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: 0.7821 (m-30) REVERT: F 57 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7826 (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: 0.7703 (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: 0.8546 (mm) REVERT: H 99 LYS cc_start: 0.7386 (pttp) cc_final: 0.7160 (pttp) REVERT: H 143 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (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: 0.7796 (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: 0.8682 (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: 0.4588 time to fit residues: 592.9113 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 : 2.859 ------------------------------------------------------------------------------- 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 303 optimal weight: 1.9990 chunk 272 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 326 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.179497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135023 restraints weight = 29258.802| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.64 r_work: 0.3182 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28860 Z= 0.173 Angle : 0.537 12.580 39048 Z= 0.295 Chirality : 0.049 0.172 4620 Planarity : 0.003 0.030 4992 Dihedral : 5.292 46.693 3975 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.07 % Allowed : 13.20 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3660 helix: 1.39 (0.14), residues: 1512 sheet: -0.11 (0.17), residues: 948 loop : -0.52 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 162 HIS 0.004 0.001 HIS E 123 PHE 0.011 0.002 PHE C 253 TYR 0.012 0.002 TYR L 146 ARG 0.004 0.000 ARG J 302 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1428) hydrogen bonds : angle 5.00671 ( 3996) covalent geometry : bond 0.00395 (28860) covalent geometry : angle 0.53694 (39048) *********************** 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 843 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 715 time to evaluate : 2.869 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9152 (pt) cc_final: 0.8903 (mm) REVERT: A 99 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7507 (pttt) REVERT: A 158 ASN cc_start: 0.8187 (m-40) cc_final: 0.7900 (m110) REVERT: A 291 ASP cc_start: 0.8633 (t70) cc_final: 0.8147 (t70) REVERT: A 307 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 260 ARG cc_start: 0.7459 (mtt180) cc_final: 0.7110 (mtt180) REVERT: C 5 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8634 (mmtp) REVERT: C 263 ASN cc_start: 0.8273 (m-40) cc_final: 0.7775 (m-40) REVERT: C 291 ASP cc_start: 0.8516 (t70) cc_final: 0.8308 (t70) REVERT: D 17 GLN cc_start: 0.8096 (tp40) cc_final: 0.7677 (tp40) REVERT: D 37 ASN cc_start: 0.8796 (p0) cc_final: 0.8482 (p0) REVERT: D 281 MET cc_start: 0.7655 (mtp) cc_final: 0.7443 (mtp) REVERT: D 305 ASN cc_start: 0.8873 (m-40) cc_final: 0.8443 (m-40) REVERT: E 143 ASP cc_start: 0.8488 (m-30) cc_final: 0.8218 (m-30) REVERT: E 220 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7618 (t70) REVERT: E 307 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 157 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7292 (mt-10) REVERT: F 262 ASN cc_start: 0.8813 (m-40) cc_final: 0.8567 (m-40) REVERT: G 17 GLN cc_start: 0.7735 (tp40) cc_final: 0.7021 (tp40) REVERT: G 21 ASP cc_start: 0.7586 (m-30) cc_final: 0.7040 (m-30) REVERT: G 38 GLN cc_start: 0.8385 (mt0) cc_final: 0.8159 (mt0) REVERT: G 62 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: G 263 ASN cc_start: 0.8806 (m-40) cc_final: 0.8516 (m110) REVERT: G 286 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8654 (ptpt) REVERT: H 139 ASP cc_start: 0.6864 (m-30) cc_final: 0.6623 (m-30) REVERT: H 143 ASP cc_start: 0.8454 (m-30) cc_final: 0.8169 (m-30) REVERT: H 220 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7557 (t0) REVERT: I 17 GLN cc_start: 0.7714 (tp40) cc_final: 0.7303 (tp-100) REVERT: I 267 GLU cc_start: 0.8891 (tp30) cc_final: 0.8645 (tp30) REVERT: J 5 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8415 (mmmm) REVERT: J 39 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7753 (mt-10) REVERT: J 78 LYS cc_start: 0.8821 (tptm) cc_final: 0.8574 (ttpp) REVERT: J 143 ASP cc_start: 0.8552 (m-30) cc_final: 0.8350 (m-30) REVERT: J 263 ASN cc_start: 0.8337 (m-40) cc_final: 0.7836 (m-40) REVERT: K 156 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.8014 (mtt90) REVERT: K 260 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7274 (mtt180) REVERT: L 68 MET cc_start: 0.8945 (tpt) cc_final: 0.8685 (tpt) REVERT: L 79 ILE cc_start: 0.9052 (pt) cc_final: 0.8825 (mm) REVERT: L 156 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.8115 (mtt90) REVERT: L 158 ASN cc_start: 0.7780 (m-40) cc_final: 0.7575 (m-40) outliers start: 128 outliers final: 64 residues processed: 799 average time/residue: 0.4388 time to fit residues: 551.7018 Evaluate side-chains 727 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 659 time to evaluate : 3.177 ------------------------------------------------------------------------------- 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 C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU 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 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 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 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 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 193 HIS Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 249 THR 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 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 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 27 optimal weight: 0.6980 chunk 140 optimal weight: 0.0170 chunk 238 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 273 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 37 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN G 37 ASN G 305 ASN H 158 ASN I 37 ASN J 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 37 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.164006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.115310 restraints weight = 28902.063| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.86 r_work: 0.2895 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28860 Z= 0.115 Angle : 0.475 10.421 39048 Z= 0.260 Chirality : 0.047 0.175 4620 Planarity : 0.003 0.043 4992 Dihedral : 4.700 46.550 3951 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.74 % Allowed : 16.70 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3660 helix: 1.74 (0.14), residues: 1512 sheet: -0.58 (0.15), residues: 1080 loop : -0.71 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.004 0.001 HIS J 12 PHE 0.014 0.001 PHE F 35 TYR 0.010 0.001 TYR E 146 ARG 0.004 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1428) hydrogen bonds : angle 4.76863 ( 3996) covalent geometry : bond 0.00257 (28860) covalent geometry : angle 0.47463 (39048) *********************** 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 797 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 711 time to evaluate : 2.945 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8601 (mmtp) REVERT: A 38 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8138 (mm-40) REVERT: A 99 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7792 (pttm) REVERT: A 158 ASN cc_start: 0.8298 (m-40) cc_final: 0.8012 (m110) REVERT: A 272 THR cc_start: 0.8809 (p) cc_final: 0.8601 (t) REVERT: A 291 ASP cc_start: 0.8696 (t70) cc_final: 0.8190 (t70) REVERT: A 307 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8479 (mt-10) REVERT: B 96 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7973 (mtp85) REVERT: C 78 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8594 (tmtm) REVERT: C 263 ASN cc_start: 0.8212 (m-40) cc_final: 0.7725 (m-40) REVERT: C 291 ASP cc_start: 0.8617 (t70) cc_final: 0.8109 (t70) REVERT: C 312 LEU cc_start: 0.8977 (mt) cc_final: 0.8769 (mt) REVERT: D 17 GLN cc_start: 0.7984 (tp40) cc_final: 0.7446 (tp-100) REVERT: D 22 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7849 (tpp80) REVERT: D 37 ASN cc_start: 0.8619 (p0) cc_final: 0.8215 (p0) REVERT: D 267 GLU cc_start: 0.8443 (tt0) cc_final: 0.8226 (tt0) REVERT: E 65 ASP cc_start: 0.8419 (m-30) cc_final: 0.8189 (m-30) REVERT: E 143 ASP cc_start: 0.8395 (m-30) cc_final: 0.8194 (m-30) REVERT: E 220 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7409 (t70) REVERT: F 157 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7118 (mt-10) REVERT: F 263 ASN cc_start: 0.8794 (m-40) cc_final: 0.8559 (m110) REVERT: F 305 ASN cc_start: 0.8872 (m110) cc_final: 0.8582 (m-40) REVERT: G 17 GLN cc_start: 0.7692 (tp40) cc_final: 0.6842 (tp40) REVERT: G 21 ASP cc_start: 0.7659 (m-30) cc_final: 0.6881 (m-30) REVERT: G 62 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6290 (pm20) REVERT: G 68 MET cc_start: 0.8348 (tpp) cc_final: 0.8019 (tpt) REVERT: G 118 VAL cc_start: 0.9210 (p) cc_final: 0.9009 (p) REVERT: G 263 ASN cc_start: 0.8695 (m-40) cc_final: 0.8429 (m-40) REVERT: H 139 ASP cc_start: 0.7227 (m-30) cc_final: 0.7004 (m-30) REVERT: H 205 MET cc_start: 0.6158 (mtp) cc_final: 0.5814 (mtp) REVERT: H 220 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7430 (t0) REVERT: I 17 GLN cc_start: 0.7641 (tp40) cc_final: 0.7313 (tp40) REVERT: I 305 ASN cc_start: 0.8803 (m110) cc_final: 0.8402 (m-40) REVERT: J 5 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8281 (mmmm) REVERT: J 78 LYS cc_start: 0.8756 (tptm) cc_final: 0.8468 (ttpp) REVERT: J 158 ASN cc_start: 0.8211 (m-40) cc_final: 0.7768 (m110) REVERT: J 263 ASN cc_start: 0.8247 (m-40) cc_final: 0.7769 (m-40) REVERT: J 291 ASP cc_start: 0.8614 (t70) cc_final: 0.8144 (t70) REVERT: K 260 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7085 (ttm170) REVERT: K 286 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8339 (ptpp) REVERT: L 98 ASP cc_start: 0.8410 (p0) cc_final: 0.8000 (p0) REVERT: L 158 ASN cc_start: 0.7838 (m-40) cc_final: 0.7603 (m-40) REVERT: L 267 GLU cc_start: 0.8154 (tp30) cc_final: 0.7908 (tp30) REVERT: L 307 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8419 (mt-10) outliers start: 86 outliers final: 39 residues processed: 760 average time/residue: 0.4186 time to fit residues: 497.1939 Evaluate side-chains 724 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 681 time to evaluate : 2.920 ------------------------------------------------------------------------------- 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 222 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 220 ASP 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 128 ASP 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 237 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain F residue 83 SER 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 83 SER Chi-restraints excluded: chain H residue 220 ASP 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 237 LEU Chi-restraints excluded: chain I residue 244 VAL 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 K residue 83 SER Chi-restraints excluded: chain K residue 193 HIS 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 128 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 149 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 319 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 123 HIS B 17 GLN B 123 HIS 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 3 ASN G 123 HIS G 305 ASN H 158 ASN I 37 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN L 57 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.108123 restraints weight = 29247.144| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.03 r_work: 0.2817 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28860 Z= 0.196 Angle : 0.512 9.752 39048 Z= 0.280 Chirality : 0.048 0.201 4620 Planarity : 0.003 0.035 4992 Dihedral : 4.629 46.994 3942 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.99 % Allowed : 16.95 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3660 helix: 1.76 (0.14), residues: 1512 sheet: -0.72 (0.15), residues: 1044 loop : -0.94 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.006 0.001 HIS A 12 PHE 0.010 0.001 PHE E 266 TYR 0.010 0.001 TYR E 146 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1428) hydrogen bonds : angle 4.71600 ( 3996) covalent geometry : bond 0.00457 (28860) covalent geometry : angle 0.51246 (39048) *********************** 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 802 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 708 time to evaluate : 3.053 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8559 (mmtp) REVERT: A 51 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 98 ASP cc_start: 0.8649 (p0) cc_final: 0.8311 (p0) REVERT: A 158 ASN cc_start: 0.8376 (m-40) cc_final: 0.7967 (m110) REVERT: A 291 ASP cc_start: 0.8736 (t70) cc_final: 0.8304 (t0) REVERT: A 292 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 307 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 38 GLN cc_start: 0.8768 (mt0) cc_final: 0.8510 (mt0) REVERT: B 260 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6816 (mtm180) REVERT: B 267 GLU cc_start: 0.8603 (tt0) cc_final: 0.8335 (tt0) REVERT: C 5 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8319 (mmmm) REVERT: C 13 GLN cc_start: 0.8442 (tp40) cc_final: 0.8181 (tp40) REVERT: C 263 ASN cc_start: 0.8133 (m-40) cc_final: 0.7859 (m-40) REVERT: C 292 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8520 (pp) REVERT: D 17 GLN cc_start: 0.8257 (tp40) cc_final: 0.7734 (tp40) REVERT: D 22 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7852 (tpp80) REVERT: D 37 ASN cc_start: 0.8921 (p0) cc_final: 0.8491 (p0) REVERT: D 99 LYS cc_start: 0.8266 (pttp) cc_final: 0.7972 (pttp) REVERT: D 286 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8454 (mtmm) REVERT: D 298 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7941 (mm-30) REVERT: E 13 GLN cc_start: 0.8203 (tp40) cc_final: 0.7953 (tp40) REVERT: E 65 ASP cc_start: 0.8393 (m-30) cc_final: 0.8181 (m-30) REVERT: E 98 ASP cc_start: 0.8430 (p0) cc_final: 0.8225 (p0) REVERT: E 143 ASP cc_start: 0.8495 (m-30) cc_final: 0.8182 (m-30) REVERT: F 17 GLN cc_start: 0.7772 (tp40) cc_final: 0.7429 (tp40) REVERT: F 51 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8083 (mm-30) REVERT: F 157 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7077 (mt-10) REVERT: F 260 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6874 (mtt180) REVERT: G 17 GLN cc_start: 0.7761 (tp40) cc_final: 0.7067 (tp40) REVERT: G 21 ASP cc_start: 0.7720 (m-30) cc_final: 0.7060 (m-30) REVERT: G 62 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: G 68 MET cc_start: 0.8390 (tpp) cc_final: 0.8031 (tpt) REVERT: H 5 LYS cc_start: 0.8840 (mmtm) cc_final: 0.8537 (mmtp) REVERT: H 34 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7135 (mttt) REVERT: I 17 GLN cc_start: 0.7907 (tp40) cc_final: 0.7664 (tp40) REVERT: I 305 ASN cc_start: 0.8771 (m110) cc_final: 0.8341 (m-40) REVERT: J 5 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8367 (mmmm) REVERT: J 25 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (mt) REVERT: J 78 LYS cc_start: 0.8763 (tptm) cc_final: 0.8433 (ttpt) REVERT: J 158 ASN cc_start: 0.8264 (m-40) cc_final: 0.7822 (m-40) REVERT: J 263 ASN cc_start: 0.8167 (m-40) cc_final: 0.7892 (m-40) REVERT: J 292 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8742 (pp) REVERT: L 98 ASP cc_start: 0.8647 (p0) cc_final: 0.8276 (p0) REVERT: L 156 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7947 (mtt90) REVERT: L 158 ASN cc_start: 0.7957 (m-40) cc_final: 0.7669 (m-40) REVERT: L 267 GLU cc_start: 0.8191 (tp30) cc_final: 0.7935 (tp30) REVERT: L 291 ASP cc_start: 0.8801 (t70) cc_final: 0.8096 (t0) REVERT: L 292 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8538 (pp) REVERT: L 307 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8258 (mt-10) outliers start: 94 outliers final: 65 residues processed: 762 average time/residue: 0.4135 time to fit residues: 489.6981 Evaluate side-chains 748 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 676 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 62 GLU 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 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 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 292 ILE 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 12 HIS 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 270 VAL 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 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 G residue 222 MET Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 286 LYS 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 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 VAL 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 J residue 292 ILE 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 249 THR 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 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 357 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 280 optimal weight: 0.0870 chunk 17 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 305 ASN B 158 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.105655 restraints weight = 28926.077| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.05 r_work: 0.2814 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28860 Z= 0.118 Angle : 0.461 9.311 39048 Z= 0.251 Chirality : 0.046 0.193 4620 Planarity : 0.003 0.037 4992 Dihedral : 4.359 46.617 3938 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.83 % Allowed : 17.88 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3660 helix: 1.91 (0.14), residues: 1512 sheet: -0.62 (0.16), residues: 900 loop : -1.05 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.011 0.001 HIS A 12 PHE 0.013 0.001 PHE F 35 TYR 0.008 0.001 TYR H 146 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 1428) hydrogen bonds : angle 4.56773 ( 3996) covalent geometry : bond 0.00267 (28860) covalent geometry : angle 0.46067 (39048) *********************** 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 792 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 703 time to evaluate : 3.286 Fit side-chains REVERT: A 98 ASP cc_start: 0.8661 (p0) cc_final: 0.8287 (p0) REVERT: A 99 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7878 (pttm) REVERT: A 158 ASN cc_start: 0.8392 (m-40) cc_final: 0.7986 (m110) REVERT: A 291 ASP cc_start: 0.8794 (t70) cc_final: 0.8358 (t0) REVERT: A 292 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8578 (pp) REVERT: A 307 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8404 (mt-10) REVERT: B 38 GLN cc_start: 0.8719 (mt0) cc_final: 0.8499 (mm110) REVERT: B 96 ARG cc_start: 0.8231 (mtp85) cc_final: 0.8030 (mtp85) REVERT: B 260 ARG cc_start: 0.7241 (ttm170) cc_final: 0.6787 (mtm180) REVERT: B 267 GLU cc_start: 0.8636 (tt0) cc_final: 0.8369 (tt0) REVERT: C 5 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8425 (mmtp) REVERT: C 13 GLN cc_start: 0.8425 (tp40) cc_final: 0.8198 (tp-100) REVERT: C 158 ASN cc_start: 0.8159 (m-40) cc_final: 0.7695 (m110) REVERT: C 263 ASN cc_start: 0.8104 (m-40) cc_final: 0.7838 (m-40) REVERT: C 286 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7764 (mtpt) REVERT: C 292 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8598 (pp) REVERT: D 37 ASN cc_start: 0.8884 (p0) cc_final: 0.8462 (p0) REVERT: D 158 ASN cc_start: 0.7796 (m-40) cc_final: 0.7566 (m-40) REVERT: D 286 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8424 (mtmm) REVERT: E 13 GLN cc_start: 0.8336 (tp40) cc_final: 0.8101 (tp40) REVERT: E 65 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (m-30) REVERT: E 98 ASP cc_start: 0.8454 (p0) cc_final: 0.8235 (p0) REVERT: F 17 GLN cc_start: 0.7819 (tp40) cc_final: 0.7517 (tp40) REVERT: F 38 GLN cc_start: 0.8735 (mt0) cc_final: 0.8397 (mm-40) REVERT: F 51 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8074 (mm-30) REVERT: F 157 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7027 (mt-10) REVERT: G 17 GLN cc_start: 0.7763 (tp40) cc_final: 0.6820 (tp40) REVERT: G 21 ASP cc_start: 0.7751 (m-30) cc_final: 0.6952 (m-30) REVERT: G 22 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7887 (tpp80) REVERT: G 37 ASN cc_start: 0.8807 (p0) cc_final: 0.8479 (p0) REVERT: G 62 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: G 68 MET cc_start: 0.8458 (tpp) cc_final: 0.8082 (tpt) REVERT: G 118 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8980 (p) REVERT: G 212 LYS cc_start: 0.8847 (mptt) cc_final: 0.8639 (mptt) REVERT: H 5 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8603 (mmtp) REVERT: H 35 PHE cc_start: 0.7719 (m-10) cc_final: 0.7506 (m-10) REVERT: I 17 GLN cc_start: 0.7927 (tp40) cc_final: 0.7704 (tp40) REVERT: I 37 ASN cc_start: 0.8454 (p0) cc_final: 0.8011 (p0) REVERT: I 99 LYS cc_start: 0.8173 (pttp) cc_final: 0.7858 (pttp) REVERT: I 305 ASN cc_start: 0.8804 (m110) cc_final: 0.8354 (m-40) REVERT: J 5 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8366 (mmmm) REVERT: J 13 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8211 (mm110) REVERT: J 78 LYS cc_start: 0.8745 (tptm) cc_final: 0.8417 (ttpt) REVERT: J 158 ASN cc_start: 0.8219 (m-40) cc_final: 0.7761 (m-40) REVERT: J 263 ASN cc_start: 0.8128 (m-40) cc_final: 0.7854 (m-40) REVERT: K 114 ASN cc_start: 0.9309 (m-40) cc_final: 0.9093 (m-40) REVERT: K 260 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6583 (mtt90) REVERT: L 5 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8538 (mmtp) REVERT: L 98 ASP cc_start: 0.8662 (p0) cc_final: 0.8322 (p0) REVERT: L 158 ASN cc_start: 0.7849 (m-40) cc_final: 0.7567 (m-40) REVERT: L 267 GLU cc_start: 0.8234 (tp30) cc_final: 0.8009 (tp30) REVERT: L 286 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7845 (mtmt) REVERT: L 291 ASP cc_start: 0.8778 (t70) cc_final: 0.8330 (t70) REVERT: L 292 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8560 (pp) REVERT: L 307 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8353 (mt-10) outliers start: 89 outliers final: 53 residues processed: 749 average time/residue: 0.4188 time to fit residues: 483.3101 Evaluate side-chains 718 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 658 time to evaluate : 2.982 ------------------------------------------------------------------------------- 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 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 292 ILE 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 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 292 ILE 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 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 222 MET Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER 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 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 219 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 270 VAL 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 107 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 309 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 276 optimal weight: 0.5980 chunk 312 optimal weight: 5.9990 chunk 246 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN L 57 GLN L 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.106123 restraints weight = 28968.663| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.98 r_work: 0.2828 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28860 Z= 0.123 Angle : 0.457 9.066 39048 Z= 0.249 Chirality : 0.046 0.191 4620 Planarity : 0.003 0.034 4992 Dihedral : 4.254 47.155 3936 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 17.56 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3660 helix: 2.01 (0.14), residues: 1512 sheet: -0.68 (0.16), residues: 900 loop : -0.99 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.010 0.001 HIS A 12 PHE 0.017 0.001 PHE L 266 TYR 0.008 0.001 TYR H 245 ARG 0.005 0.000 ARG I 177 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 1428) hydrogen bonds : angle 4.47544 ( 3996) covalent geometry : bond 0.00283 (28860) covalent geometry : angle 0.45727 (39048) *********************** 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 762 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 674 time to evaluate : 3.126 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.8033 (t70) REVERT: A 98 ASP cc_start: 0.8654 (p0) cc_final: 0.8292 (p0) REVERT: A 99 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7876 (pttm) REVERT: A 158 ASN cc_start: 0.8363 (m-40) cc_final: 0.7958 (m110) REVERT: A 291 ASP cc_start: 0.8778 (t70) cc_final: 0.8305 (t0) REVERT: A 292 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8601 (pp) REVERT: A 307 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8363 (mt-10) REVERT: B 96 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7926 (mmm-85) REVERT: B 260 ARG cc_start: 0.7222 (ttm170) cc_final: 0.6819 (mtm180) REVERT: B 267 GLU cc_start: 0.8587 (tt0) cc_final: 0.8298 (tt0) REVERT: C 5 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8398 (mmtp) REVERT: C 33 LYS cc_start: 0.7182 (pttt) cc_final: 0.6981 (pttm) REVERT: C 64 ASN cc_start: 0.8908 (m-40) cc_final: 0.8679 (m-40) REVERT: C 158 ASN cc_start: 0.8132 (m-40) cc_final: 0.7674 (m-40) REVERT: C 263 ASN cc_start: 0.8048 (m-40) cc_final: 0.7751 (m-40) REVERT: C 292 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 294 MET cc_start: 0.8626 (pmm) cc_final: 0.7858 (pmm) REVERT: D 37 ASN cc_start: 0.8814 (p0) cc_final: 0.8400 (p0) REVERT: D 158 ASN cc_start: 0.7763 (m-40) cc_final: 0.7519 (m-40) REVERT: D 286 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8411 (mtmm) REVERT: E 13 GLN cc_start: 0.8274 (tp40) cc_final: 0.7967 (tp40) REVERT: E 65 ASP cc_start: 0.8433 (m-30) cc_final: 0.8208 (m-30) REVERT: E 98 ASP cc_start: 0.8509 (p0) cc_final: 0.8302 (p0) REVERT: F 17 GLN cc_start: 0.7859 (tp40) cc_final: 0.7200 (tp40) REVERT: F 38 GLN cc_start: 0.8692 (mt0) cc_final: 0.8400 (mm-40) REVERT: F 51 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8102 (mm-30) REVERT: F 118 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8950 (p) REVERT: F 157 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6940 (mt-10) REVERT: F 260 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6975 (mtm180) REVERT: G 17 GLN cc_start: 0.7755 (tp40) cc_final: 0.6781 (tp40) REVERT: G 21 ASP cc_start: 0.7743 (m-30) cc_final: 0.6910 (m-30) REVERT: G 37 ASN cc_start: 0.8800 (p0) cc_final: 0.8407 (p0) REVERT: G 62 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: G 68 MET cc_start: 0.8464 (tpp) cc_final: 0.8082 (tpt) REVERT: G 212 LYS cc_start: 0.8871 (mptt) cc_final: 0.8620 (mmtm) REVERT: H 5 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8618 (mmtp) REVERT: H 13 GLN cc_start: 0.8406 (tp40) cc_final: 0.8152 (mm110) REVERT: H 35 PHE cc_start: 0.7663 (m-10) cc_final: 0.7349 (m-10) REVERT: H 286 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: I 17 GLN cc_start: 0.7946 (tp40) cc_final: 0.7723 (tp40) REVERT: I 51 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7698 (mm-30) REVERT: I 99 LYS cc_start: 0.8140 (pttp) cc_final: 0.7860 (pttp) REVERT: I 286 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8404 (mtmt) REVERT: J 5 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8366 (mmmm) REVERT: J 13 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8071 (mm110) REVERT: J 78 LYS cc_start: 0.8712 (tptm) cc_final: 0.8389 (ttpt) REVERT: J 158 ASN cc_start: 0.8162 (m-40) cc_final: 0.7739 (m-40) REVERT: J 263 ASN cc_start: 0.8100 (m-40) cc_final: 0.7809 (m-40) REVERT: K 96 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7804 (mmm-85) REVERT: K 260 ARG cc_start: 0.7086 (ttm170) cc_final: 0.6399 (mtt90) REVERT: L 98 ASP cc_start: 0.8743 (p0) cc_final: 0.8416 (p0) REVERT: L 158 ASN cc_start: 0.7814 (m-40) cc_final: 0.7502 (m-40) REVERT: L 291 ASP cc_start: 0.8790 (t70) cc_final: 0.8370 (t70) REVERT: L 292 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8626 (pp) REVERT: L 307 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8299 (mt-10) outliers start: 88 outliers final: 60 residues processed: 723 average time/residue: 0.4186 time to fit residues: 466.9717 Evaluate side-chains 714 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 645 time to evaluate : 3.039 ------------------------------------------------------------------------------- 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 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 118 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 289 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 237 LEU 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 152 LEU 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 128 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 292 ILE 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 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 83 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 286 LYS 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 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 237 LEU 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 294 MET 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 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 126 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 340 optimal weight: 0.0020 chunk 190 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 ASN K 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.162937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.110323 restraints weight = 28921.118| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.11 r_work: 0.2858 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 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 = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28860 Z= 0.135 Angle : 0.464 8.929 39048 Z= 0.252 Chirality : 0.047 0.168 4620 Planarity : 0.003 0.029 4992 Dihedral : 4.253 47.899 3936 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.89 % Allowed : 18.23 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3660 helix: 2.03 (0.14), residues: 1512 sheet: -0.72 (0.16), residues: 900 loop : -0.95 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 162 HIS 0.010 0.001 HIS A 12 PHE 0.013 0.001 PHE F 35 TYR 0.007 0.001 TYR H 146 ARG 0.004 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 1428) hydrogen bonds : angle 4.42445 ( 3996) covalent geometry : bond 0.00312 (28860) covalent geometry : angle 0.46367 (39048) *********************** 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 757 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 666 time to evaluate : 3.026 Fit side-chains revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8673 (p0) cc_final: 0.8305 (p0) REVERT: A 99 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (pttt) REVERT: A 158 ASN cc_start: 0.8349 (m-40) cc_final: 0.7928 (m110) REVERT: A 222 MET cc_start: 0.7981 (ptm) cc_final: 0.7665 (ttm) REVERT: A 291 ASP cc_start: 0.8760 (t70) cc_final: 0.8245 (t0) REVERT: A 292 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8605 (pp) REVERT: A 307 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8335 (mt-10) REVERT: B 96 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7903 (mmm-85) REVERT: B 260 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6809 (mtm180) REVERT: B 267 GLU cc_start: 0.8568 (tt0) cc_final: 0.8289 (tt0) REVERT: C 5 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8443 (mmtp) REVERT: C 13 GLN cc_start: 0.8119 (tp40) cc_final: 0.7222 (tp40) REVERT: C 33 LYS cc_start: 0.7169 (pttt) cc_final: 0.6931 (ptpp) REVERT: C 64 ASN cc_start: 0.8889 (m-40) cc_final: 0.8656 (m-40) REVERT: C 158 ASN cc_start: 0.8115 (m-40) cc_final: 0.7672 (m-40) REVERT: C 263 ASN cc_start: 0.7691 (m-40) cc_final: 0.7371 (m-40) REVERT: C 291 ASP cc_start: 0.8709 (t70) cc_final: 0.8501 (t70) REVERT: C 292 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (pp) REVERT: C 294 MET cc_start: 0.8613 (pmm) cc_final: 0.8028 (pmm) REVERT: D 37 ASN cc_start: 0.8819 (p0) cc_final: 0.8404 (p0) REVERT: D 158 ASN cc_start: 0.7743 (m-40) cc_final: 0.7427 (m110) REVERT: D 286 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: E 13 GLN cc_start: 0.8208 (tp40) cc_final: 0.7959 (tp40) REVERT: E 286 LYS cc_start: 0.8123 (ptpt) cc_final: 0.7829 (mtmt) REVERT: F 17 GLN cc_start: 0.7898 (tp40) cc_final: 0.7212 (tp40) REVERT: F 38 GLN cc_start: 0.8670 (mt0) cc_final: 0.8406 (mm-40) REVERT: F 51 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8091 (mm-30) REVERT: F 118 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8998 (p) REVERT: F 157 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6993 (mt-10) REVERT: F 260 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6908 (mtm180) REVERT: G 17 GLN cc_start: 0.7783 (tp40) cc_final: 0.6798 (tp40) REVERT: G 21 ASP cc_start: 0.7750 (m-30) cc_final: 0.6912 (m-30) REVERT: G 37 ASN cc_start: 0.8767 (p0) cc_final: 0.8455 (p0) REVERT: G 38 GLN cc_start: 0.8529 (mt0) cc_final: 0.8220 (mm-40) REVERT: G 62 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: G 68 MET cc_start: 0.8466 (tpp) cc_final: 0.8080 (tpt) REVERT: G 212 LYS cc_start: 0.8871 (mptt) cc_final: 0.8663 (mmtm) REVERT: H 35 PHE cc_start: 0.7705 (m-10) cc_final: 0.7297 (m-10) REVERT: H 286 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7816 (mtmt) REVERT: I 17 GLN cc_start: 0.7968 (tp40) cc_final: 0.7757 (tp40) REVERT: I 37 ASN cc_start: 0.8446 (p0) cc_final: 0.7991 (p0) REVERT: I 51 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7594 (mm-30) REVERT: I 64 ASN cc_start: 0.8987 (m-40) cc_final: 0.8745 (m-40) REVERT: I 102 LYS cc_start: 0.8550 (mttp) cc_final: 0.8334 (mptt) REVERT: I 158 ASN cc_start: 0.7708 (m-40) cc_final: 0.7433 (m-40) REVERT: I 286 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8412 (mtmt) REVERT: I 305 ASN cc_start: 0.8802 (m110) cc_final: 0.8339 (m-40) REVERT: J 5 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8355 (mmmm) REVERT: J 13 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8130 (mm110) REVERT: J 33 LYS cc_start: 0.7169 (pttm) cc_final: 0.6811 (ptmm) REVERT: J 78 LYS cc_start: 0.8715 (tptm) cc_final: 0.8423 (ttpt) REVERT: J 158 ASN cc_start: 0.8077 (m-40) cc_final: 0.7676 (m-40) REVERT: J 263 ASN cc_start: 0.8075 (m-40) cc_final: 0.7782 (m-40) REVERT: K 96 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7896 (mtp85) REVERT: K 260 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6757 (mtm180) REVERT: L 98 ASP cc_start: 0.8796 (p0) cc_final: 0.8457 (p0) REVERT: L 158 ASN cc_start: 0.7873 (m-40) cc_final: 0.7565 (m-40) REVERT: L 162 TRP cc_start: 0.8479 (p-90) cc_final: 0.7934 (p-90) REVERT: L 291 ASP cc_start: 0.8784 (t70) cc_final: 0.8376 (t70) REVERT: L 292 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8586 (pp) REVERT: L 307 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8272 (mt-10) outliers start: 91 outliers final: 73 residues processed: 722 average time/residue: 0.4115 time to fit residues: 460.8640 Evaluate side-chains 736 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 655 time to evaluate : 3.059 ------------------------------------------------------------------------------- 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 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 208 VAL Chi-restraints excluded: chain C residue 237 LEU 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 152 LEU Chi-restraints excluded: chain D residue 193 HIS 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 128 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU 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 G residue 222 MET Chi-restraints excluded: chain H residue 62 GLU 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 25 LEU 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 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 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 63 ILE Chi-restraints excluded: chain L residue 78 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 0.0670 chunk 222 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 0.6980 chunk 333 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS B 17 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN E 12 HIS ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN H 12 HIS H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 64 ASN K 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.164739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112056 restraints weight = 29064.773| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.16 r_work: 0.2859 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3897 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= 0.114 Angle : 0.451 8.791 39048 Z= 0.244 Chirality : 0.046 0.217 4620 Planarity : 0.003 0.027 4992 Dihedral : 4.167 48.260 3936 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 18.16 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3660 helix: 2.12 (0.14), residues: 1512 sheet: -0.71 (0.17), residues: 900 loop : -0.90 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 162 HIS 0.010 0.001 HIS H 12 PHE 0.010 0.001 PHE E 266 TYR 0.006 0.001 TYR C 146 ARG 0.006 0.000 ARG L 184 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 1428) hydrogen bonds : angle 4.35965 ( 3996) covalent geometry : bond 0.00261 (28860) covalent geometry : angle 0.45079 (39048) *********************** 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 762 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 668 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8663 (p0) cc_final: 0.8281 (p0) REVERT: A 99 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (pttt) REVERT: A 158 ASN cc_start: 0.8310 (m-40) cc_final: 0.7908 (m110) REVERT: A 291 ASP cc_start: 0.8740 (t70) cc_final: 0.8251 (t0) REVERT: A 292 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 307 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8396 (mt-10) REVERT: B 260 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6769 (mtm180) REVERT: B 267 GLU cc_start: 0.8540 (tt0) cc_final: 0.8271 (tt0) REVERT: C 5 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8425 (mmtp) REVERT: C 39 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 158 ASN cc_start: 0.8099 (m-40) cc_final: 0.7646 (m-40) REVERT: C 263 ASN cc_start: 0.7692 (m-40) cc_final: 0.7372 (m-40) REVERT: C 291 ASP cc_start: 0.8636 (t70) cc_final: 0.8412 (t70) REVERT: C 294 MET cc_start: 0.8590 (pmm) cc_final: 0.7966 (pmm) REVERT: D 37 ASN cc_start: 0.8763 (p0) cc_final: 0.8346 (p0) REVERT: D 96 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7876 (mtp85) REVERT: D 158 ASN cc_start: 0.7732 (m-40) cc_final: 0.7408 (m110) REVERT: E 13 GLN cc_start: 0.8278 (tp40) cc_final: 0.7966 (tp40) REVERT: F 17 GLN cc_start: 0.7900 (tp40) cc_final: 0.7229 (tp40) REVERT: F 38 GLN cc_start: 0.8675 (mt0) cc_final: 0.8348 (mm-40) REVERT: F 51 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8070 (mm-30) REVERT: F 62 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: F 118 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8952 (p) REVERT: F 157 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6947 (mt-10) REVERT: F 260 ARG cc_start: 0.7247 (mtt180) cc_final: 0.6915 (mtm180) REVERT: F 263 ASN cc_start: 0.8745 (m-40) cc_final: 0.8535 (m-40) REVERT: F 305 ASN cc_start: 0.8939 (m110) cc_final: 0.8546 (m-40) REVERT: G 17 GLN cc_start: 0.7791 (tp40) cc_final: 0.6831 (tp40) REVERT: G 21 ASP cc_start: 0.7744 (m-30) cc_final: 0.6912 (m-30) REVERT: G 37 ASN cc_start: 0.8738 (p0) cc_final: 0.8443 (p0) REVERT: G 38 GLN cc_start: 0.8546 (mt0) cc_final: 0.8260 (mm-40) REVERT: G 62 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: G 68 MET cc_start: 0.8441 (tpp) cc_final: 0.8050 (tpt) REVERT: G 212 LYS cc_start: 0.8882 (mptt) cc_final: 0.8670 (mmtm) REVERT: G 260 ARG cc_start: 0.7167 (mtt90) cc_final: 0.6957 (mtt90) REVERT: H 35 PHE cc_start: 0.7658 (m-10) cc_final: 0.7136 (m-10) REVERT: H 237 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7258 (mt) REVERT: H 286 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7859 (mtmt) REVERT: I 51 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7590 (mm-30) REVERT: I 64 ASN cc_start: 0.8945 (m-40) cc_final: 0.8733 (m-40) REVERT: J 5 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8345 (mmmm) REVERT: J 13 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8147 (mm110) REVERT: J 33 LYS cc_start: 0.7134 (pttm) cc_final: 0.6782 (ptmm) REVERT: J 38 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7810 (mp10) REVERT: J 39 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7914 (mt-10) REVERT: J 78 LYS cc_start: 0.8725 (tptm) cc_final: 0.8405 (ttpt) REVERT: J 158 ASN cc_start: 0.8011 (m-40) cc_final: 0.7617 (m-40) REVERT: J 263 ASN cc_start: 0.8014 (m-40) cc_final: 0.7713 (m-40) REVERT: K 96 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7833 (mmm-85) REVERT: K 157 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7461 (mt-10) REVERT: K 260 ARG cc_start: 0.7125 (ttm170) cc_final: 0.6427 (mtt90) REVERT: K 267 GLU cc_start: 0.8498 (tt0) cc_final: 0.8276 (tt0) REVERT: L 98 ASP cc_start: 0.8835 (p0) cc_final: 0.8474 (p0) REVERT: L 158 ASN cc_start: 0.7829 (m-40) cc_final: 0.7528 (m-40) REVERT: L 162 TRP cc_start: 0.8446 (p-90) cc_final: 0.7909 (p-90) REVERT: L 291 ASP cc_start: 0.8735 (t70) cc_final: 0.8357 (t70) REVERT: L 292 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8562 (pp) REVERT: L 307 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8287 (mt-10) outliers start: 94 outliers final: 73 residues processed: 725 average time/residue: 0.4180 time to fit residues: 468.3591 Evaluate side-chains 734 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 653 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG 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 222 MET 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 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 152 LEU 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 128 ASP Chi-restraints excluded: chain E residue 208 VAL 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 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 G residue 222 MET Chi-restraints excluded: chain H residue 62 GLU 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 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 25 LEU 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 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 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 L residue 25 LEU Chi-restraints excluded: chain L residue 78 LYS 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 258 optimal weight: 10.0000 chunk 278 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 158 ASN ** J 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.160511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.105839 restraints weight = 29193.193| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.19 r_work: 0.2767 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 28860 Z= 0.256 Angle : 0.552 8.641 39048 Z= 0.298 Chirality : 0.049 0.202 4620 Planarity : 0.004 0.035 4992 Dihedral : 4.566 49.584 3936 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.12 % Allowed : 18.48 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3660 helix: 1.84 (0.14), residues: 1512 sheet: -0.84 (0.17), residues: 900 loop : -1.00 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.012 0.001 HIS C 12 PHE 0.022 0.001 PHE F 35 TYR 0.012 0.002 TYR A 54 ARG 0.008 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1428) hydrogen bonds : angle 4.49527 ( 3996) covalent geometry : bond 0.00603 (28860) covalent geometry : angle 0.55212 (39048) *********************** 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 778 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 680 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8724 (p0) cc_final: 0.8337 (p0) REVERT: A 158 ASN cc_start: 0.8388 (m-40) cc_final: 0.7935 (m110) REVERT: A 291 ASP cc_start: 0.8844 (t70) cc_final: 0.8583 (t70) REVERT: A 292 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8605 (pp) REVERT: A 307 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8373 (mt-10) REVERT: B 133 GLN cc_start: 0.8891 (mp10) cc_final: 0.8571 (mp10) REVERT: B 267 GLU cc_start: 0.8613 (tt0) cc_final: 0.8368 (tt0) REVERT: C 5 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8390 (mmmt) REVERT: C 39 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7995 (mt-10) REVERT: C 158 ASN cc_start: 0.8079 (m-40) cc_final: 0.7850 (m-40) REVERT: C 263 ASN cc_start: 0.7994 (m-40) cc_final: 0.7696 (m-40) REVERT: C 291 ASP cc_start: 0.8740 (t70) cc_final: 0.8470 (t70) REVERT: C 294 MET cc_start: 0.8595 (pmm) cc_final: 0.7926 (pmm) REVERT: D 3 ASN cc_start: 0.7966 (m-40) cc_final: 0.7743 (m-40) REVERT: D 22 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7734 (ttm-80) REVERT: D 37 ASN cc_start: 0.8796 (p0) cc_final: 0.8355 (p0) REVERT: D 104 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8418 (mtm-85) REVERT: D 158 ASN cc_start: 0.7854 (m-40) cc_final: 0.7531 (m-40) REVERT: D 298 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7973 (mm-30) REVERT: E 237 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7258 (mt) REVERT: F 17 GLN cc_start: 0.7870 (tp40) cc_final: 0.7352 (tp40) REVERT: F 38 GLN cc_start: 0.8691 (mt0) cc_final: 0.8461 (mm-40) REVERT: F 51 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8192 (mm-30) REVERT: F 62 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: F 157 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6991 (mt-10) REVERT: F 260 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6778 (mtp85) REVERT: G 17 GLN cc_start: 0.7824 (tp40) cc_final: 0.7037 (tp40) REVERT: G 21 ASP cc_start: 0.7864 (m-30) cc_final: 0.7219 (m-30) REVERT: G 38 GLN cc_start: 0.8549 (mt0) cc_final: 0.8239 (mm-40) REVERT: G 62 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: G 212 LYS cc_start: 0.8905 (mptt) cc_final: 0.8681 (mmtm) REVERT: H 35 PHE cc_start: 0.7685 (m-10) cc_final: 0.7275 (m-10) REVERT: H 237 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7109 (mt) REVERT: H 286 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7798 (mtmt) REVERT: I 51 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7753 (mm-30) REVERT: I 158 ASN cc_start: 0.7795 (m-40) cc_final: 0.7485 (m110) REVERT: I 305 ASN cc_start: 0.8768 (m110) cc_final: 0.8316 (m-40) REVERT: J 5 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8365 (mmmt) REVERT: J 25 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8435 (mt) REVERT: J 39 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7968 (mt-10) REVERT: J 78 LYS cc_start: 0.8650 (tptm) cc_final: 0.8226 (tmtm) REVERT: J 100 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7614 (mtpp) REVERT: J 158 ASN cc_start: 0.8078 (m-40) cc_final: 0.7807 (m-40) REVERT: J 263 ASN cc_start: 0.8001 (m-40) cc_final: 0.7702 (m-40) REVERT: K 133 GLN cc_start: 0.8985 (mp10) cc_final: 0.8646 (mp10) REVERT: K 157 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7448 (mt-10) REVERT: K 260 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6713 (mtm180) REVERT: L 98 ASP cc_start: 0.8868 (p0) cc_final: 0.8450 (p0) REVERT: L 158 ASN cc_start: 0.8067 (m-40) cc_final: 0.7733 (m-40) REVERT: L 205 MET cc_start: 0.6703 (mtp) cc_final: 0.6313 (mtp) REVERT: L 291 ASP cc_start: 0.8872 (t70) cc_final: 0.8660 (t70) REVERT: L 292 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8505 (pp) REVERT: L 307 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8312 (mt-10) outliers start: 98 outliers final: 80 residues processed: 741 average time/residue: 0.3962 time to fit residues: 461.0573 Evaluate side-chains 746 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 658 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 62 GLU 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 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 152 LEU 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 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 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 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 G residue 222 MET 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 208 VAL Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 99 LYS 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 272 THR 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 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 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 78 LYS 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 127 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 263 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS H 158 ASN I 193 HIS J 13 GLN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 158 ASN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.108812 restraints weight = 28999.030| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.23 r_work: 0.2812 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 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 = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28860 Z= 0.149 Angle : 0.487 8.559 39048 Z= 0.264 Chirality : 0.047 0.196 4620 Planarity : 0.003 0.054 4992 Dihedral : 4.484 49.042 3936 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.83 % Allowed : 18.96 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3660 helix: 1.97 (0.14), residues: 1512 sheet: -0.85 (0.17), residues: 900 loop : -0.95 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.011 0.001 HIS C 12 PHE 0.010 0.001 PHE E 266 TYR 0.013 0.001 TYR K 311 ARG 0.008 0.000 ARG K 177 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 1428) hydrogen bonds : angle 4.39272 ( 3996) covalent geometry : bond 0.00347 (28860) covalent geometry : angle 0.48698 (39048) ********************** 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 781 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 692 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8623 (p0) cc_final: 0.8173 (p0) REVERT: A 99 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7901 (pttt) REVERT: A 158 ASN cc_start: 0.8375 (m-40) cc_final: 0.7952 (m110) REVERT: A 291 ASP cc_start: 0.8794 (t70) cc_final: 0.8571 (t70) REVERT: A 292 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8598 (pp) REVERT: A 307 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 133 GLN cc_start: 0.8837 (mp10) cc_final: 0.8511 (mp10) REVERT: B 222 MET cc_start: 0.8211 (ttp) cc_final: 0.7909 (ttm) REVERT: B 267 GLU cc_start: 0.8588 (tt0) cc_final: 0.8319 (tt0) REVERT: C 5 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8384 (mmmt) REVERT: C 39 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 158 ASN cc_start: 0.8021 (m-40) cc_final: 0.7629 (m-40) REVERT: C 263 ASN cc_start: 0.7688 (m-40) cc_final: 0.7374 (m-40) REVERT: C 294 MET cc_start: 0.8652 (pmm) cc_final: 0.7942 (pmm) REVERT: D 3 ASN cc_start: 0.8098 (m-40) cc_final: 0.7888 (m-40) REVERT: D 37 ASN cc_start: 0.8756 (p0) cc_final: 0.8326 (p0) REVERT: D 96 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7937 (mtp85) REVERT: D 158 ASN cc_start: 0.7821 (m-40) cc_final: 0.7542 (m-40) REVERT: D 212 LYS cc_start: 0.8703 (tttt) cc_final: 0.8344 (mmtm) REVERT: D 286 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8361 (mtmt) REVERT: E 35 PHE cc_start: 0.7649 (m-10) cc_final: 0.7412 (m-10) REVERT: E 237 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7268 (mt) REVERT: E 286 LYS cc_start: 0.8143 (ptpt) cc_final: 0.7870 (mtmt) REVERT: F 17 GLN cc_start: 0.7914 (tp40) cc_final: 0.7530 (tp40) REVERT: F 38 GLN cc_start: 0.8721 (mt0) cc_final: 0.8359 (mm-40) REVERT: F 51 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8146 (mm-30) REVERT: F 62 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: F 157 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6978 (mt-10) REVERT: F 260 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6909 (mtm180) REVERT: G 17 GLN cc_start: 0.7851 (tp40) cc_final: 0.7170 (tp40) REVERT: G 21 ASP cc_start: 0.7835 (m-30) cc_final: 0.7139 (m-30) REVERT: G 38 GLN cc_start: 0.8568 (mt0) cc_final: 0.8260 (mm-40) REVERT: G 62 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: G 68 MET cc_start: 0.8446 (tpp) cc_final: 0.8136 (tpt) REVERT: G 212 LYS cc_start: 0.8881 (mptt) cc_final: 0.8660 (mmtm) REVERT: G 263 ASN cc_start: 0.8418 (m-40) cc_final: 0.8200 (m110) REVERT: H 35 PHE cc_start: 0.7693 (m-10) cc_final: 0.7180 (m-10) REVERT: H 237 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7198 (mt) REVERT: H 286 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7877 (mtmt) REVERT: I 37 ASN cc_start: 0.8356 (p0) cc_final: 0.7926 (p0) REVERT: I 38 GLN cc_start: 0.8658 (mt0) cc_final: 0.8451 (mm-40) REVERT: I 51 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7647 (mm-30) REVERT: I 102 LYS cc_start: 0.8569 (mttp) cc_final: 0.8330 (mptt) REVERT: I 158 ASN cc_start: 0.7737 (m-40) cc_final: 0.7385 (m-40) REVERT: I 305 ASN cc_start: 0.8797 (m110) cc_final: 0.8330 (m-40) REVERT: J 5 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8339 (mmmt) REVERT: J 25 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (mt) REVERT: J 39 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7936 (mt-10) REVERT: J 78 LYS cc_start: 0.8714 (tptm) cc_final: 0.8354 (ttpt) REVERT: J 158 ASN cc_start: 0.8019 (m-40) cc_final: 0.7639 (m-40) REVERT: J 263 ASN cc_start: 0.7756 (m-40) cc_final: 0.7450 (m-40) REVERT: J 305 ASN cc_start: 0.9084 (m110) cc_final: 0.8504 (m110) REVERT: K 38 GLN cc_start: 0.8795 (mm110) cc_final: 0.8568 (mm-40) REVERT: K 133 GLN cc_start: 0.8907 (mp10) cc_final: 0.8570 (mp10) REVERT: K 157 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7350 (mt-10) REVERT: K 260 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6723 (mtm180) REVERT: L 98 ASP cc_start: 0.8866 (p0) cc_final: 0.8416 (p0) REVERT: L 158 ASN cc_start: 0.8014 (m-40) cc_final: 0.7687 (m-40) REVERT: L 205 MET cc_start: 0.6598 (mtp) cc_final: 0.6234 (mtp) REVERT: L 292 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8439 (pp) REVERT: L 307 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8399 (mt-10) outliers start: 89 outliers final: 78 residues processed: 748 average time/residue: 0.4135 time to fit residues: 482.1114 Evaluate side-chains 750 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 663 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 31 VAL 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 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 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 152 LEU 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 83 SER 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 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 G residue 222 MET Chi-restraints excluded: chain H residue 62 GLU 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 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 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 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 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 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 63 ILE Chi-restraints excluded: chain L residue 78 LYS 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 270 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 357 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 338 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 323 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 17 GLN B 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN H 13 GLN K 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.165170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.107663 restraints weight = 28957.310| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.99 r_work: 0.2840 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4185 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= 0.114 Angle : 0.463 8.531 39048 Z= 0.250 Chirality : 0.046 0.189 4620 Planarity : 0.003 0.051 4992 Dihedral : 4.274 48.771 3936 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.70 % Allowed : 19.40 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3660 helix: 2.15 (0.14), residues: 1512 sheet: -0.80 (0.17), residues: 900 loop : -0.90 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 162 HIS 0.010 0.001 HIS C 12 PHE 0.018 0.001 PHE F 35 TYR 0.012 0.001 TYR K 311 ARG 0.007 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 1428) hydrogen bonds : angle 4.30857 ( 3996) covalent geometry : bond 0.00260 (28860) covalent geometry : angle 0.46315 (39048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17487.14 seconds wall clock time: 302 minutes 19.00 seconds (18139.00 seconds total)