Starting phenix.real_space_refine on Sat Sep 12 11:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.cif" model { file = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8br2_16197/09_2026/8br2_16197.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 58 5.49 5 S 78 5.16 5 C 9477 2.51 5 N 2757 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15574 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "B" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "C" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "D" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "E" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "F" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 residue: pdb=" N AARG A 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 254 " occ=0.50 residue: pdb=" N AARG B 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 130 " occ=0.50 residue: pdb=" N AARG B 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 254 " occ=0.50 residue: pdb=" N AARG C 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 130 " occ=0.50 residue: pdb=" N AARG C 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 254 " occ=0.50 residue: pdb=" N AARG D 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 130 " occ=0.50 residue: pdb=" N AARG D 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 254 " occ=0.50 residue: pdb=" N AARG E 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 130 " occ=0.50 residue: pdb=" N AARG E 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 254 " occ=0.50 residue: pdb=" N AARG F 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 130 " occ=0.50 residue: pdb=" N AARG F 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 254 " occ=0.50 Time building chain proxies: 6.10, per 1000 atoms: 0.39 Number of scatterers: 15574 At special positions: 0 Unit cell: (126.488, 138.224, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 78 16.00 P 58 15.00 O 3192 8.00 N 2757 7.00 C 9477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 18 sheets defined 52.5% alpha, 17.0% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.876A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.853A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.576A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.590A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.657A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 196 through 214 removed outlier: 3.885A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.885A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.876A pdb=" N GLN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.853A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.576A pdb=" N GLU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.590A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.657A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.884A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.885A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.876A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.852A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.576A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.590A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.657A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.885A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.886A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.876A pdb=" N GLN D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.852A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.576A pdb=" N GLU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.590A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.657A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'D' and resid 196 through 214 removed outlier: 3.884A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.885A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 removed outlier: 3.876A pdb=" N GLN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.852A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 98 removed outlier: 3.575A pdb=" N GLU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.589A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.658A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.885A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.886A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 3.877A pdb=" N GLN F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.853A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.531A pdb=" N LYS F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.576A pdb=" N GLU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.590A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.657A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.885A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.664A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.886A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.321A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 127 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.321A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 5.321A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.321A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE D 122 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU D 300 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE D 126 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LYS D 304 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 88 removed outlier: 5.321A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 127 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.322A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 218 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'F' and resid 269 through 271 719 hydrogen bonds defined for protein. 2058 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2549 1.31 - 1.43: 4095 1.43 - 1.56: 8890 1.56 - 1.68: 108 1.68 - 1.80: 126 Bond restraints: 15768 Sorted by residual: bond pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " ideal model delta sigma weight residual 1.367 1.440 -0.073 6.00e-03 2.78e+04 1.47e+02 bond pdb=" N1 DT H 17 " pdb=" C6 DT H 17 " ideal model delta sigma weight residual 1.378 1.460 -0.082 7.00e-03 2.04e+04 1.36e+02 bond pdb=" N1 DT H 11 " pdb=" C6 DT H 11 " ideal model delta sigma weight residual 1.378 1.446 -0.068 7.00e-03 2.04e+04 9.45e+01 bond pdb=" C5 DA H 20 " pdb=" C6 DA H 20 " ideal model delta sigma weight residual 1.406 1.492 -0.086 9.00e-03 1.23e+04 9.03e+01 bond pdb=" C5 DT H 11 " pdb=" C6 DT H 11 " ideal model delta sigma weight residual 1.339 1.403 -0.064 7.00e-03 2.04e+04 8.32e+01 ... (remaining 15763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20622 1.28 - 2.55: 703 2.55 - 3.83: 131 3.83 - 5.10: 20 5.10 - 6.38: 12 Bond angle restraints: 21488 Sorted by residual: angle pdb=" N9 DA H 20 " pdb=" C4 DA H 20 " pdb=" C5 DA H 20 " ideal model delta sigma weight residual 105.80 101.99 3.81 4.00e-01 6.25e+00 9.08e+01 angle pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " pdb=" C5 DC H 8 " ideal model delta sigma weight residual 121.00 117.54 3.46 5.00e-01 4.00e+00 4.80e+01 angle pdb=" C6 DA H 20 " pdb=" C5 DA H 20 " pdb=" C4 DA H 20 " ideal model delta sigma weight residual 117.00 113.56 3.44 5.00e-01 4.00e+00 4.74e+01 angle pdb=" N9 DA H 14 " pdb=" C8 DA H 14 " pdb=" N7 DA H 14 " ideal model delta sigma weight residual 113.80 110.51 3.29 5.00e-01 4.00e+00 4.32e+01 angle pdb=" N7 DA H 20 " pdb=" C5 DA H 20 " pdb=" C4 DA H 20 " ideal model delta sigma weight residual 110.70 113.98 -3.28 5.00e-01 4.00e+00 4.30e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8076 17.38 - 34.75: 931 34.75 - 52.12: 256 52.12 - 69.50: 115 69.50 - 86.87: 26 Dihedral angle restraints: 9404 sinusoidal: 4034 harmonic: 5370 Sorted by residual: dihedral pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CD ARG E 303 " pdb=" NE ARG E 303 " pdb=" CZ ARG E 303 " pdb=" NH1 ARG E 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CD ARG C 303 " pdb=" NE ARG C 303 " pdb=" CZ ARG C 303 " pdb=" NH1 ARG C 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 9401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1526 0.037 - 0.074: 618 0.074 - 0.112: 237 0.112 - 0.149: 40 0.149 - 0.186: 13 Chirality restraints: 2434 Sorted by residual: chirality pdb=" C3' DT G 7 " pdb=" C4' DT G 7 " pdb=" O3' DT G 7 " pdb=" C2' DT G 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA BARG A 130 " pdb=" N BARG A 130 " pdb=" C BARG A 130 " pdb=" CB BARG A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA BARG C 130 " pdb=" N BARG C 130 " pdb=" C BARG C 130 " pdb=" CB BARG C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2431 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 303 " -1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 303 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 303 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 303 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG B 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 303 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG F 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG F 303 " 0.016 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 482 2.67 - 3.23: 14595 3.23 - 3.79: 24938 3.79 - 4.34: 37527 4.34 - 4.90: 58002 Nonbonded interactions: 135544 Sorted by model distance: nonbonded pdb=" OG1 THR F 134 " pdb="CA CA F 401 " model vdw 2.117 2.510 nonbonded pdb=" OG1 THR A 134 " pdb="CA CA A 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR E 134 " pdb="CA CA E 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR B 134 " pdb="CA CA B 401 " model vdw 2.118 2.510 ... (remaining 135539 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'B' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'C' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'D' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'E' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'F' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.070 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.008 0.086 15768 Z= 0.469 Angle : 0.581 6.377 21488 Z= 0.400 Chirality : 0.046 0.186 2434 Planarity : 0.024 0.490 2632 Dihedral : 17.500 86.872 5972 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.80 % Allowed : 22.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.17), residues: 1878 helix: -2.43 (0.13), residues: 894 sheet: 0.23 (0.30), residues: 306 loop : -1.87 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 247 TYR 0.010 0.002 TYR A 159 PHE 0.008 0.002 PHE D 129 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.47 (15768) covalent geometry : angle 0.58147 / 0.40 (21488) hydrogen bonds : bond 0.21623 / 14.40 ( 761) hydrogen bonds : angle 7.78207 / 5.53 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 444 time to evaluate : 0.442 Fit side-chains REVERT: A 176 GLU cc_start: 0.7387 (tp30) cc_final: 0.7039 (tp30) REVERT: A 243 MET cc_start: 0.8725 (mtp) cc_final: 0.8365 (mtt) REVERT: A 266 THR cc_start: 0.8968 (m) cc_final: 0.8599 (m) REVERT: A 268 GLN cc_start: 0.9032 (mt0) cc_final: 0.8641 (mt0) REVERT: B 40 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7273 (mttt) REVERT: B 95 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7879 (mtm110) REVERT: B 187 ASP cc_start: 0.8264 (m-30) cc_final: 0.7922 (m-30) REVERT: C 39 LYS cc_start: 0.8098 (mttt) cc_final: 0.7681 (ttpt) REVERT: C 70 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6556 (mmmm) REVERT: C 176 GLU cc_start: 0.7955 (tp30) cc_final: 0.7549 (tp30) REVERT: C 205 TYR cc_start: 0.8273 (m-80) cc_final: 0.8024 (m-80) REVERT: C 211 MET cc_start: 0.8173 (mtt) cc_final: 0.7794 (mtt) REVERT: C 235 ARG cc_start: 0.9057 (ttp-170) cc_final: 0.8532 (ttp-170) REVERT: D 43 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7339 (mm-30) REVERT: D 108 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7637 (tp30) REVERT: D 111 LYS cc_start: 0.8070 (mttp) cc_final: 0.7812 (mtmt) REVERT: D 210 MET cc_start: 0.9015 (mtp) cc_final: 0.8799 (mtm) REVERT: E 40 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6882 (mmtp) REVERT: E 111 LYS cc_start: 0.7993 (mttp) cc_final: 0.7712 (mttt) REVERT: E 200 GLN cc_start: 0.9231 (tt0) cc_final: 0.8999 (tt0) REVERT: E 284 LYS cc_start: 0.8046 (pttm) cc_final: 0.7673 (ptmt) REVERT: F 70 LYS cc_start: 0.5470 (mmtt) cc_final: 0.5072 (mmtt) REVERT: F 210 MET cc_start: 0.8417 (mtp) cc_final: 0.7983 (mtp) REVERT: F 330 ASN cc_start: 0.8432 (m-40) cc_final: 0.8217 (m110) outliers start: 6 outliers final: 5 residues processed: 450 average time/residue: 0.7926 time to fit residues: 384.6813 Evaluate side-chains 246 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain E residue 31 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 206 GLN A 290 ASN B 23 GLN B 145 GLN B 202 GLN B 330 ASN C 23 GLN C 101 GLN C 138 HIS C 145 GLN C 202 GLN C 206 GLN D 114 GLN D 145 GLN D 196 ASN D 202 GLN E 206 GLN E 290 ASN F 202 GLN F 206 GLN F 290 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.134998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098527 restraints weight = 77485.784| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 5.18 r_work: 0.2517 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15768 Z= 0.162 Angle : 0.587 6.400 21488 Z= 0.325 Chirality : 0.043 0.177 2434 Planarity : 0.005 0.103 2632 Dihedral : 14.303 81.200 2521 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.65 % Allowed : 23.17 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 1878 helix: -0.52 (0.16), residues: 894 sheet: 0.01 (0.29), residues: 348 loop : -1.24 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 303 TYR 0.019 0.002 TYR F 178 PHE 0.014 0.002 PHE F 46 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (15768) covalent geometry : angle 0.58725 / 0.32 (21488) hydrogen bonds : bond 0.04793 / 3.25 ( 761) hydrogen bonds : angle 4.79342 / 3.40 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.605 Fit side-chains REVERT: A 42 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7042 (tp30) REVERT: A 57 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6501 (tttp) REVERT: A 107 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7750 (mtpt) REVERT: A 206 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: A 266 THR cc_start: 0.9174 (m) cc_final: 0.8822 (m) REVERT: B 43 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7274 (mm-30) REVERT: B 94 GLN cc_start: 0.7998 (mt0) cc_final: 0.7743 (mt0) REVERT: B 165 THR cc_start: 0.8952 (m) cc_final: 0.8664 (p) REVERT: B 210 MET cc_start: 0.8885 (mtp) cc_final: 0.8526 (mtp) REVERT: C 39 LYS cc_start: 0.7625 (mttt) cc_final: 0.7019 (ttpt) REVERT: C 70 LYS cc_start: 0.6945 (mmtt) cc_final: 0.6324 (mmmm) REVERT: C 176 GLU cc_start: 0.8561 (tp30) cc_final: 0.8060 (tp30) REVERT: C 205 TYR cc_start: 0.8751 (m-80) cc_final: 0.8411 (m-80) REVERT: C 326 MET cc_start: 0.9211 (ttm) cc_final: 0.8869 (ttm) REVERT: D 43 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7182 (mm-30) REVERT: D 64 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7364 (pttt) REVERT: D 108 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8141 (mm-30) REVERT: D 111 LYS cc_start: 0.8537 (mttp) cc_final: 0.8024 (mtmt) REVERT: D 176 GLU cc_start: 0.7960 (tp30) cc_final: 0.7728 (tm-30) REVERT: E 39 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7140 (ptmt) REVERT: E 40 LYS cc_start: 0.6756 (mmtt) cc_final: 0.6409 (mmtp) REVERT: E 43 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7118 (mt-10) REVERT: E 70 LYS cc_start: 0.6623 (tptt) cc_final: 0.6367 (tppt) REVERT: E 111 LYS cc_start: 0.7329 (mttp) cc_final: 0.6840 (mttt) REVERT: E 267 ASN cc_start: 0.9388 (t0) cc_final: 0.9091 (t0) REVERT: E 285 LYS cc_start: 0.8991 (ptmm) cc_final: 0.8779 (ptmt) REVERT: E 310 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8364 (mtt-85) REVERT: F 70 LYS cc_start: 0.5985 (mmtt) cc_final: 0.5384 (mtpp) REVERT: F 108 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: F 210 MET cc_start: 0.8567 (mtp) cc_final: 0.8101 (mtp) REVERT: F 211 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8167 (mtt) outliers start: 50 outliers final: 12 residues processed: 290 average time/residue: 0.8532 time to fit residues: 265.9014 Evaluate side-chains 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 138 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 196 ASN D 202 GLN D 272 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092966 restraints weight = 78183.365| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 5.28 r_work: 0.2471 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2457 r_free = 0.2457 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15768 Z= 0.232 Angle : 0.590 6.717 21488 Z= 0.322 Chirality : 0.044 0.143 2434 Planarity : 0.005 0.049 2632 Dihedral : 14.235 81.171 2520 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.12 % Allowed : 22.84 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 1878 helix: 0.10 (0.17), residues: 900 sheet: -0.05 (0.28), residues: 342 loop : -1.04 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.023 0.002 TYR B 159 PHE 0.018 0.002 PHE B 327 HIS 0.008 0.002 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (15768) covalent geometry : angle 0.59030 / 0.32 (21488) hydrogen bonds : bond 0.04369 / 3.00 ( 761) hydrogen bonds : angle 4.52158 / 3.21 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.570 Fit side-chains REVERT: A 42 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7117 (tp30) REVERT: A 57 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6816 (tttp) REVERT: A 66 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7388 (mp) REVERT: A 202 GLN cc_start: 0.7169 (tm130) cc_final: 0.6872 (tt0) REVERT: A 266 THR cc_start: 0.9343 (m) cc_final: 0.9064 (m) REVERT: B 43 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7267 (mm-30) REVERT: B 94 GLN cc_start: 0.8072 (mt0) cc_final: 0.7866 (mt0) REVERT: B 98 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7238 (pp20) REVERT: B 161 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8653 (t70) REVERT: B 165 THR cc_start: 0.8972 (m) cc_final: 0.8695 (p) REVERT: C 39 LYS cc_start: 0.7709 (mttt) cc_final: 0.7087 (ttpt) REVERT: C 70 LYS cc_start: 0.6572 (mmtt) cc_final: 0.5914 (mmmm) REVERT: C 169 GLU cc_start: 0.8634 (pm20) cc_final: 0.8264 (mm-30) REVERT: C 176 GLU cc_start: 0.8689 (tp30) cc_final: 0.8174 (tp30) REVERT: C 205 TYR cc_start: 0.8771 (m-80) cc_final: 0.8368 (m-80) REVERT: C 326 MET cc_start: 0.9158 (ttm) cc_final: 0.8955 (ttm) REVERT: D 43 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7170 (mm-30) REVERT: D 64 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7340 (pttt) REVERT: D 111 LYS cc_start: 0.8509 (mttp) cc_final: 0.8065 (mtmt) REVERT: E 39 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7030 (ptmt) REVERT: E 40 LYS cc_start: 0.6807 (mmtt) cc_final: 0.6494 (mmtp) REVERT: E 43 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 70 LYS cc_start: 0.6615 (tptt) cc_final: 0.6336 (tppt) REVERT: E 111 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7242 (mttt) REVERT: E 310 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8206 (mtt-85) REVERT: F 70 LYS cc_start: 0.6022 (mmtt) cc_final: 0.5380 (mtpp) REVERT: F 108 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: F 210 MET cc_start: 0.8650 (mtp) cc_final: 0.8205 (mtp) REVERT: F 213 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7387 (mp0) REVERT: F 253 LEU cc_start: 0.8510 (tp) cc_final: 0.8303 (tp) outliers start: 52 outliers final: 23 residues processed: 280 average time/residue: 0.8515 time to fit residues: 256.3926 Evaluate side-chains 262 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN B 290 ASN C 23 GLN C 30 GLN C 202 GLN D 202 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.132609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094423 restraints weight = 71495.336| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 5.03 r_work: 0.2508 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15768 Z= 0.142 Angle : 0.515 7.002 21488 Z= 0.282 Chirality : 0.041 0.145 2434 Planarity : 0.004 0.047 2632 Dihedral : 14.102 81.449 2519 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.65 % Allowed : 23.51 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1878 helix: 0.52 (0.17), residues: 900 sheet: 0.06 (0.31), residues: 300 loop : -0.95 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 310 TYR 0.012 0.001 TYR B 159 PHE 0.012 0.001 PHE F 46 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15768) covalent geometry : angle 0.51504 / 0.28 (21488) hydrogen bonds : bond 0.03271 / 2.24 ( 761) hydrogen bonds : angle 4.17140 / 2.95 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.543 Fit side-chains REVERT: A 42 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7209 (tp30) REVERT: A 57 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6762 (mmtt) REVERT: A 66 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7468 (mp) REVERT: A 184 ASP cc_start: 0.7725 (m-30) cc_final: 0.7508 (m-30) REVERT: A 202 GLN cc_start: 0.7432 (tm130) cc_final: 0.6989 (tt0) REVERT: A 266 THR cc_start: 0.9268 (m) cc_final: 0.8973 (m) REVERT: B 43 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7328 (tp30) REVERT: B 98 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7244 (pp20) REVERT: B 154 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8079 (mt-10) REVERT: B 161 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8594 (t70) REVERT: B 165 THR cc_start: 0.8928 (m) cc_final: 0.8661 (p) REVERT: B 285 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8527 (ptpt) REVERT: C 39 LYS cc_start: 0.7653 (mttt) cc_final: 0.7065 (ttpt) REVERT: C 70 LYS cc_start: 0.6561 (mmtt) cc_final: 0.5909 (mmmm) REVERT: C 114 GLN cc_start: 0.8919 (mt0) cc_final: 0.8717 (mt0) REVERT: C 169 GLU cc_start: 0.8585 (pm20) cc_final: 0.8309 (mm-30) REVERT: C 176 GLU cc_start: 0.8668 (tp30) cc_final: 0.8152 (tp30) REVERT: C 205 TYR cc_start: 0.8764 (m-80) cc_final: 0.8354 (m-80) REVERT: C 326 MET cc_start: 0.9100 (ttm) cc_final: 0.8875 (ttm) REVERT: D 43 GLU cc_start: 0.7949 (mt-10) cc_final: 0.6948 (mp0) REVERT: D 64 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7271 (pttt) REVERT: D 72 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: D 111 LYS cc_start: 0.8512 (mttp) cc_final: 0.8061 (mtmt) REVERT: D 177 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8525 (ttt-90) REVERT: E 39 LYS cc_start: 0.7806 (mmmm) cc_final: 0.7095 (ptmt) REVERT: E 40 LYS cc_start: 0.6782 (mmtt) cc_final: 0.6478 (mmtp) REVERT: E 43 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7071 (mt-10) REVERT: E 70 LYS cc_start: 0.6621 (tptt) cc_final: 0.6317 (tppt) REVERT: E 111 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7271 (mttt) REVERT: E 215 ARG cc_start: 0.9036 (ttt90) cc_final: 0.8690 (ttt90) REVERT: E 267 ASN cc_start: 0.9470 (t0) cc_final: 0.9184 (t0) REVERT: E 285 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8632 (ptmm) REVERT: F 70 LYS cc_start: 0.6005 (mmtt) cc_final: 0.5248 (mtpp) REVERT: F 108 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: F 210 MET cc_start: 0.8606 (mtp) cc_final: 0.8225 (mtp) REVERT: F 213 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7401 (mp0) REVERT: F 253 LEU cc_start: 0.8674 (tp) cc_final: 0.8271 (tp) REVERT: F 324 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7690 (mt-10) outliers start: 44 outliers final: 18 residues processed: 283 average time/residue: 0.8408 time to fit residues: 255.9279 Evaluate side-chains 263 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN B 94 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 34 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.091801 restraints weight = 69085.285| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.88 r_work: 0.2480 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15768 Z= 0.226 Angle : 0.587 7.600 21488 Z= 0.316 Chirality : 0.044 0.147 2434 Planarity : 0.005 0.047 2632 Dihedral : 13.977 81.581 2519 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.52 % Allowed : 23.17 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1878 helix: 0.50 (0.17), residues: 900 sheet: 0.04 (0.39), residues: 210 loop : -1.14 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 250 TYR 0.017 0.002 TYR B 159 PHE 0.015 0.002 PHE A 92 HIS 0.009 0.002 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (15768) covalent geometry : angle 0.58710 / 0.32 (21488) hydrogen bonds : bond 0.03763 / 2.58 ( 761) hydrogen bonds : angle 4.31650 / 3.06 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6888 (mtt-85) REVERT: A 42 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7232 (tp30) REVERT: A 184 ASP cc_start: 0.7779 (m-30) cc_final: 0.7510 (m-30) REVERT: A 202 GLN cc_start: 0.7427 (tm130) cc_final: 0.6933 (tt0) REVERT: A 266 THR cc_start: 0.9412 (m) cc_final: 0.9178 (m) REVERT: B 31 CYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7218 (t) REVERT: B 43 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7341 (tp30) REVERT: B 98 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7294 (pp20) REVERT: B 154 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8098 (mt-10) REVERT: B 161 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8646 (t70) REVERT: B 165 THR cc_start: 0.8979 (m) cc_final: 0.8708 (p) REVERT: C 39 LYS cc_start: 0.7764 (mttt) cc_final: 0.7179 (ttpt) REVERT: C 70 LYS cc_start: 0.6575 (mmtt) cc_final: 0.5903 (mmmm) REVERT: C 114 GLN cc_start: 0.8903 (mt0) cc_final: 0.8694 (mt0) REVERT: C 176 GLU cc_start: 0.8722 (tp30) cc_final: 0.8233 (tp30) REVERT: C 205 TYR cc_start: 0.8787 (m-80) cc_final: 0.8368 (m-80) REVERT: D 43 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7090 (mp0) REVERT: D 64 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7286 (pttt) REVERT: D 72 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: D 111 LYS cc_start: 0.8599 (mttp) cc_final: 0.8066 (mtmt) REVERT: E 39 LYS cc_start: 0.7818 (mmmm) cc_final: 0.7018 (ptmt) REVERT: E 40 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6642 (mmtp) REVERT: E 43 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7052 (mt-10) REVERT: E 70 LYS cc_start: 0.6694 (tptt) cc_final: 0.6365 (tppt) REVERT: E 84 MET cc_start: 0.8480 (mtm) cc_final: 0.8241 (mmm) REVERT: E 111 LYS cc_start: 0.7811 (mttp) cc_final: 0.7243 (mttt) REVERT: E 215 ARG cc_start: 0.9086 (ttt90) cc_final: 0.8639 (ttt180) REVERT: F 70 LYS cc_start: 0.5929 (mmtt) cc_final: 0.5190 (mtpp) REVERT: F 108 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: F 210 MET cc_start: 0.8644 (mtp) cc_final: 0.8205 (mtp) REVERT: F 213 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7428 (mp0) REVERT: F 214 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8192 (t) REVERT: F 253 LEU cc_start: 0.8661 (tp) cc_final: 0.8175 (tp) outliers start: 43 outliers final: 28 residues processed: 278 average time/residue: 0.8695 time to fit residues: 259.6578 Evaluate side-chains 270 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 0.0970 chunk 149 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN B 202 GLN C 30 GLN C 202 GLN C 290 ASN D 202 GLN E 206 GLN F 202 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.094877 restraints weight = 75330.610| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 5.04 r_work: 0.2522 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15768 Z= 0.108 Angle : 0.489 6.497 21488 Z= 0.268 Chirality : 0.039 0.136 2434 Planarity : 0.004 0.045 2632 Dihedral : 13.946 82.048 2518 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 24.24 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1878 helix: 0.81 (0.18), residues: 900 sheet: 0.24 (0.39), residues: 210 loop : -1.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 250 TYR 0.009 0.001 TYR F 178 PHE 0.008 0.001 PHE D 126 HIS 0.002 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (15768) covalent geometry : angle 0.48894 / 0.27 (21488) hydrogen bonds : bond 0.02710 / 1.85 ( 761) hydrogen bonds : angle 3.99182 / 2.82 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.585 Fit side-chains REVERT: A 42 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7204 (tp30) REVERT: A 57 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6724 (mttp) REVERT: A 184 ASP cc_start: 0.7715 (m-30) cc_final: 0.7461 (m-30) REVERT: A 202 GLN cc_start: 0.7453 (tm130) cc_final: 0.6969 (tt0) REVERT: A 251 MET cc_start: 0.8727 (mtp) cc_final: 0.8139 (mmm) REVERT: A 266 THR cc_start: 0.9244 (m) cc_final: 0.8944 (m) REVERT: B 43 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7337 (tp30) REVERT: B 68 GLU cc_start: 0.7445 (mp0) cc_final: 0.7156 (mp0) REVERT: B 98 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7380 (pp20) REVERT: B 154 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8052 (mt-10) REVERT: B 161 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8585 (t70) REVERT: B 165 THR cc_start: 0.8992 (m) cc_final: 0.8681 (p) REVERT: B 202 GLN cc_start: 0.8480 (tp40) cc_final: 0.8192 (mm110) REVERT: C 39 LYS cc_start: 0.7735 (mttt) cc_final: 0.7183 (ttpt) REVERT: C 99 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8122 (mm) REVERT: C 169 GLU cc_start: 0.8568 (pm20) cc_final: 0.8307 (mm-30) REVERT: C 176 GLU cc_start: 0.8599 (tp30) cc_final: 0.8131 (tp30) REVERT: C 205 TYR cc_start: 0.8773 (m-80) cc_final: 0.8353 (m-80) REVERT: D 43 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7041 (mp0) REVERT: D 177 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8185 (ttt-90) REVERT: E 27 ARG cc_start: 0.6945 (mtm180) cc_final: 0.6309 (mtt-85) REVERT: E 39 LYS cc_start: 0.7740 (mmmm) cc_final: 0.7042 (ptmt) REVERT: E 40 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6718 (mmtp) REVERT: E 43 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7081 (mt-10) REVERT: E 84 MET cc_start: 0.8426 (mtm) cc_final: 0.8193 (mmm) REVERT: E 111 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7266 (mttt) REVERT: E 215 ARG cc_start: 0.9067 (ttt90) cc_final: 0.8770 (ttt90) REVERT: E 267 ASN cc_start: 0.9456 (t0) cc_final: 0.9171 (t0) REVERT: E 285 LYS cc_start: 0.8963 (ptmt) cc_final: 0.8662 (ptmm) REVERT: F 70 LYS cc_start: 0.5752 (mmtt) cc_final: 0.5083 (mtpp) REVERT: F 108 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: F 210 MET cc_start: 0.8604 (mtp) cc_final: 0.8147 (mtp) REVERT: F 213 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7409 (mp0) REVERT: F 214 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8208 (t) REVERT: F 253 LEU cc_start: 0.8654 (tp) cc_final: 0.8161 (tp) REVERT: F 326 MET cc_start: 0.8385 (ttm) cc_final: 0.8015 (tpt) outliers start: 36 outliers final: 17 residues processed: 265 average time/residue: 0.8451 time to fit residues: 240.9262 Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 163 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN E 206 GLN F 200 GLN F 202 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.095692 restraints weight = 72776.339| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.93 r_work: 0.2535 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15768 Z= 0.109 Angle : 0.479 6.664 21488 Z= 0.263 Chirality : 0.040 0.136 2434 Planarity : 0.004 0.044 2632 Dihedral : 13.843 81.664 2517 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.99 % Allowed : 24.57 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1878 helix: 0.96 (0.18), residues: 900 sheet: 0.35 (0.40), residues: 210 loop : -0.95 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 250 TYR 0.008 0.001 TYR B 232 PHE 0.010 0.001 PHE F 46 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15768) covalent geometry : angle 0.47886 / 0.26 (21488) hydrogen bonds : bond 0.02541 / 1.73 ( 761) hydrogen bonds : angle 3.82948 / 2.70 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.580 Fit side-chains REVERT: A 27 ARG cc_start: 0.7277 (mmm-85) cc_final: 0.6860 (mtt-85) REVERT: A 42 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7197 (tp30) REVERT: A 57 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6724 (mmtt) REVERT: A 184 ASP cc_start: 0.7755 (m-30) cc_final: 0.7497 (m-30) REVERT: A 202 GLN cc_start: 0.7457 (tm130) cc_final: 0.6907 (tt0) REVERT: A 206 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: A 266 THR cc_start: 0.9209 (m) cc_final: 0.8874 (m) REVERT: B 43 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7488 (tp30) REVERT: B 98 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7343 (pp20) REVERT: B 154 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8029 (mt-10) REVERT: B 161 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8582 (t70) REVERT: B 165 THR cc_start: 0.9006 (m) cc_final: 0.8705 (p) REVERT: B 202 GLN cc_start: 0.8456 (tp40) cc_final: 0.8231 (mm-40) REVERT: B 326 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8212 (tmm) REVERT: C 39 LYS cc_start: 0.7733 (mttt) cc_final: 0.7181 (ttpt) REVERT: C 169 GLU cc_start: 0.8555 (pm20) cc_final: 0.8303 (mm-30) REVERT: C 176 GLU cc_start: 0.8640 (tp30) cc_final: 0.8143 (tp30) REVERT: C 205 TYR cc_start: 0.8766 (m-80) cc_final: 0.8387 (m-80) REVERT: D 43 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7077 (mp0) REVERT: D 111 LYS cc_start: 0.8612 (mttp) cc_final: 0.8061 (mtmt) REVERT: D 177 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8248 (ttt-90) REVERT: E 39 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7048 (ptmt) REVERT: E 40 LYS cc_start: 0.7033 (mmtt) cc_final: 0.6757 (mmtp) REVERT: E 43 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7061 (mt-10) REVERT: E 72 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: E 84 MET cc_start: 0.8378 (mtm) cc_final: 0.8157 (mmm) REVERT: E 111 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7262 (mttt) REVERT: E 215 ARG cc_start: 0.9096 (ttt90) cc_final: 0.8778 (tmt90) REVERT: E 267 ASN cc_start: 0.9456 (t0) cc_final: 0.9152 (t0) REVERT: E 285 LYS cc_start: 0.8966 (ptmt) cc_final: 0.8669 (ptmm) REVERT: F 50 GLU cc_start: 0.7887 (mp0) cc_final: 0.7504 (mp0) REVERT: F 70 LYS cc_start: 0.5768 (mmtt) cc_final: 0.5144 (mtpp) REVERT: F 210 MET cc_start: 0.8573 (mtp) cc_final: 0.8023 (mtp) REVERT: F 213 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7415 (mp0) REVERT: F 214 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8214 (t) REVERT: F 253 LEU cc_start: 0.8820 (tp) cc_final: 0.8343 (tp) outliers start: 35 outliers final: 17 residues processed: 268 average time/residue: 0.8579 time to fit residues: 246.9224 Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 202 GLN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 206 GLN F 196 ASN F 200 GLN F 202 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.130937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.092476 restraints weight = 77218.582| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 5.11 r_work: 0.2476 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15768 Z= 0.231 Angle : 0.569 8.687 21488 Z= 0.306 Chirality : 0.044 0.152 2434 Planarity : 0.005 0.049 2632 Dihedral : 13.841 80.951 2517 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.05 % Allowed : 24.30 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1878 helix: 0.72 (0.17), residues: 906 sheet: 0.79 (0.40), residues: 192 loop : -1.05 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 250 TYR 0.017 0.002 TYR B 159 PHE 0.016 0.002 PHE A 92 HIS 0.008 0.002 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (15768) covalent geometry : angle 0.56941 / 0.31 (21488) hydrogen bonds : bond 0.03377 / 2.31 ( 761) hydrogen bonds : angle 4.15281 / 2.95 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7214 (mtt90) REVERT: A 42 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7234 (tp30) REVERT: A 57 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6754 (tttt) REVERT: A 202 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6978 (tt0) REVERT: A 206 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: A 266 THR cc_start: 0.9370 (m) cc_final: 0.9103 (m) REVERT: B 43 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7488 (tp30) REVERT: B 98 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7368 (pp20) REVERT: B 154 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8091 (mt-10) REVERT: B 161 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8670 (t70) REVERT: B 165 THR cc_start: 0.8998 (m) cc_final: 0.8745 (p) REVERT: B 202 GLN cc_start: 0.8505 (tp40) cc_final: 0.8263 (mm-40) REVERT: B 326 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: C 39 LYS cc_start: 0.7639 (mttt) cc_final: 0.7074 (ttpt) REVERT: C 70 LYS cc_start: 0.6615 (mmtm) cc_final: 0.6390 (mmmm) REVERT: C 176 GLU cc_start: 0.8727 (tp30) cc_final: 0.8225 (tp30) REVERT: C 205 TYR cc_start: 0.8794 (m-80) cc_final: 0.8359 (m-80) REVERT: D 43 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7097 (mp0) REVERT: D 111 LYS cc_start: 0.8616 (mttp) cc_final: 0.8066 (mtmt) REVERT: D 177 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8322 (ttt-90) REVERT: E 39 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7021 (ptmt) REVERT: E 40 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6721 (mmtp) REVERT: E 43 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7110 (mt-10) REVERT: E 84 MET cc_start: 0.8452 (mtm) cc_final: 0.8231 (mmm) REVERT: E 111 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7229 (mttt) REVERT: F 50 GLU cc_start: 0.7890 (mp0) cc_final: 0.7465 (mp0) REVERT: F 70 LYS cc_start: 0.5922 (mmtt) cc_final: 0.5376 (mtpp) REVERT: F 210 MET cc_start: 0.8649 (mtp) cc_final: 0.8154 (mtp) REVERT: F 213 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7274 (mp0) REVERT: F 214 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8200 (t) REVERT: F 253 LEU cc_start: 0.8841 (tp) cc_final: 0.8403 (tp) REVERT: F 326 MET cc_start: 0.8509 (ttm) cc_final: 0.8238 (tpp) outliers start: 38 outliers final: 22 residues processed: 264 average time/residue: 0.8009 time to fit residues: 226.8004 Evaluate side-chains 261 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 45 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 196 ASN E 206 GLN F 200 GLN F 202 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.094719 restraints weight = 69160.208| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.95 r_work: 0.2532 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15768 Z= 0.105 Angle : 0.487 6.803 21488 Z= 0.266 Chirality : 0.039 0.136 2434 Planarity : 0.004 0.044 2632 Dihedral : 13.851 82.024 2517 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.26 % Allowed : 25.56 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1878 helix: 0.92 (0.18), residues: 906 sheet: 0.94 (0.41), residues: 192 loop : -1.00 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 250 TYR 0.013 0.001 TYR A 205 PHE 0.009 0.001 PHE D 126 HIS 0.002 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (15768) covalent geometry : angle 0.48685 / 0.27 (21488) hydrogen bonds : bond 0.02570 / 1.75 ( 761) hydrogen bonds : angle 3.91717 / 2.77 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.577 Fit side-chains REVERT: A 42 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7201 (tp30) REVERT: A 57 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6581 (mttp) REVERT: A 184 ASP cc_start: 0.7787 (m-30) cc_final: 0.7527 (m-30) REVERT: A 202 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6818 (tt0) REVERT: A 251 MET cc_start: 0.8698 (mtp) cc_final: 0.8169 (mmm) REVERT: A 266 THR cc_start: 0.9226 (m) cc_final: 0.8919 (m) REVERT: B 43 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7481 (tp30) REVERT: B 95 ARG cc_start: 0.8598 (mtp180) cc_final: 0.8307 (mtm110) REVERT: B 98 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7344 (pp20) REVERT: B 154 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8055 (mt-10) REVERT: B 161 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8566 (t70) REVERT: B 165 THR cc_start: 0.9081 (m) cc_final: 0.8730 (p) REVERT: B 202 GLN cc_start: 0.8494 (tp40) cc_final: 0.8260 (mm-40) REVERT: B 326 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8211 (tmm) REVERT: C 39 LYS cc_start: 0.7697 (mttt) cc_final: 0.7136 (ttpt) REVERT: C 70 LYS cc_start: 0.6594 (mmtm) cc_final: 0.6333 (mmmm) REVERT: C 176 GLU cc_start: 0.8610 (tp30) cc_final: 0.8156 (tp30) REVERT: C 205 TYR cc_start: 0.8782 (m-80) cc_final: 0.8372 (m-80) REVERT: D 43 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7075 (mp0) REVERT: D 111 LYS cc_start: 0.8612 (mttp) cc_final: 0.8058 (mtmt) REVERT: D 177 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8250 (ttt-90) REVERT: E 39 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7064 (ptmt) REVERT: E 40 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6675 (mmtp) REVERT: E 43 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7099 (mt-10) REVERT: E 84 MET cc_start: 0.8410 (mtm) cc_final: 0.8187 (mmm) REVERT: E 111 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7206 (mttt) REVERT: E 267 ASN cc_start: 0.9447 (t0) cc_final: 0.9130 (t0) REVERT: E 285 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8689 (ptmm) REVERT: F 50 GLU cc_start: 0.7861 (mp0) cc_final: 0.7444 (mp0) REVERT: F 70 LYS cc_start: 0.5754 (mmtt) cc_final: 0.5282 (mtpp) REVERT: F 210 MET cc_start: 0.8612 (mtp) cc_final: 0.8135 (mtp) REVERT: F 213 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7277 (mp0) REVERT: F 253 LEU cc_start: 0.8852 (tp) cc_final: 0.8383 (tp) REVERT: F 326 MET cc_start: 0.8508 (ttm) cc_final: 0.8202 (tpp) outliers start: 26 outliers final: 15 residues processed: 250 average time/residue: 0.8733 time to fit residues: 234.3724 Evaluate side-chains 251 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 188 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN E 206 GLN F 196 ASN F 200 GLN F 202 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.093749 restraints weight = 71515.973| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.07 r_work: 0.2473 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15768 Z= 0.248 Angle : 0.580 8.487 21488 Z= 0.311 Chirality : 0.045 0.154 2434 Planarity : 0.005 0.049 2632 Dihedral : 13.831 81.121 2517 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.59 % Allowed : 25.10 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1878 helix: 0.70 (0.17), residues: 906 sheet: 0.78 (0.40), residues: 192 loop : -1.04 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 27 TYR 0.018 0.002 TYR B 159 PHE 0.017 0.002 PHE A 92 HIS 0.008 0.002 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (15768) covalent geometry : angle 0.58020 / 0.31 (21488) hydrogen bonds : bond 0.03492 / 2.39 ( 761) hydrogen bonds : angle 4.23289 / 3.00 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6989 (mtt-85) REVERT: A 42 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7237 (tp30) REVERT: A 57 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6637 (mttp) REVERT: A 202 GLN cc_start: 0.7362 (tm-30) cc_final: 0.6856 (tt0) REVERT: A 266 THR cc_start: 0.9414 (m) cc_final: 0.9178 (m) REVERT: B 43 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7456 (tp30) REVERT: B 98 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7400 (pp20) REVERT: B 161 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8694 (t70) REVERT: B 165 THR cc_start: 0.9021 (m) cc_final: 0.8761 (p) REVERT: B 202 GLN cc_start: 0.8504 (tp40) cc_final: 0.8258 (mm-40) REVERT: B 326 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8492 (tmm) REVERT: C 39 LYS cc_start: 0.7633 (mttt) cc_final: 0.7073 (ttpt) REVERT: C 70 LYS cc_start: 0.6603 (mmtm) cc_final: 0.6337 (mmmm) REVERT: C 176 GLU cc_start: 0.8726 (tp30) cc_final: 0.8228 (tp30) REVERT: C 205 TYR cc_start: 0.8828 (m-80) cc_final: 0.8405 (m-80) REVERT: C 306 ARG cc_start: 0.7760 (tmm-80) cc_final: 0.7141 (tmm160) REVERT: D 43 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7121 (mp0) REVERT: D 64 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7244 (pttt) REVERT: D 111 LYS cc_start: 0.8620 (mttp) cc_final: 0.8067 (mtmt) REVERT: D 177 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8330 (ttt-90) REVERT: E 39 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7038 (ptmt) REVERT: E 40 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6725 (mmtp) REVERT: E 43 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7178 (mt-10) REVERT: E 84 MET cc_start: 0.8447 (mtm) cc_final: 0.8212 (mmm) REVERT: E 111 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7279 (mttt) REVERT: F 50 GLU cc_start: 0.7916 (mp0) cc_final: 0.7478 (mp0) REVERT: F 59 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7213 (mp0) REVERT: F 70 LYS cc_start: 0.5945 (mmtt) cc_final: 0.5394 (mtpp) REVERT: F 210 MET cc_start: 0.8669 (mtp) cc_final: 0.8162 (mtp) REVERT: F 213 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7254 (mp0) REVERT: F 214 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8200 (t) REVERT: F 253 LEU cc_start: 0.8846 (tp) cc_final: 0.8587 (tp) outliers start: 31 outliers final: 20 residues processed: 254 average time/residue: 0.8800 time to fit residues: 239.2931 Evaluate side-chains 255 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 206 GLN F 200 GLN F 202 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.094662 restraints weight = 72558.641| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 5.02 r_work: 0.2524 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15768 Z= 0.113 Angle : 0.490 6.927 21488 Z= 0.268 Chirality : 0.039 0.134 2434 Planarity : 0.004 0.044 2632 Dihedral : 13.856 82.105 2517 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 25.03 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1878 helix: 0.91 (0.18), residues: 906 sheet: 0.70 (0.39), residues: 210 loop : -0.99 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.009 0.001 TYR E 315 PHE 0.008 0.001 PHE F 46 HIS 0.002 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15768) covalent geometry : angle 0.48974 / 0.27 (21488) hydrogen bonds : bond 0.02563 / 1.75 ( 761) hydrogen bonds : angle 3.93206 / 2.77 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6682.09 seconds wall clock time: 114 minutes 20.53 seconds (6860.53 seconds total)