Starting phenix.real_space_refine on Tue Jun 24 07:38:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbd_27280/06_2025/8dbd_27280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbd_27280/06_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_27280/06_2025/8dbd_27280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbd_27280/06_2025/8dbd_27280.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbd_27280/06_2025/8dbd_27280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbd_27280/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.78, per 1000 atoms: 0.52 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: 6.32 Conformation dependent library (CDL) restraints added in 3.5 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: 4.10 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: 10.56 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9014 1.33 - 1.45: 3429 1.45 - 1.57: 16117 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 28860 Sorted by residual: bond pdb=" O4 PO4 I 402 " pdb=" P PO4 I 402 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O4 PO4 K 402 " pdb=" P PO4 K 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 28855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 35459 1.17 - 2.33: 2827 2.33 - 3.50: 475 3.50 - 4.66: 218 4.66 - 5.83: 69 Bond angle restraints: 39048 Sorted by residual: angle pdb=" C LEU H 27 " pdb=" N GLY H 28 " pdb=" CA GLY H 28 " ideal model delta sigma weight residual 120.10 115.70 4.40 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta sigma weight residual 120.10 115.71 4.39 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU E 27 " pdb=" N GLY E 28 " pdb=" CA GLY E 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 ... (remaining 39043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 15588 15.96 - 31.92: 1428 31.92 - 47.88: 432 47.88 - 63.84: 144 63.84 - 79.80: 48 Dihedral angle restraints: 17640 sinusoidal: 6888 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER I 8 " pdb=" C SER I 8 " pdb=" N GLY I 9 " pdb=" CA GLY I 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 17637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2891 0.047 - 0.095: 1294 0.095 - 0.142: 326 0.142 - 0.189: 73 0.189 - 0.236: 36 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LEU L 27 " pdb=" N LEU L 27 " pdb=" C LEU L 27 " pdb=" CB LEU L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU J 27 " pdb=" N LEU J 27 " pdb=" C LEU J 27 " pdb=" CB LEU J 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4617 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 26 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C GLU I 26 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU I 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU I 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU G 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU G 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU G 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU D 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU D 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU D 27 " 0.021 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 496 2.68 - 3.23: 27371 3.23 - 3.79: 47180 3.79 - 4.34: 64031 4.34 - 4.90: 104172 Nonbonded interactions: 243250 Sorted by model distance: nonbonded pdb=" NZ LYS K 176 " pdb=" OD2 ASP L 101 " model vdw 2.119 3.120 nonbonded pdb=" NZ LYS E 176 " pdb=" OD2 ASP F 101 " model vdw 2.120 3.120 nonbonded pdb=" O ILE G 6 " pdb=" N GLY G 28 " model vdw 2.217 3.120 nonbonded pdb=" O ILE A 6 " pdb=" N GLY A 28 " model vdw 2.218 3.120 nonbonded pdb=" O ILE H 6 " pdb=" N GLY H 28 " model vdw 2.218 3.120 ... (remaining 243245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.28 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.910 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.460 ------------------------------------------------------------------------------- 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 : 2.946 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: 0.4440 time to fit residues: 571.9821 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 : 3.306 ------------------------------------------------------------------------------- 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 = 0.135026 restraints weight = 29258.806| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.63 r_work: 0.3181 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 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 = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- 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 : 3.220 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9150 (pt) cc_final: 0.8901 (mm) REVERT: A 99 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7508 (pttt) REVERT: A 158 ASN cc_start: 0.8187 (m-40) cc_final: 0.7900 (m110) REVERT: A 291 ASP cc_start: 0.8630 (t70) cc_final: 0.8143 (t70) REVERT: A 307 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8399 (mt-10) REVERT: B 260 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7105 (mtt180) REVERT: C 5 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8635 (mmtp) REVERT: C 263 ASN cc_start: 0.8271 (m-40) cc_final: 0.7771 (m-40) REVERT: C 291 ASP cc_start: 0.8515 (t70) cc_final: 0.8307 (t70) REVERT: D 17 GLN cc_start: 0.8093 (tp40) cc_final: 0.7675 (tp40) REVERT: D 37 ASN cc_start: 0.8794 (p0) cc_final: 0.8481 (p0) REVERT: D 281 MET cc_start: 0.7662 (mtp) cc_final: 0.7448 (mtp) REVERT: D 305 ASN cc_start: 0.8872 (m-40) cc_final: 0.8442 (m-40) REVERT: E 143 ASP cc_start: 0.8489 (m-30) cc_final: 0.8219 (m-30) REVERT: E 220 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7615 (t70) REVERT: E 307 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 157 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7297 (mt-10) REVERT: F 262 ASN cc_start: 0.8812 (m-40) cc_final: 0.8567 (m-40) REVERT: G 17 GLN cc_start: 0.7732 (tp40) cc_final: 0.7017 (tp40) REVERT: G 21 ASP cc_start: 0.7587 (m-30) cc_final: 0.7041 (m-30) REVERT: G 38 GLN cc_start: 0.8385 (mt0) cc_final: 0.8159 (mt0) REVERT: G 62 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6497 (pm20) REVERT: G 263 ASN cc_start: 0.8804 (m-40) cc_final: 0.8515 (m110) REVERT: G 286 LYS cc_start: 0.8858 (ptpp) cc_final: 0.8652 (ptpt) REVERT: H 139 ASP cc_start: 0.6868 (m-30) cc_final: 0.6627 (m-30) REVERT: H 143 ASP cc_start: 0.8454 (m-30) cc_final: 0.8169 (m-30) REVERT: H 220 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7555 (t0) REVERT: I 17 GLN cc_start: 0.7712 (tp40) cc_final: 0.7301 (tp-100) REVERT: I 267 GLU cc_start: 0.8894 (tp30) cc_final: 0.8645 (tp30) REVERT: J 5 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8414 (mmmm) REVERT: J 39 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7753 (mt-10) REVERT: J 78 LYS cc_start: 0.8820 (tptm) cc_final: 0.8572 (ttpp) REVERT: J 143 ASP cc_start: 0.8553 (m-30) cc_final: 0.8351 (m-30) REVERT: J 263 ASN cc_start: 0.8335 (m-40) cc_final: 0.7833 (m-40) REVERT: K 156 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.8013 (mtt90) REVERT: K 260 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7267 (mtt180) REVERT: L 68 MET cc_start: 0.8941 (tpt) cc_final: 0.8680 (tpt) REVERT: L 79 ILE cc_start: 0.9051 (pt) cc_final: 0.8823 (mm) REVERT: L 156 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8108 (mtt90) REVERT: L 158 ASN cc_start: 0.7786 (m-40) cc_final: 0.7579 (m-40) outliers start: 128 outliers final: 64 residues processed: 799 average time/residue: 0.4496 time to fit residues: 565.4808 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 : 2.940 ------------------------------------------------------------------------------- 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: 9.9990 chunk 140 optimal weight: 0.0270 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: 0.7980 chunk 330 optimal weight: 0.7980 chunk 273 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.166679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117376 restraints weight = 28660.178| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.88 r_work: 0.2892 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28860 Z= 0.121 Angle : 0.476 10.257 39048 Z= 0.261 Chirality : 0.047 0.175 4620 Planarity : 0.003 0.042 4992 Dihedral : 4.673 46.651 3951 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.77 % Allowed : 16.83 % Favored : 80.41 % 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: 1.75 (0.14), residues: 1512 sheet: -0.59 (0.15), residues: 1080 loop : -0.70 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.005 0.001 HIS H 193 PHE 0.015 0.001 PHE F 35 TYR 0.011 0.001 TYR C 146 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1428) hydrogen bonds : angle 4.74364 ( 3996) covalent geometry : bond 0.00270 (28860) covalent geometry : angle 0.47646 (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 812 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 725 time to evaluate : 2.981 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8885 (mmtp) cc_final: 0.8593 (mmtp) REVERT: A 34 LYS cc_start: 0.7802 (mttt) cc_final: 0.7593 (mmtp) REVERT: A 38 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8140 (mm-40) REVERT: A 99 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7807 (pttm) REVERT: A 158 ASN cc_start: 0.8323 (m-40) cc_final: 0.8025 (m110) REVERT: A 291 ASP cc_start: 0.8705 (t70) cc_final: 0.8221 (t70) REVERT: A 307 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8468 (mt-10) REVERT: B 96 ARG cc_start: 0.8271 (mtp85) cc_final: 0.8042 (mtp85) REVERT: B 104 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8398 (mtm-85) REVERT: C 13 GLN cc_start: 0.8414 (tp40) cc_final: 0.8212 (tp40) REVERT: C 78 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8594 (tmtm) REVERT: C 263 ASN cc_start: 0.8210 (m-40) cc_final: 0.7720 (m-40) REVERT: C 291 ASP cc_start: 0.8607 (t70) cc_final: 0.8113 (t70) REVERT: D 17 GLN cc_start: 0.8002 (tp40) cc_final: 0.7454 (tp-100) REVERT: D 22 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7843 (tpp80) REVERT: D 37 ASN cc_start: 0.8732 (p0) cc_final: 0.8325 (p0) REVERT: D 96 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7911 (mtp85) REVERT: E 34 LYS cc_start: 0.7923 (mttt) cc_final: 0.7590 (mttt) REVERT: E 65 ASP cc_start: 0.8361 (m-30) cc_final: 0.8115 (m-30) REVERT: E 143 ASP cc_start: 0.8396 (m-30) cc_final: 0.8195 (m-30) REVERT: E 220 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7453 (t0) REVERT: E 291 ASP cc_start: 0.8697 (t0) cc_final: 0.8475 (t70) REVERT: F 3 ASN cc_start: 0.7668 (m-40) cc_final: 0.7374 (m-40) REVERT: F 17 GLN cc_start: 0.7543 (tp40) cc_final: 0.6849 (tp40) REVERT: F 21 ASP cc_start: 0.7473 (m-30) cc_final: 0.6730 (m-30) REVERT: F 51 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7952 (mm-30) REVERT: F 157 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7109 (mt-10) REVERT: F 263 ASN cc_start: 0.8794 (m-40) cc_final: 0.8570 (m110) REVERT: F 305 ASN cc_start: 0.8872 (m110) cc_final: 0.8571 (m-40) REVERT: G 17 GLN cc_start: 0.7673 (tp40) cc_final: 0.6792 (tp40) REVERT: G 21 ASP cc_start: 0.7684 (m-30) cc_final: 0.6891 (m-30) REVERT: G 22 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7879 (tpp80) REVERT: G 62 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: G 68 MET cc_start: 0.8337 (tpp) cc_final: 0.8019 (tpt) REVERT: G 118 VAL cc_start: 0.9214 (p) cc_final: 0.9013 (p) REVERT: G 263 ASN cc_start: 0.8691 (m-40) cc_final: 0.8415 (m-40) REVERT: H 139 ASP cc_start: 0.7252 (m-30) cc_final: 0.7026 (m-30) REVERT: H 205 MET cc_start: 0.6101 (mtp) cc_final: 0.5893 (mtp) REVERT: H 220 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7451 (t0) REVERT: I 17 GLN cc_start: 0.7664 (tp40) cc_final: 0.7306 (tp40) REVERT: I 96 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7899 (mtp85) REVERT: I 267 GLU cc_start: 0.8860 (tp30) cc_final: 0.8653 (tp30) REVERT: I 305 ASN cc_start: 0.8822 (m110) cc_final: 0.8410 (m-40) REVERT: J 5 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8352 (mmmm) REVERT: J 78 LYS cc_start: 0.8759 (tptm) cc_final: 0.8468 (ttpt) REVERT: J 158 ASN cc_start: 0.8206 (m-40) cc_final: 0.7764 (m110) REVERT: J 263 ASN cc_start: 0.8233 (m-40) cc_final: 0.7756 (m-40) REVERT: J 291 ASP cc_start: 0.8629 (t70) cc_final: 0.8164 (t70) REVERT: K 260 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7088 (ttm170) REVERT: K 286 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8356 (ptpp) REVERT: L 98 ASP cc_start: 0.8484 (p0) cc_final: 0.8093 (p0) REVERT: L 158 ASN cc_start: 0.7847 (m-40) cc_final: 0.7610 (m-40) REVERT: L 267 GLU cc_start: 0.8185 (tp30) cc_final: 0.7942 (tp30) REVERT: L 307 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8421 (mt-10) outliers start: 87 outliers final: 37 residues processed: 775 average time/residue: 0.4284 time to fit residues: 515.7885 Evaluate side-chains 728 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 687 time to evaluate : 3.200 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 A 305 ASN B 17 GLN B 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.160659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104018 restraints weight = 29255.964| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.95 r_work: 0.2798 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28860 Z= 0.209 Angle : 0.517 9.994 39048 Z= 0.282 Chirality : 0.048 0.214 4620 Planarity : 0.003 0.034 4992 Dihedral : 4.634 47.191 3942 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.96 % Allowed : 16.92 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.14), residues: 3660 helix: 1.75 (0.14), residues: 1512 sheet: -0.73 (0.15), residues: 1044 loop : -0.95 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.008 0.001 HIS A 12 PHE 0.010 0.001 PHE E 266 TYR 0.011 0.001 TYR H 146 ARG 0.004 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1428) hydrogen bonds : angle 4.71723 ( 3996) covalent geometry : bond 0.00488 (28860) covalent geometry : angle 0.51710 (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 798 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 705 time to evaluate : 2.933 Fit side-chains REVERT: A 5 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8589 (mmtp) REVERT: A 98 ASP cc_start: 0.8639 (p0) cc_final: 0.8299 (p0) REVERT: A 158 ASN cc_start: 0.8389 (m-40) cc_final: 0.7992 (m110) REVERT: A 291 ASP cc_start: 0.8826 (t70) cc_final: 0.8300 (t0) REVERT: A 292 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8594 (pp) REVERT: A 307 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 38 GLN cc_start: 0.8772 (mt0) cc_final: 0.8489 (mm-40) REVERT: B 69 GLU cc_start: 0.8537 (tt0) cc_final: 0.8199 (tt0) REVERT: B 260 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6802 (mtm180) REVERT: C 263 ASN cc_start: 0.8132 (m-40) cc_final: 0.7867 (m-40) REVERT: C 292 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 17 GLN cc_start: 0.8310 (tp40) cc_final: 0.7787 (tp40) REVERT: D 22 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7859 (tpp80) REVERT: D 37 ASN cc_start: 0.8939 (p0) cc_final: 0.8515 (p0) REVERT: D 96 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8065 (mtp85) REVERT: D 99 LYS cc_start: 0.8262 (pttp) cc_final: 0.7973 (pttp) REVERT: D 286 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8465 (mtmm) REVERT: D 298 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7871 (mm-30) REVERT: E 13 GLN cc_start: 0.8217 (tp40) cc_final: 0.7971 (tp40) REVERT: E 98 ASP cc_start: 0.8395 (p0) cc_final: 0.8191 (p0) REVERT: E 143 ASP cc_start: 0.8512 (m-30) cc_final: 0.8197 (m-30) REVERT: E 307 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8767 (mt-10) REVERT: F 21 ASP cc_start: 0.7621 (m-30) cc_final: 0.7366 (m-30) REVERT: F 38 GLN cc_start: 0.8677 (mt0) cc_final: 0.8281 (mm-40) REVERT: F 51 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8146 (mm-30) REVERT: F 157 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7063 (mt-10) REVERT: F 260 ARG cc_start: 0.7372 (mtt180) cc_final: 0.6937 (mtt180) REVERT: G 17 GLN cc_start: 0.7773 (tp40) cc_final: 0.7080 (tp40) REVERT: G 21 ASP cc_start: 0.7750 (m-30) cc_final: 0.7082 (m-30) REVERT: G 62 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: G 68 MET cc_start: 0.8423 (tpp) cc_final: 0.8052 (tpt) REVERT: H 5 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8546 (mmtp) REVERT: H 34 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7031 (mttt) REVERT: I 17 GLN cc_start: 0.7949 (tp40) cc_final: 0.7703 (tp40) REVERT: I 267 GLU cc_start: 0.8918 (tp30) cc_final: 0.8630 (tp30) REVERT: I 305 ASN cc_start: 0.8790 (m110) cc_final: 0.8362 (m-40) REVERT: J 5 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8346 (mmmm) REVERT: J 25 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8463 (mt) REVERT: J 78 LYS cc_start: 0.8756 (tptm) cc_final: 0.8422 (ttpt) REVERT: J 158 ASN cc_start: 0.8272 (m-40) cc_final: 0.7831 (m-40) REVERT: J 263 ASN cc_start: 0.8244 (m-40) cc_final: 0.7961 (m-40) REVERT: L 98 ASP cc_start: 0.8671 (p0) cc_final: 0.8333 (p0) REVERT: L 158 ASN cc_start: 0.7882 (m-40) cc_final: 0.7607 (m-40) REVERT: L 267 GLU cc_start: 0.8233 (tp30) cc_final: 0.8020 (tp30) REVERT: L 291 ASP cc_start: 0.8811 (t70) cc_final: 0.8091 (t0) REVERT: L 292 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8534 (pp) REVERT: L 307 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8277 (mt-10) outliers start: 93 outliers final: 64 residues processed: 759 average time/residue: 0.4159 time to fit residues: 489.7598 Evaluate side-chains 757 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 687 time to evaluate : 2.884 ------------------------------------------------------------------------------- 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 25 LEU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP 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 F residue 31 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain 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 H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 237 LEU 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 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 244 VAL 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: 0.9990 chunk 151 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 357 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 280 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.106713 restraints weight = 28924.733| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.97 r_work: 0.2826 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 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 = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28860 Z= 0.122 Angle : 0.459 9.430 39048 Z= 0.250 Chirality : 0.046 0.163 4620 Planarity : 0.003 0.036 4992 Dihedral : 4.354 46.478 3938 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.54 % Allowed : 18.07 % Favored : 79.39 % 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: 1.92 (0.14), residues: 1512 sheet: -0.81 (0.15), residues: 1068 loop : -0.83 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.012 0.001 HIS A 12 PHE 0.018 0.001 PHE L 266 TYR 0.009 0.001 TYR H 146 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1428) hydrogen bonds : angle 4.56214 ( 3996) covalent geometry : bond 0.00278 (28860) covalent geometry : angle 0.45923 (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 783 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 703 time to evaluate : 2.930 Fit side-chains REVERT: A 96 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8048 (mtp85) REVERT: A 98 ASP cc_start: 0.8620 (p0) cc_final: 0.8263 (p0) REVERT: A 99 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7861 (pttm) REVERT: A 158 ASN cc_start: 0.8381 (m-40) cc_final: 0.7963 (m110) REVERT: A 291 ASP cc_start: 0.8774 (t70) cc_final: 0.8290 (t0) REVERT: A 292 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8569 (pp) REVERT: A 307 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 96 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8140 (mtp85) REVERT: B 260 ARG cc_start: 0.7228 (ttm170) cc_final: 0.6803 (mtm180) REVERT: B 267 GLU cc_start: 0.8594 (tt0) cc_final: 0.8325 (tt0) REVERT: C 64 ASN cc_start: 0.8905 (m-40) cc_final: 0.8689 (m-40) REVERT: C 158 ASN cc_start: 0.8155 (m-40) cc_final: 0.7689 (m110) REVERT: C 263 ASN cc_start: 0.8079 (m-40) cc_final: 0.7820 (m-40) REVERT: C 292 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8604 (pp) REVERT: D 22 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7680 (ttm-80) REVERT: D 37 ASN cc_start: 0.8891 (p0) cc_final: 0.8465 (p0) REVERT: D 96 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8034 (mtp85) REVERT: D 158 ASN cc_start: 0.7772 (m-40) cc_final: 0.7539 (m-40) REVERT: D 286 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8424 (mtmm) REVERT: E 13 GLN cc_start: 0.8315 (tp40) cc_final: 0.8072 (tp40) REVERT: E 98 ASP cc_start: 0.8450 (p0) cc_final: 0.8239 (p0) REVERT: E 307 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8799 (mt-10) REVERT: F 17 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7219 (tp40) REVERT: F 21 ASP cc_start: 0.7622 (m-30) cc_final: 0.7144 (m-30) REVERT: F 38 GLN cc_start: 0.8691 (mt0) cc_final: 0.8371 (mm-40) REVERT: F 51 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8045 (mm-30) REVERT: F 96 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7907 (mtp85) REVERT: F 157 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 260 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7141 (mtm180) REVERT: G 17 GLN cc_start: 0.7747 (tp40) cc_final: 0.6808 (tp40) REVERT: G 21 ASP cc_start: 0.7733 (m-30) cc_final: 0.6938 (m-30) REVERT: G 37 ASN cc_start: 0.8757 (p0) cc_final: 0.8341 (p0) REVERT: G 62 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: G 68 MET cc_start: 0.8477 (tpp) cc_final: 0.8110 (tpt) REVERT: G 118 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8967 (p) REVERT: H 5 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8599 (mmtp) REVERT: H 13 GLN cc_start: 0.8253 (tp40) cc_final: 0.7998 (tp40) REVERT: H 35 PHE cc_start: 0.7731 (m-10) cc_final: 0.7529 (m-10) REVERT: I 17 GLN cc_start: 0.7936 (tp40) cc_final: 0.7712 (tp40) REVERT: I 37 ASN cc_start: 0.8497 (p0) cc_final: 0.8050 (p0) REVERT: I 99 LYS cc_start: 0.8145 (pttp) cc_final: 0.7852 (pttp) REVERT: I 267 GLU cc_start: 0.8897 (tp30) cc_final: 0.8597 (tp30) REVERT: I 305 ASN cc_start: 0.8801 (m110) cc_final: 0.8348 (m-40) REVERT: J 5 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8288 (mmmm) REVERT: J 38 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8124 (mm-40) REVERT: J 78 LYS cc_start: 0.8733 (tptm) cc_final: 0.8423 (ttpt) REVERT: J 158 ASN cc_start: 0.8217 (m-40) cc_final: 0.7751 (m-40) REVERT: J 263 ASN cc_start: 0.8114 (m-40) cc_final: 0.7843 (m-40) REVERT: K 114 ASN cc_start: 0.9299 (m-40) cc_final: 0.9084 (m-40) REVERT: K 260 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6508 (mtt90) REVERT: L 5 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8644 (mmtp) REVERT: L 98 ASP cc_start: 0.8646 (p0) cc_final: 0.8318 (p0) REVERT: L 158 ASN cc_start: 0.7849 (m-40) cc_final: 0.7546 (m-40) REVERT: L 267 GLU cc_start: 0.8274 (tp30) cc_final: 0.8072 (tp30) REVERT: L 286 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7855 (mtmt) REVERT: L 291 ASP cc_start: 0.8765 (t70) cc_final: 0.8343 (t70) REVERT: L 292 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8523 (pp) REVERT: L 307 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8329 (mt-10) outliers start: 80 outliers final: 54 residues processed: 749 average time/residue: 0.4314 time to fit residues: 497.2834 Evaluate side-chains 718 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 657 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain C residue 292 ILE 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 220 ASP Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain 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 152 LEU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 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 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 219 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 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: 3.9990 chunk 115 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 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: 0.4980 chunk 178 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN C 13 GLN C 123 HIS ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 305 ASN K 17 GLN K 158 ASN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 193 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.162721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.105071 restraints weight = 29076.389| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.98 r_work: 0.2816 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28860 Z= 0.138 Angle : 0.464 9.219 39048 Z= 0.253 Chirality : 0.047 0.195 4620 Planarity : 0.003 0.037 4992 Dihedral : 4.303 47.170 3936 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: 0.44 (0.14), residues: 3660 helix: 2.00 (0.14), residues: 1512 sheet: -0.82 (0.16), residues: 1044 loop : -0.88 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.012 0.001 HIS A 12 PHE 0.010 0.001 PHE E 266 TYR 0.008 0.001 TYR H 146 ARG 0.006 0.000 ARG K 177 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1428) hydrogen bonds : angle 4.49739 ( 3996) covalent geometry : bond 0.00319 (28860) covalent geometry : angle 0.46421 (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 763 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 674 time to evaluate : 3.048 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8124 (t70) REVERT: A 98 ASP cc_start: 0.8695 (p0) cc_final: 0.8329 (p0) REVERT: A 99 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7830 (pttm) REVERT: A 158 ASN cc_start: 0.8364 (m-40) cc_final: 0.7944 (m110) REVERT: A 291 ASP cc_start: 0.8786 (t70) cc_final: 0.8263 (t0) REVERT: A 292 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8641 (pp) REVERT: A 307 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 96 ARG cc_start: 0.8229 (mtp85) cc_final: 0.8005 (mtp85) REVERT: B 260 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6828 (mtm180) REVERT: B 267 GLU cc_start: 0.8597 (tt0) cc_final: 0.8316 (tt0) REVERT: C 158 ASN cc_start: 0.8132 (m-40) cc_final: 0.7666 (m-40) REVERT: C 263 ASN cc_start: 0.8052 (m-40) cc_final: 0.7754 (m-40) REVERT: C 291 ASP cc_start: 0.8802 (t70) cc_final: 0.8585 (t70) REVERT: C 292 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8625 (pp) REVERT: D 22 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7685 (ttm-80) REVERT: D 37 ASN cc_start: 0.8824 (p0) cc_final: 0.8418 (p0) REVERT: D 96 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8040 (mtp85) REVERT: D 158 ASN cc_start: 0.7815 (m-40) cc_final: 0.7536 (m-40) REVERT: D 286 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8415 (mtmm) REVERT: D 294 MET cc_start: 0.8538 (pmm) cc_final: 0.8316 (pmm) REVERT: E 13 GLN cc_start: 0.8165 (tp40) cc_final: 0.7912 (tp40) REVERT: E 98 ASP cc_start: 0.8526 (p0) cc_final: 0.8303 (p0) REVERT: F 17 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7133 (tp-100) REVERT: F 21 ASP cc_start: 0.7634 (m-30) cc_final: 0.7013 (m-30) REVERT: F 38 GLN cc_start: 0.8707 (mt0) cc_final: 0.8375 (mm-40) REVERT: F 51 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8088 (mm-30) REVERT: F 96 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7929 (mtp85) REVERT: F 157 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 260 ARG cc_start: 0.7364 (mtt180) cc_final: 0.7112 (mtm180) REVERT: G 17 GLN cc_start: 0.7788 (tp40) cc_final: 0.7122 (tp40) REVERT: G 21 ASP cc_start: 0.7760 (m-30) cc_final: 0.7070 (m-30) REVERT: G 37 ASN cc_start: 0.8791 (p0) cc_final: 0.8463 (p0) REVERT: G 62 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: G 68 MET cc_start: 0.8449 (tpp) cc_final: 0.8052 (tpt) REVERT: H 13 GLN cc_start: 0.8322 (tp40) cc_final: 0.8008 (tp40) REVERT: H 35 PHE cc_start: 0.7675 (m-10) cc_final: 0.7319 (m-10) REVERT: H 286 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7820 (mtmt) REVERT: I 17 GLN cc_start: 0.7970 (tp40) cc_final: 0.7738 (tp40) REVERT: I 37 ASN cc_start: 0.8455 (p0) cc_final: 0.8014 (p0) REVERT: I 51 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7735 (mm-30) REVERT: I 99 LYS cc_start: 0.8160 (pttp) cc_final: 0.7886 (pttp) REVERT: I 102 LYS cc_start: 0.8541 (mttp) cc_final: 0.8308 (mptt) REVERT: I 158 ASN cc_start: 0.7755 (m-40) cc_final: 0.7453 (m-40) REVERT: I 267 GLU cc_start: 0.8872 (tp30) cc_final: 0.8597 (tp30) REVERT: I 286 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8433 (mtmt) REVERT: I 305 ASN cc_start: 0.8810 (m110) cc_final: 0.8353 (m-40) REVERT: J 5 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8292 (mmmm) REVERT: J 13 GLN cc_start: 0.8265 (mm110) cc_final: 0.8024 (tp40) REVERT: J 38 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8131 (mm-40) REVERT: J 78 LYS cc_start: 0.8722 (tptm) cc_final: 0.8417 (ttpt) REVERT: J 158 ASN cc_start: 0.8176 (m-40) cc_final: 0.7749 (m-40) REVERT: J 263 ASN cc_start: 0.8091 (m-40) cc_final: 0.7793 (m-40) REVERT: K 260 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6745 (mtm180) REVERT: L 5 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8482 (mmtp) REVERT: L 98 ASP cc_start: 0.8744 (p0) cc_final: 0.8401 (p0) REVERT: L 158 ASN cc_start: 0.7880 (m-40) cc_final: 0.7564 (m-40) REVERT: L 162 TRP cc_start: 0.8457 (p-90) cc_final: 0.7930 (p-90) REVERT: L 291 ASP cc_start: 0.8791 (t70) cc_final: 0.8383 (t70) REVERT: L 292 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8614 (pp) REVERT: L 307 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8292 (mt-10) outliers start: 89 outliers final: 65 residues processed: 726 average time/residue: 0.4191 time to fit residues: 469.7192 Evaluate side-chains 739 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 666 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 115 MET 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 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 128 ASP 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 193 HIS Chi-restraints excluded: chain D residue 220 ASP 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 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 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 193 HIS Chi-restraints excluded: chain H residue 36 SER 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 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 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 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 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: 1.9990 chunk 340 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.104444 restraints weight = 29137.667| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.18 r_work: 0.2772 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- 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 = 0.51 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: 0.8192 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28860 Z= 0.243 Angle : 0.536 8.978 39048 Z= 0.291 Chirality : 0.049 0.178 4620 Planarity : 0.003 0.039 4992 Dihedral : 4.604 48.968 3936 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.40 % Allowed : 17.62 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3660 helix: 1.78 (0.14), residues: 1512 sheet: -0.92 (0.16), residues: 1044 loop : -0.96 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 162 HIS 0.013 0.001 HIS A 12 PHE 0.018 0.001 PHE F 35 TYR 0.011 0.002 TYR H 146 ARG 0.006 0.000 ARG L 184 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1428) hydrogen bonds : angle 4.55896 ( 3996) covalent geometry : bond 0.00573 (28860) covalent geometry : angle 0.53613 (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 820 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 713 time to evaluate : 4.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8631 (p0) cc_final: 0.8189 (p0) REVERT: A 99 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7934 (pttt) REVERT: A 158 ASN cc_start: 0.8392 (m-40) cc_final: 0.8055 (m110) REVERT: A 291 ASP cc_start: 0.8869 (t70) cc_final: 0.8624 (t70) REVERT: A 292 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8616 (pp) REVERT: A 307 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 133 GLN cc_start: 0.8884 (mp10) cc_final: 0.8556 (mp10) REVERT: B 260 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6835 (mtm180) REVERT: B 267 GLU cc_start: 0.8604 (tt0) cc_final: 0.8372 (tt0) REVERT: C 158 ASN cc_start: 0.8077 (m-40) cc_final: 0.7852 (m-40) REVERT: C 263 ASN cc_start: 0.8027 (m-40) cc_final: 0.7743 (m-40) REVERT: C 292 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8534 (pp) REVERT: D 22 ARG cc_start: 0.8169 (mtt-85) cc_final: 0.7834 (tpp80) REVERT: D 37 ASN cc_start: 0.8771 (p0) cc_final: 0.8333 (p0) REVERT: D 96 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8046 (mtp85) REVERT: D 139 ASP cc_start: 0.8206 (m-30) cc_final: 0.7999 (m-30) REVERT: D 158 ASN cc_start: 0.7886 (m-40) cc_final: 0.7573 (m-40) REVERT: D 286 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: D 298 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8009 (mm-30) REVERT: E 13 GLN cc_start: 0.8249 (tp40) cc_final: 0.8008 (tp40) REVERT: E 98 ASP cc_start: 0.8485 (p0) cc_final: 0.8268 (p0) REVERT: E 222 MET cc_start: 0.8226 (ptm) cc_final: 0.7964 (ptm) REVERT: F 21 ASP cc_start: 0.7713 (m-30) cc_final: 0.7476 (m-30) REVERT: F 38 GLN cc_start: 0.8637 (mt0) cc_final: 0.8364 (mm-40) REVERT: F 51 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8186 (mm-30) REVERT: F 62 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7035 (pm20) REVERT: F 96 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7921 (mtp85) REVERT: F 157 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7045 (mt-10) REVERT: F 260 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7119 (mtp85) REVERT: G 17 GLN cc_start: 0.7812 (tp40) cc_final: 0.7047 (tp40) REVERT: G 21 ASP cc_start: 0.7864 (m-30) cc_final: 0.7234 (m-30) REVERT: G 38 GLN cc_start: 0.8550 (mt0) cc_final: 0.8250 (mm-40) REVERT: G 62 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: H 286 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: I 17 GLN cc_start: 0.8027 (tp40) cc_final: 0.7792 (tp40) REVERT: I 99 LYS cc_start: 0.8288 (pttp) cc_final: 0.7997 (pttp) REVERT: I 102 LYS cc_start: 0.8535 (mttp) cc_final: 0.8220 (mptt) REVERT: I 139 ASP cc_start: 0.8188 (m-30) cc_final: 0.7987 (m-30) REVERT: I 158 ASN cc_start: 0.7857 (m-40) cc_final: 0.7521 (m-40) REVERT: I 267 GLU cc_start: 0.8921 (tp30) cc_final: 0.8584 (tp30) REVERT: I 286 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8368 (mtmm) REVERT: I 305 ASN cc_start: 0.8776 (m110) cc_final: 0.8313 (m-40) REVERT: J 5 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8364 (mmmt) REVERT: J 25 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8402 (mt) REVERT: J 38 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8113 (mm-40) REVERT: J 78 LYS cc_start: 0.8675 (tptm) cc_final: 0.8298 (ttpt) REVERT: J 158 ASN cc_start: 0.8212 (m-40) cc_final: 0.7898 (m-40) REVERT: J 263 ASN cc_start: 0.7988 (m-40) cc_final: 0.7699 (m-40) REVERT: J 286 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7959 (mtpt) REVERT: K 133 GLN cc_start: 0.8917 (mp10) cc_final: 0.8570 (mp10) REVERT: K 260 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6762 (mtm180) REVERT: L 5 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8456 (mmtp) REVERT: L 33 LYS cc_start: 0.7284 (pttm) cc_final: 0.7006 (ptpt) REVERT: L 34 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7744 (mmtm) REVERT: L 98 ASP cc_start: 0.8792 (p0) cc_final: 0.8387 (p0) REVERT: L 158 ASN cc_start: 0.8043 (m-40) cc_final: 0.7713 (m-40) REVERT: L 292 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8526 (pp) REVERT: L 307 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8333 (mt-10) outliers start: 107 outliers final: 82 residues processed: 777 average time/residue: 0.5971 time to fit residues: 737.3225 Evaluate side-chains 769 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 678 time to evaluate : 3.864 ------------------------------------------------------------------------------- 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 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 12 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 SER 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 C residue 292 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 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 12 HIS Chi-restraints excluded: chain H residue 36 SER 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 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 272 THR 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 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 244 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: 0.9990 chunk 222 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 0.0570 chunk 333 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 193 HIS F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS I 193 HIS ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN K 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.163782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111378 restraints weight = 29159.780| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.96 r_work: 0.2866 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28860 Z= 0.121 Angle : 0.464 8.763 39048 Z= 0.252 Chirality : 0.046 0.215 4620 Planarity : 0.003 0.044 4992 Dihedral : 4.411 48.129 3936 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.89 % Allowed : 18.77 % Favored : 78.34 % 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: 0.42 (0.14), residues: 3660 helix: 2.01 (0.14), residues: 1512 sheet: -0.88 (0.16), residues: 1044 loop : -0.86 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 162 HIS 0.012 0.001 HIS A 12 PHE 0.008 0.001 PHE H 266 TYR 0.007 0.001 TYR E 146 ARG 0.007 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 1428) hydrogen bonds : angle 4.41386 ( 3996) covalent geometry : bond 0.00276 (28860) covalent geometry : angle 0.46363 (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 784 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 693 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8621 (p0) cc_final: 0.8278 (p0) REVERT: A 99 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7859 (pttt) REVERT: A 158 ASN cc_start: 0.8356 (m-40) cc_final: 0.7909 (m110) REVERT: A 291 ASP cc_start: 0.8763 (t70) cc_final: 0.8195 (t0) REVERT: A 292 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 307 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8444 (mt-10) REVERT: B 96 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7913 (mmm-85) REVERT: B 157 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7142 (mt-10) REVERT: B 260 ARG cc_start: 0.7163 (ttm170) cc_final: 0.6786 (mtm180) REVERT: B 267 GLU cc_start: 0.8603 (tt0) cc_final: 0.8342 (tt0) REVERT: C 33 LYS cc_start: 0.7185 (pttt) cc_final: 0.6905 (ptpp) REVERT: C 39 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7974 (mt-10) REVERT: C 158 ASN cc_start: 0.8071 (m-40) cc_final: 0.7672 (m-40) REVERT: C 263 ASN cc_start: 0.7675 (m-40) cc_final: 0.7366 (m-40) REVERT: C 292 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8564 (pp) REVERT: D 22 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7709 (ttm-80) REVERT: D 37 ASN cc_start: 0.8751 (p0) cc_final: 0.8306 (p0) REVERT: D 96 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8067 (mtp85) REVERT: D 139 ASP cc_start: 0.8109 (m-30) cc_final: 0.7892 (m-30) REVERT: D 158 ASN cc_start: 0.7808 (m-40) cc_final: 0.7486 (m-40) REVERT: D 286 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: E 13 GLN cc_start: 0.8234 (tp40) cc_final: 0.8011 (tp40) REVERT: E 98 ASP cc_start: 0.8533 (p0) cc_final: 0.8323 (p0) REVERT: E 234 ASP cc_start: 0.7381 (m-30) cc_final: 0.7144 (m-30) REVERT: E 286 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7869 (mtmt) REVERT: F 21 ASP cc_start: 0.7666 (m-30) cc_final: 0.7419 (m-30) REVERT: F 38 GLN cc_start: 0.8700 (mt0) cc_final: 0.8318 (mm-40) REVERT: F 51 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8089 (mm-30) REVERT: F 62 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: F 96 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8005 (mtp85) REVERT: F 157 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7012 (mt-10) REVERT: F 260 ARG cc_start: 0.7366 (mtt180) cc_final: 0.7131 (mtm180) REVERT: F 305 ASN cc_start: 0.8969 (m110) cc_final: 0.8572 (m-40) REVERT: G 17 GLN cc_start: 0.7808 (tp40) cc_final: 0.6859 (tp40) REVERT: G 21 ASP cc_start: 0.7831 (m-30) cc_final: 0.7023 (m-30) REVERT: G 38 GLN cc_start: 0.8581 (mt0) cc_final: 0.8277 (mm-40) REVERT: G 62 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: G 68 MET cc_start: 0.8462 (tpp) cc_final: 0.8118 (tpt) REVERT: G 114 ASN cc_start: 0.9178 (m-40) cc_final: 0.8838 (m-40) REVERT: G 305 ASN cc_start: 0.8976 (m110) cc_final: 0.8581 (m-40) REVERT: H 13 GLN cc_start: 0.8290 (tp40) cc_final: 0.7940 (tp40) REVERT: H 35 PHE cc_start: 0.7670 (m-10) cc_final: 0.7321 (m-10) REVERT: H 234 ASP cc_start: 0.7364 (m-30) cc_final: 0.7159 (m-30) REVERT: H 237 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7294 (mt) REVERT: H 286 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: I 17 GLN cc_start: 0.8014 (tp40) cc_final: 0.7794 (tp40) REVERT: I 37 ASN cc_start: 0.8367 (p0) cc_final: 0.7974 (p0) REVERT: I 38 GLN cc_start: 0.8661 (mt0) cc_final: 0.8459 (mm-40) REVERT: I 51 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7716 (mm-30) REVERT: I 102 LYS cc_start: 0.8523 (mttp) cc_final: 0.8311 (mptt) REVERT: I 158 ASN cc_start: 0.7791 (m-40) cc_final: 0.7441 (m-40) REVERT: I 267 GLU cc_start: 0.8824 (tp30) cc_final: 0.8515 (tp30) REVERT: I 286 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8356 (mtmt) REVERT: I 305 ASN cc_start: 0.8786 (m110) cc_final: 0.8322 (m-40) REVERT: J 5 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8251 (mmmm) REVERT: J 25 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8333 (mt) REVERT: J 33 LYS cc_start: 0.7241 (pttm) cc_final: 0.6855 (ptmm) REVERT: J 39 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7893 (mt-10) REVERT: J 78 LYS cc_start: 0.8717 (tptm) cc_final: 0.8397 (ttpt) REVERT: J 158 ASN cc_start: 0.8020 (m-40) cc_final: 0.7639 (m-40) REVERT: J 263 ASN cc_start: 0.8044 (m-40) cc_final: 0.7765 (m-40) REVERT: J 294 MET cc_start: 0.8592 (pmm) cc_final: 0.7859 (pmm) REVERT: K 157 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7435 (mt-10) REVERT: K 260 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6694 (mtm180) REVERT: K 267 GLU cc_start: 0.8558 (tt0) cc_final: 0.8336 (tt0) REVERT: L 78 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8115 (tmtm) REVERT: L 98 ASP cc_start: 0.8774 (p0) cc_final: 0.8418 (p0) REVERT: L 158 ASN cc_start: 0.7954 (m-40) cc_final: 0.7627 (m-40) REVERT: L 292 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8528 (pp) outliers start: 91 outliers final: 70 residues processed: 756 average time/residue: 0.4147 time to fit residues: 486.8214 Evaluate side-chains 752 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 671 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 SER 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 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 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 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 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 286 LYS Chi-restraints excluded: chain H residue 36 SER 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 118 VAL Chi-restraints excluded: chain I residue 193 HIS Chi-restraints excluded: chain I residue 208 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 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 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: 4.9990 chunk 278 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN G 263 ASN H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.162707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.110063 restraints weight = 29150.588| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.03 r_work: 0.2819 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28860 Z= 0.155 Angle : 0.481 8.665 39048 Z= 0.261 Chirality : 0.047 0.197 4620 Planarity : 0.003 0.044 4992 Dihedral : 4.421 48.953 3936 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.86 % Allowed : 18.80 % Favored : 78.34 % 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: 0.43 (0.14), residues: 3660 helix: 2.00 (0.14), residues: 1512 sheet: -0.86 (0.16), residues: 1044 loop : -0.86 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.014 0.001 HIS A 12 PHE 0.018 0.001 PHE F 35 TYR 0.009 0.001 TYR A 54 ARG 0.007 0.000 ARG K 177 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 1428) hydrogen bonds : angle 4.39073 ( 3996) covalent geometry : bond 0.00363 (28860) covalent geometry : angle 0.48126 (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 764 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 674 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8642 (p0) cc_final: 0.8214 (p0) REVERT: A 99 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7890 (pttt) REVERT: A 158 ASN cc_start: 0.8391 (m-40) cc_final: 0.7971 (m110) REVERT: A 291 ASP cc_start: 0.8783 (t70) cc_final: 0.8558 (t70) REVERT: A 292 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8653 (pp) REVERT: A 307 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 96 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7902 (mmm-85) REVERT: B 114 ASN cc_start: 0.9293 (m-40) cc_final: 0.9054 (m-40) REVERT: B 133 GLN cc_start: 0.8809 (mp10) cc_final: 0.8488 (mp10) REVERT: B 157 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 260 ARG cc_start: 0.7201 (ttm170) cc_final: 0.6808 (mtm180) REVERT: B 267 GLU cc_start: 0.8585 (tt0) cc_final: 0.8331 (tt0) REVERT: C 33 LYS cc_start: 0.7196 (pttt) cc_final: 0.6922 (ptpp) REVERT: C 39 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7973 (mt-10) REVERT: C 158 ASN cc_start: 0.8026 (m-40) cc_final: 0.7650 (m-40) REVERT: C 263 ASN cc_start: 0.7665 (m-40) cc_final: 0.7358 (m-40) REVERT: C 291 ASP cc_start: 0.8751 (t70) cc_final: 0.8133 (t70) REVERT: C 292 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8662 (pp) REVERT: C 294 MET cc_start: 0.8645 (pmm) cc_final: 0.7804 (pmm) REVERT: D 22 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7728 (ttm-80) REVERT: D 37 ASN cc_start: 0.8776 (p0) cc_final: 0.8315 (p0) REVERT: D 96 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8108 (mtp85) REVERT: D 139 ASP cc_start: 0.8116 (m-30) cc_final: 0.7900 (m-30) REVERT: D 158 ASN cc_start: 0.7835 (m-40) cc_final: 0.7523 (m-40) REVERT: D 286 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8376 (mtmm) REVERT: E 13 GLN cc_start: 0.8189 (tp40) cc_final: 0.7940 (tp40) REVERT: E 35 PHE cc_start: 0.7702 (m-10) cc_final: 0.7293 (m-10) REVERT: E 234 ASP cc_start: 0.7413 (m-30) cc_final: 0.7196 (m-30) REVERT: E 237 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7191 (mt) REVERT: E 286 LYS cc_start: 0.8156 (ptpt) cc_final: 0.7877 (mtmt) REVERT: F 17 GLN cc_start: 0.7771 (tp-100) cc_final: 0.6993 (tp-100) REVERT: F 21 ASP cc_start: 0.7698 (m-30) cc_final: 0.7050 (m-30) REVERT: F 38 GLN cc_start: 0.8677 (mt0) cc_final: 0.8287 (mm-40) REVERT: F 51 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8125 (mm-30) REVERT: F 62 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: F 96 ARG cc_start: 0.8242 (mtp85) cc_final: 0.8024 (mtp85) REVERT: F 157 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7002 (mt-10) REVERT: F 260 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7080 (mtm180) REVERT: G 17 GLN cc_start: 0.7855 (tp40) cc_final: 0.7156 (tp40) REVERT: G 21 ASP cc_start: 0.7829 (m-30) cc_final: 0.7209 (m-30) REVERT: G 38 GLN cc_start: 0.8558 (mt0) cc_final: 0.8251 (mm-40) REVERT: G 62 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: G 68 MET cc_start: 0.8465 (tpp) cc_final: 0.8093 (tpt) REVERT: H 13 GLN cc_start: 0.8288 (tp40) cc_final: 0.7922 (tp40) REVERT: H 35 PHE cc_start: 0.7686 (m-10) cc_final: 0.7367 (m-10) REVERT: H 234 ASP cc_start: 0.7414 (m-30) cc_final: 0.7195 (m-30) REVERT: H 237 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7180 (mt) REVERT: H 286 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7869 (mtmt) REVERT: I 37 ASN cc_start: 0.8414 (p0) cc_final: 0.8023 (p0) REVERT: I 51 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7772 (mm-30) REVERT: I 158 ASN cc_start: 0.7867 (m-40) cc_final: 0.7533 (m-40) REVERT: I 267 GLU cc_start: 0.8806 (tp30) cc_final: 0.8493 (tp30) REVERT: I 286 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8325 (mtmt) REVERT: I 305 ASN cc_start: 0.8781 (m110) cc_final: 0.8316 (m-40) REVERT: J 5 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8285 (mmmm) REVERT: J 33 LYS cc_start: 0.7227 (pttm) cc_final: 0.6843 (ptmm) REVERT: J 39 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7918 (mt-10) REVERT: J 78 LYS cc_start: 0.8711 (tptm) cc_final: 0.8393 (ttpt) REVERT: J 158 ASN cc_start: 0.8021 (m-40) cc_final: 0.7624 (m-40) REVERT: J 263 ASN cc_start: 0.8045 (m-40) cc_final: 0.7755 (m-40) REVERT: J 294 MET cc_start: 0.8608 (pmm) cc_final: 0.7845 (pmm) REVERT: K 157 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7392 (mt-10) REVERT: K 260 ARG cc_start: 0.7222 (ttm170) cc_final: 0.6739 (mtm180) REVERT: L 98 ASP cc_start: 0.8829 (p0) cc_final: 0.8483 (p0) REVERT: L 158 ASN cc_start: 0.7963 (m-40) cc_final: 0.7647 (m-40) REVERT: L 292 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (pp) outliers start: 90 outliers final: 77 residues processed: 736 average time/residue: 0.4335 time to fit residues: 497.1013 Evaluate side-chains 754 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 667 time to evaluate : 3.469 ------------------------------------------------------------------------------- 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 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 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 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 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 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 286 LYS Chi-restraints excluded: chain H residue 36 SER 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 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 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 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 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: 0.6980 chunk 273 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 263 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.165053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.111645 restraints weight = 28975.437| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.09 r_work: 0.2824 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28860 Z= 0.125 Angle : 0.464 8.637 39048 Z= 0.251 Chirality : 0.046 0.188 4620 Planarity : 0.003 0.053 4992 Dihedral : 4.327 49.219 3936 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.83 % Allowed : 18.92 % Favored : 78.24 % 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: 0.51 (0.14), residues: 3660 helix: 2.10 (0.14), residues: 1512 sheet: -0.82 (0.16), residues: 1044 loop : -0.86 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.013 0.001 HIS A 12 PHE 0.010 0.001 PHE K 35 TYR 0.006 0.001 TYR E 146 ARG 0.007 0.000 ARG K 177 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 1428) hydrogen bonds : angle 4.32832 ( 3996) covalent geometry : bond 0.00290 (28860) covalent geometry : angle 0.46356 (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 767 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 678 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8610 (p0) cc_final: 0.8256 (p0) REVERT: A 99 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7846 (pttt) REVERT: A 158 ASN cc_start: 0.8352 (m-40) cc_final: 0.7950 (m110) REVERT: A 291 ASP cc_start: 0.8769 (t70) cc_final: 0.8202 (t0) REVERT: A 292 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 307 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8434 (mt-10) REVERT: B 96 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7912 (mmm-85) REVERT: B 157 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 267 GLU cc_start: 0.8578 (tt0) cc_final: 0.8335 (tt0) REVERT: C 33 LYS cc_start: 0.7174 (pttt) cc_final: 0.6943 (ptpp) REVERT: C 39 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7990 (mt-10) REVERT: C 158 ASN cc_start: 0.7981 (m-40) cc_final: 0.7632 (m-40) REVERT: C 263 ASN cc_start: 0.7660 (m-40) cc_final: 0.7348 (m-40) REVERT: C 291 ASP cc_start: 0.8737 (t70) cc_final: 0.8106 (t70) REVERT: C 292 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8719 (pp) REVERT: C 294 MET cc_start: 0.8630 (pmm) cc_final: 0.7749 (pmm) REVERT: D 22 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7737 (ttm-80) REVERT: D 37 ASN cc_start: 0.8737 (p0) cc_final: 0.8288 (p0) REVERT: D 96 ARG cc_start: 0.8301 (mtp85) cc_final: 0.8078 (mtp85) REVERT: D 139 ASP cc_start: 0.8125 (m-30) cc_final: 0.7913 (m-30) REVERT: D 158 ASN cc_start: 0.7828 (m-40) cc_final: 0.7515 (m-40) REVERT: D 212 LYS cc_start: 0.8707 (tttt) cc_final: 0.8339 (mmtm) REVERT: D 286 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8384 (mtmm) REVERT: E 13 GLN cc_start: 0.8199 (tp40) cc_final: 0.7948 (tp40) REVERT: E 35 PHE cc_start: 0.7648 (m-10) cc_final: 0.7163 (m-10) REVERT: E 234 ASP cc_start: 0.7437 (m-30) cc_final: 0.7204 (m-30) REVERT: E 286 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7864 (mtmt) REVERT: E 291 ASP cc_start: 0.8714 (t70) cc_final: 0.8364 (t0) REVERT: F 17 GLN cc_start: 0.7799 (tp-100) cc_final: 0.6979 (tp-100) REVERT: F 21 ASP cc_start: 0.7716 (m-30) cc_final: 0.6975 (m-30) REVERT: F 38 GLN cc_start: 0.8679 (mt0) cc_final: 0.8313 (mm-40) REVERT: F 51 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8091 (mm-30) REVERT: F 62 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: F 157 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6952 (mt-10) REVERT: F 260 ARG cc_start: 0.7304 (mtt180) cc_final: 0.7060 (mtm180) REVERT: F 305 ASN cc_start: 0.8956 (m110) cc_final: 0.8560 (m-40) REVERT: G 17 GLN cc_start: 0.7858 (tp40) cc_final: 0.6858 (tp40) REVERT: G 21 ASP cc_start: 0.7835 (m-30) cc_final: 0.6998 (m-30) REVERT: G 38 GLN cc_start: 0.8596 (mt0) cc_final: 0.8312 (mm-40) REVERT: G 62 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: G 68 MET cc_start: 0.8502 (tpp) cc_final: 0.8151 (tpt) REVERT: G 158 ASN cc_start: 0.8468 (m-40) cc_final: 0.8216 (m110) REVERT: G 305 ASN cc_start: 0.9023 (m110) cc_final: 0.8614 (m-40) REVERT: H 13 GLN cc_start: 0.8302 (tp40) cc_final: 0.7945 (tp40) REVERT: H 35 PHE cc_start: 0.7652 (m-10) cc_final: 0.7152 (m-10) REVERT: H 234 ASP cc_start: 0.7406 (m-30) cc_final: 0.7189 (m-30) REVERT: H 237 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7324 (mt) REVERT: H 286 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: I 37 ASN cc_start: 0.8394 (p0) cc_final: 0.7997 (p0) REVERT: I 51 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7776 (mm-30) REVERT: I 52 ASP cc_start: 0.8762 (t0) cc_final: 0.8304 (t0) REVERT: I 158 ASN cc_start: 0.7845 (m-40) cc_final: 0.7540 (m-40) REVERT: I 267 GLU cc_start: 0.8764 (tp30) cc_final: 0.8467 (tp30) REVERT: I 286 LYS cc_start: 0.8670 (ptpp) cc_final: 0.8315 (mtmt) REVERT: I 305 ASN cc_start: 0.8817 (m110) cc_final: 0.8345 (m-40) REVERT: J 5 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8325 (mmmm) REVERT: J 33 LYS cc_start: 0.7239 (pttm) cc_final: 0.6884 (ptmm) REVERT: J 39 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7918 (mt-10) REVERT: J 78 LYS cc_start: 0.8735 (tptm) cc_final: 0.8431 (ttpt) REVERT: J 158 ASN cc_start: 0.7978 (m-40) cc_final: 0.7633 (m-40) REVERT: J 263 ASN cc_start: 0.7999 (m-40) cc_final: 0.7713 (m-40) REVERT: J 294 MET cc_start: 0.8616 (pmm) cc_final: 0.7858 (pmm) REVERT: K 157 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7407 (mt-10) REVERT: K 260 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6699 (mtm180) REVERT: K 267 GLU cc_start: 0.8541 (tt0) cc_final: 0.8319 (tt0) REVERT: K 286 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8136 (mtpt) REVERT: L 78 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8157 (tmtm) REVERT: L 98 ASP cc_start: 0.8808 (p0) cc_final: 0.8437 (p0) REVERT: L 158 ASN cc_start: 0.7923 (m-40) cc_final: 0.7605 (m-40) outliers start: 89 outliers final: 75 residues processed: 738 average time/residue: 0.5025 time to fit residues: 586.3611 Evaluate side-chains 753 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 669 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 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 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 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 C residue 292 ILE Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 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 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 286 LYS Chi-restraints excluded: chain H residue 36 SER 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 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 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 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 152 LEU Chi-restraints excluded: chain K residue 193 HIS Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 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 78 LYS Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 270 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 357 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 338 optimal weight: 0.3980 chunk 165 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** D 263 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 57 GLN ** F 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** J 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN K 158 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.162374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.109732 restraints weight = 29239.963| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.02 r_work: 0.2823 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 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 = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28860 Z= 0.140 Angle : 0.472 8.600 39048 Z= 0.256 Chirality : 0.047 0.184 4620 Planarity : 0.003 0.050 4992 Dihedral : 4.345 49.528 3936 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.86 % Allowed : 18.92 % 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: 0.51 (0.14), residues: 3660 helix: 2.08 (0.14), residues: 1512 sheet: -0.81 (0.16), residues: 1044 loop : -0.85 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.013 0.001 HIS A 12 PHE 0.020 0.001 PHE F 35 TYR 0.009 0.001 TYR E 146 ARG 0.007 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 1428) hydrogen bonds : angle 4.32659 ( 3996) covalent geometry : bond 0.00326 (28860) covalent geometry : angle 0.47202 (39048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18826.44 seconds wall clock time: 327 minutes 29.37 seconds (19649.37 seconds total)