Starting phenix.real_space_refine on Sun Aug 24 00:03:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8br2_16197/08_2025/8br2_16197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8br2_16197/08_2025/8br2_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_16197/08_2025/8br2_16197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8br2_16197/08_2025/8br2_16197.map" model { file = "/net/cci-nas-00/data/ceres_data/8br2_16197/08_2025/8br2_16197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8br2_16197/08_2025/8br2_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.04, 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: 1.16 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.93 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: 2.60 Time building geometry restraints manager: 1.59 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=" C5 DA H 20 " pdb=" C6 DA H 20 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" N1 DT H 17 " pdb=" C6 DT H 17 " ideal model delta sigma weight residual 1.380 1.460 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" N9 DA H 14 " pdb=" C8 DA H 14 " ideal model delta sigma weight residual 1.367 1.446 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " ideal model delta sigma weight residual 1.364 1.440 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" SD MET D 251 " pdb=" CE MET D 251 " ideal model delta sigma weight residual 1.791 1.706 0.085 2.50e-02 1.60e+03 1.16e+01 ... (remaining 15763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20742 1.28 - 2.55: 596 2.55 - 3.83: 119 3.83 - 5.10: 19 5.10 - 6.38: 12 Bond angle restraints: 21488 Sorted by residual: angle pdb=" CA BARG F 130 " pdb=" CB BARG F 130 " pdb=" CG BARG F 130 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA BARG C 130 " pdb=" CB BARG C 130 " pdb=" CG BARG C 130 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG E 130 " pdb=" CB BARG E 130 " pdb=" CG BARG E 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG D 130 " pdb=" CB BARG D 130 " pdb=" CG BARG D 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG A 130 " pdb=" CB BARG A 130 " pdb=" CG BARG A 130 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8212 17.90 - 35.81: 967 35.81 - 53.71: 272 53.71 - 71.61: 101 71.61 - 89.51: 38 Dihedral angle restraints: 9590 sinusoidal: 4220 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 9587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1418 0.033 - 0.066: 715 0.066 - 0.099: 201 0.099 - 0.132: 87 0.132 - 0.165: 13 Chirality restraints: 2434 Sorted by residual: 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 chirality pdb=" CA BARG E 130 " pdb=" N BARG E 130 " pdb=" C BARG E 130 " pdb=" CB BARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-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: 0.490 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.085 15768 Z= 0.344 Angle : 0.556 6.377 21488 Z= 0.311 Chirality : 0.045 0.165 2434 Planarity : 0.024 0.490 2632 Dihedral : 18.028 89.513 6158 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 aren 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 covalent geometry : bond 0.00778 (15768) covalent geometry : angle 0.55650 (21488) hydrogen bonds : bond 0.21623 ( 761) hydrogen bonds : angle 7.78207 ( 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 : 0.392 Fit side-chains REVERT: A 176 GLU cc_start: 0.7387 (tp30) cc_final: 0.7040 (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: 0.8598 (m) REVERT: A 268 GLN cc_start: 0.9032 (mt0) cc_final: 0.8642 (mt0) REVERT: B 40 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7275 (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: 0.7550 (tp30) REVERT: C 205 TYR cc_start: 0.8273 (m-80) cc_final: 0.8025 (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: 0.8529 (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: 0.7636 (tp30) REVERT: D 111 LYS cc_start: 0.8070 (mttp) cc_final: 0.7811 (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: 0.6883 (mmtp) REVERT: E 111 LYS cc_start: 0.7993 (mttp) cc_final: 0.7713 (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: 0.7496 time to fit residues: 362.1920 Evaluate side-chains 247 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 242 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 196 ASN A 206 GLN A 290 ASN B 23 GLN B 94 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 D 290 ASN E 206 GLN E 290 ASN F 202 GLN F 206 GLN F 290 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.134855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.097486 restraints weight = 78205.231| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 5.54 r_work: 0.2525 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 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 = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15768 Z= 0.147 Angle : 0.542 7.210 21488 Z= 0.296 Chirality : 0.041 0.140 2434 Planarity : 0.005 0.051 2632 Dihedral : 15.606 89.914 2707 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.25 % Allowed : 23.24 % Favored : 73.51 % 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 aren not related in a simple way. whole: -1.02 (0.18), residues: 1878 helix: -0.47 (0.16), residues: 900 sheet: 0.10 (0.30), residues: 342 loop : -1.18 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 306 TYR 0.015 0.001 TYR B 159 PHE 0.014 0.002 PHE F 46 HIS 0.006 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00330 (15768) covalent geometry : angle 0.54174 (21488) hydrogen bonds : bond 0.03523 ( 761) hydrogen bonds : angle 4.53757 ( 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 301 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.567 Fit side-chains REVERT: A 37 ASP cc_start: 0.6601 (m-30) cc_final: 0.6141 (m-30) REVERT: A 42 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7129 (tp30) REVERT: A 57 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6599 (tttp) REVERT: A 94 GLN cc_start: 0.8367 (tp40) cc_final: 0.8148 (tp-100) REVERT: A 95 ARG cc_start: 0.8510 (mtp180) cc_final: 0.8305 (mtm-85) REVERT: A 107 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7704 (mtpt) REVERT: A 202 GLN cc_start: 0.7349 (tm-30) cc_final: 0.7134 (tt0) REVERT: A 206 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: A 266 THR cc_start: 0.9168 (m) cc_final: 0.8829 (m) REVERT: B 43 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7262 (mm-30) REVERT: B 161 ASP cc_start: 0.8875 (t70) cc_final: 0.8623 (t70) REVERT: B 165 THR cc_start: 0.8920 (m) cc_final: 0.8616 (p) REVERT: B 210 MET cc_start: 0.8871 (mtp) cc_final: 0.8482 (mtp) REVERT: C 39 LYS cc_start: 0.7572 (mttt) cc_final: 0.7000 (ttpt) REVERT: C 70 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6110 (mmmm) REVERT: C 169 GLU cc_start: 0.8573 (pm20) cc_final: 0.8247 (mm-30) REVERT: C 176 GLU cc_start: 0.8656 (tp30) cc_final: 0.8171 (tp30) REVERT: C 205 TYR cc_start: 0.8759 (m-80) cc_final: 0.8372 (m-80) REVERT: C 306 ARG cc_start: 0.7496 (tmm160) cc_final: 0.7288 (tmm160) REVERT: C 326 MET cc_start: 0.9140 (ttm) cc_final: 0.8938 (ttm) REVERT: D 43 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7063 (mp0) REVERT: D 64 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7308 (pttt) REVERT: D 111 LYS cc_start: 0.8483 (mttp) cc_final: 0.7982 (mtmt) REVERT: D 176 GLU cc_start: 0.7925 (tp30) cc_final: 0.7574 (tm-30) REVERT: D 306 ARG cc_start: 0.7135 (tmm160) cc_final: 0.6924 (tmm160) REVERT: E 27 ARG cc_start: 0.7222 (mtm180) cc_final: 0.6690 (mtt-85) REVERT: E 39 LYS cc_start: 0.7582 (mmmm) cc_final: 0.6844 (ptmt) REVERT: E 40 LYS cc_start: 0.6746 (mmtt) cc_final: 0.6382 (mmtp) REVERT: E 43 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7075 (mt-10) REVERT: E 70 LYS cc_start: 0.6654 (tptt) cc_final: 0.6400 (tppt) REVERT: E 111 LYS cc_start: 0.7333 (mttp) cc_final: 0.6832 (mttt) REVERT: E 267 ASN cc_start: 0.9488 (t0) cc_final: 0.9214 (t0) REVERT: E 285 LYS cc_start: 0.9033 (ptmm) cc_final: 0.8816 (ptmm) REVERT: F 42 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7358 (mt-10) REVERT: F 70 LYS cc_start: 0.6073 (mmtt) cc_final: 0.5338 (mtpp) REVERT: F 210 MET cc_start: 0.8638 (mtp) cc_final: 0.8242 (mtp) REVERT: F 211 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8307 (mtt) REVERT: F 213 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7440 (mp0) REVERT: F 253 LEU cc_start: 0.8440 (tp) cc_final: 0.8084 (tp) outliers start: 42 outliers final: 10 residues processed: 290 average time/residue: 0.7261 time to fit residues: 226.2834 Evaluate side-chains 242 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 206 GLN 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 181 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain F residue 211 MET 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: 0.8980 chunk 90 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 202 GLN B 272 GLN C 23 GLN C 202 GLN D 196 ASN E 34 ASN E 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 = 0.3375 r_free = 0.3375 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094047 restraints weight = 77858.128| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 5.21 r_work: 0.2497 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2483 r_free = 0.2483 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15768 Z= 0.168 Angle : 0.534 7.353 21488 Z= 0.288 Chirality : 0.041 0.142 2434 Planarity : 0.004 0.050 2632 Dihedral : 15.224 89.605 2704 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.45 % Allowed : 23.17 % Favored : 73.37 % 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 aren not related in a simple way. whole: -0.47 (0.19), residues: 1878 helix: 0.32 (0.17), residues: 900 sheet: 0.31 (0.36), residues: 246 loop : -1.26 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 250 TYR 0.015 0.001 TYR B 159 PHE 0.013 0.002 PHE F 46 HIS 0.005 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00388 (15768) covalent geometry : angle 0.53380 (21488) hydrogen bonds : bond 0.03288 ( 761) hydrogen bonds : angle 4.18699 ( 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 299 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.399 Fit side-chains REVERT: A 37 ASP cc_start: 0.6691 (m-30) cc_final: 0.6249 (m-30) REVERT: A 42 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7261 (tp30) REVERT: A 57 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6565 (tttp) REVERT: A 95 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8235 (mtm-85) REVERT: A 107 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7636 (mtpt) REVERT: A 202 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7203 (tt0) REVERT: A 243 MET cc_start: 0.8949 (mtp) cc_final: 0.8515 (mtt) REVERT: A 251 MET cc_start: 0.8642 (mtp) cc_final: 0.8046 (mmm) REVERT: A 266 THR cc_start: 0.9285 (m) cc_final: 0.9015 (m) REVERT: A 326 MET cc_start: 0.8670 (ttp) cc_final: 0.8406 (mtp) REVERT: B 43 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7470 (tp30) REVERT: B 82 VAL cc_start: 0.8355 (t) cc_final: 0.8137 (m) REVERT: B 161 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8648 (t70) REVERT: B 165 THR cc_start: 0.8976 (m) cc_final: 0.8674 (p) REVERT: B 196 ASN cc_start: 0.9367 (p0) cc_final: 0.9135 (p0) REVERT: B 202 GLN cc_start: 0.8534 (tp40) cc_final: 0.8321 (mm-40) REVERT: C 39 LYS cc_start: 0.7665 (mttt) cc_final: 0.7097 (ttpt) REVERT: C 70 LYS cc_start: 0.6561 (mmtt) cc_final: 0.5895 (mmmm) REVERT: C 169 GLU cc_start: 0.8624 (pm20) cc_final: 0.8233 (mm-30) REVERT: C 176 GLU cc_start: 0.8692 (tp30) cc_final: 0.8206 (tp30) REVERT: C 205 TYR cc_start: 0.8779 (m-80) cc_final: 0.8365 (m-80) REVERT: C 303 ARG cc_start: 0.9201 (ptt-90) cc_final: 0.8851 (ptt-90) REVERT: C 306 ARG cc_start: 0.7549 (tmm160) cc_final: 0.7160 (tmm160) REVERT: D 43 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7035 (mp0) REVERT: D 64 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7394 (pttt) REVERT: D 80 LYS cc_start: 0.7559 (pttp) cc_final: 0.7338 (pttp) REVERT: D 111 LYS cc_start: 0.8537 (mttp) cc_final: 0.8013 (mtmt) REVERT: E 39 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7059 (ptmt) REVERT: E 40 LYS cc_start: 0.6968 (mmtt) cc_final: 0.6667 (mmtp) REVERT: E 43 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7114 (mt-10) REVERT: E 80 LYS cc_start: 0.7023 (pptt) cc_final: 0.6819 (pptt) REVERT: E 84 MET cc_start: 0.8439 (mtm) cc_final: 0.8053 (mmm) REVERT: E 111 LYS cc_start: 0.7782 (mttp) cc_final: 0.7177 (mttt) REVERT: E 215 ARG cc_start: 0.9018 (ttt90) cc_final: 0.8669 (ttt90) REVERT: E 267 ASN cc_start: 0.9475 (t0) cc_final: 0.9168 (t0) REVERT: E 330 ASN cc_start: 0.8743 (m-40) cc_final: 0.8517 (m110) REVERT: F 42 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 70 LYS cc_start: 0.5919 (mmtt) cc_final: 0.5187 (mtpp) REVERT: F 108 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: F 210 MET cc_start: 0.8585 (mtp) cc_final: 0.8096 (mtp) REVERT: F 213 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7453 (mp0) REVERT: F 253 LEU cc_start: 0.8567 (tp) cc_final: 0.8237 (tp) REVERT: F 326 MET cc_start: 0.8568 (ttm) cc_final: 0.8137 (tpp) outliers start: 40 outliers final: 14 residues processed: 285 average time/residue: 0.7172 time to fit residues: 219.1438 Evaluate side-chains 262 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 285 LYS 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 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 181 SER 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 237 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 202 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 = 0.3395 r_free = 0.3395 target = 0.133796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.095263 restraints weight = 71025.861| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.95 r_work: 0.2536 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 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 = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15768 Z= 0.126 Angle : 0.487 7.249 21488 Z= 0.262 Chirality : 0.040 0.131 2434 Planarity : 0.004 0.048 2632 Dihedral : 15.109 89.877 2703 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.05 % Allowed : 23.77 % 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 aren not related in a simple way. whole: -0.10 (0.19), residues: 1878 helix: 0.71 (0.18), residues: 900 sheet: 0.27 (0.36), residues: 252 loop : -1.11 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 250 TYR 0.011 0.001 TYR B 159 PHE 0.011 0.001 PHE F 46 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00284 (15768) covalent geometry : angle 0.48737 (21488) hydrogen bonds : bond 0.02639 ( 761) hydrogen bonds : angle 3.94780 ( 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 289 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.531 Fit side-chains REVERT: A 37 ASP cc_start: 0.6593 (m-30) cc_final: 0.6244 (m-30) REVERT: A 42 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7166 (tp30) REVERT: A 57 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6493 (mttp) REVERT: A 266 THR cc_start: 0.9216 (m) cc_final: 0.8907 (m) REVERT: A 326 MET cc_start: 0.8673 (ttp) cc_final: 0.8397 (mtp) REVERT: B 43 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7432 (tp30) REVERT: B 68 GLU cc_start: 0.7205 (mp0) cc_final: 0.6953 (mp0) REVERT: B 154 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7955 (mt-10) REVERT: B 161 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8602 (t70) REVERT: B 165 THR cc_start: 0.8912 (m) cc_final: 0.8626 (p) REVERT: B 196 ASN cc_start: 0.9355 (p0) cc_final: 0.9100 (p0) REVERT: B 202 GLN cc_start: 0.8475 (tp40) cc_final: 0.8237 (mm-40) REVERT: B 285 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8464 (ptpt) REVERT: B 326 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8129 (tmm) REVERT: C 39 LYS cc_start: 0.7612 (mttt) cc_final: 0.7000 (ttpt) REVERT: C 68 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7074 (mp0) REVERT: C 169 GLU cc_start: 0.8564 (pm20) cc_final: 0.8282 (mm-30) REVERT: C 176 GLU cc_start: 0.8625 (tp30) cc_final: 0.8168 (tp30) REVERT: C 205 TYR cc_start: 0.8764 (m-80) cc_final: 0.8351 (m-80) REVERT: C 306 ARG cc_start: 0.7639 (tmm160) cc_final: 0.7210 (tmm160) REVERT: C 308 GLU cc_start: 0.8546 (pm20) cc_final: 0.8313 (pm20) REVERT: D 43 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7015 (mp0) REVERT: D 64 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7272 (pttt) REVERT: E 39 LYS cc_start: 0.7746 (mmmm) cc_final: 0.7051 (ptmt) REVERT: E 40 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6707 (mmtp) REVERT: E 43 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7197 (mt-10) REVERT: E 111 LYS cc_start: 0.7763 (mttp) cc_final: 0.7156 (mttt) REVERT: E 215 ARG cc_start: 0.9063 (ttt90) cc_final: 0.8745 (ttt90) REVERT: E 267 ASN cc_start: 0.9488 (t0) cc_final: 0.9181 (t0) REVERT: E 285 LYS cc_start: 0.9077 (ptmm) cc_final: 0.8820 (ptmm) REVERT: E 330 ASN cc_start: 0.8714 (m-40) cc_final: 0.8501 (m110) REVERT: F 42 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7481 (mt-10) REVERT: F 58 LYS cc_start: 0.7325 (mtpt) cc_final: 0.6636 (mtpt) REVERT: F 70 LYS cc_start: 0.5752 (mmtt) cc_final: 0.5284 (mtpp) REVERT: F 108 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: F 210 MET cc_start: 0.8571 (mtp) cc_final: 0.8151 (mtp) REVERT: F 213 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7260 (mp0) REVERT: F 253 LEU cc_start: 0.8655 (tp) cc_final: 0.8173 (tp) REVERT: F 296 SER cc_start: 0.8418 (m) cc_final: 0.8149 (p) outliers start: 35 outliers final: 15 residues processed: 276 average time/residue: 0.8332 time to fit residues: 245.6049 Evaluate side-chains 259 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 B residue 326 MET Chi-restraints excluded: chain B residue 332 ASP 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 181 SER 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 237 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 202 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.097121 restraints weight = 68732.349| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 5.28 r_work: 0.2517 rms_B_bonded: 4.64 restraints_weight: 0.5000 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15768 Z= 0.145 Angle : 0.496 7.496 21488 Z= 0.267 Chirality : 0.040 0.132 2434 Planarity : 0.004 0.047 2632 Dihedral : 15.068 89.778 2702 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.92 % Allowed : 23.97 % Favored : 73.11 % 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 aren not related in a simple way. whole: 0.08 (0.20), residues: 1878 helix: 0.86 (0.18), residues: 900 sheet: 0.49 (0.35), residues: 246 loop : -1.08 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 250 TYR 0.011 0.001 TYR B 315 PHE 0.012 0.001 PHE F 46 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00333 (15768) covalent geometry : angle 0.49626 (21488) hydrogen bonds : bond 0.02796 ( 761) hydrogen bonds : angle 3.94607 ( 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 287 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.530 Fit side-chains REVERT: A 42 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7200 (tp30) REVERT: A 57 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6750 (mttp) REVERT: A 243 MET cc_start: 0.9028 (mtp) cc_final: 0.8572 (mtt) REVERT: A 266 THR cc_start: 0.9264 (m) cc_final: 0.8973 (m) REVERT: A 326 MET cc_start: 0.8685 (ttp) cc_final: 0.8377 (mtp) REVERT: B 43 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7413 (tp30) REVERT: B 68 GLU cc_start: 0.7203 (mp0) cc_final: 0.6896 (mp0) REVERT: B 161 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8610 (t70) REVERT: B 165 THR cc_start: 0.9088 (m) cc_final: 0.8721 (p) REVERT: B 196 ASN cc_start: 0.9371 (p0) cc_final: 0.9112 (p0) REVERT: B 202 GLN cc_start: 0.8501 (tp40) cc_final: 0.8255 (mm-40) REVERT: B 326 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: C 39 LYS cc_start: 0.7632 (mttt) cc_final: 0.7056 (ttpt) REVERT: C 68 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7061 (mp0) REVERT: C 70 LYS cc_start: 0.6567 (mmtm) cc_final: 0.6282 (mmmm) REVERT: C 169 GLU cc_start: 0.8585 (pm20) cc_final: 0.8360 (mm-30) REVERT: C 176 GLU cc_start: 0.8672 (tp30) cc_final: 0.8204 (tp30) REVERT: C 205 TYR cc_start: 0.8822 (m-80) cc_final: 0.8400 (m-80) REVERT: C 306 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7154 (tmm160) REVERT: C 308 GLU cc_start: 0.8590 (pm20) cc_final: 0.8383 (pm20) REVERT: D 43 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7049 (mp0) REVERT: D 64 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7267 (pttt) REVERT: D 215 ARG cc_start: 0.8859 (ttt90) cc_final: 0.8615 (ttt90) REVERT: E 27 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6286 (mtt-85) REVERT: E 39 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7059 (ptmt) REVERT: E 40 LYS cc_start: 0.6944 (mmtt) cc_final: 0.6672 (mmtp) REVERT: E 43 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7273 (mt-10) REVERT: E 84 MET cc_start: 0.8395 (mtm) cc_final: 0.8142 (mmm) REVERT: E 111 LYS cc_start: 0.7814 (mttp) cc_final: 0.7170 (mttt) REVERT: E 215 ARG cc_start: 0.9096 (ttt90) cc_final: 0.8820 (ttt90) REVERT: E 267 ASN cc_start: 0.9480 (t0) cc_final: 0.9177 (t0) REVERT: E 285 LYS cc_start: 0.9101 (ptmm) cc_final: 0.8819 (ptmm) REVERT: E 330 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (m110) REVERT: F 42 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7467 (mt-10) REVERT: F 70 LYS cc_start: 0.5915 (mmtt) cc_final: 0.5365 (mtpp) REVERT: F 108 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: F 210 MET cc_start: 0.8594 (mtp) cc_final: 0.8140 (mtp) REVERT: F 213 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7252 (mp0) REVERT: F 253 LEU cc_start: 0.8843 (tp) cc_final: 0.8590 (tp) REVERT: F 296 SER cc_start: 0.8415 (m) cc_final: 0.8149 (p) outliers start: 35 outliers final: 18 residues processed: 274 average time/residue: 0.8001 time to fit residues: 234.4773 Evaluate side-chains 259 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 285 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 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 266 THR Chi-restraints excluded: chain C residue 330 ASN 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 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 202 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 = 0.3380 r_free = 0.3380 target = 0.132560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094244 restraints weight = 74921.151| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 5.07 r_work: 0.2506 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 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 = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3643 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= 0.148 Angle : 0.500 7.193 21488 Z= 0.269 Chirality : 0.040 0.131 2434 Planarity : 0.004 0.046 2632 Dihedral : 15.056 89.207 2702 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.92 % Allowed : 23.90 % 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 aren not related in a simple way. whole: 0.14 (0.20), residues: 1878 helix: 0.90 (0.18), residues: 900 sheet: 0.33 (0.34), residues: 264 loop : -0.97 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 250 TYR 0.011 0.001 TYR B 159 PHE 0.011 0.001 PHE F 46 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00343 (15768) covalent geometry : angle 0.49978 (21488) hydrogen bonds : bond 0.02754 ( 761) hydrogen bonds : angle 3.95696 ( 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 282 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7197 (tp30) REVERT: A 57 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6445 (tttt) REVERT: A 70 LYS cc_start: 0.5510 (mmtt) cc_final: 0.5092 (mmtp) REVERT: A 266 THR cc_start: 0.9286 (m) cc_final: 0.8992 (m) REVERT: A 326 MET cc_start: 0.8693 (ttp) cc_final: 0.8359 (mtp) REVERT: B 43 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7321 (mm-30) REVERT: B 161 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8634 (t70) REVERT: B 165 THR cc_start: 0.9083 (m) cc_final: 0.8708 (p) REVERT: B 196 ASN cc_start: 0.9359 (p0) cc_final: 0.9107 (p0) REVERT: B 202 GLN cc_start: 0.8504 (tp40) cc_final: 0.8287 (mm-40) REVERT: B 326 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: C 39 LYS cc_start: 0.7617 (mttt) cc_final: 0.7014 (ttpt) REVERT: C 68 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7083 (mp0) REVERT: C 169 GLU cc_start: 0.8596 (pm20) cc_final: 0.8344 (mm-30) REVERT: C 176 GLU cc_start: 0.8586 (tp30) cc_final: 0.8154 (tp30) REVERT: C 205 TYR cc_start: 0.8850 (m-80) cc_final: 0.8399 (m-80) REVERT: C 306 ARG cc_start: 0.7828 (tmm160) cc_final: 0.7341 (tmm160) REVERT: C 308 GLU cc_start: 0.8596 (pm20) cc_final: 0.8386 (pm20) REVERT: D 43 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7091 (mp0) REVERT: D 64 LYS cc_start: 0.7743 (mmtm) cc_final: 0.7285 (pttt) REVERT: E 39 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7182 (ptmt) REVERT: E 40 LYS cc_start: 0.6944 (mmtt) cc_final: 0.6661 (mmtp) REVERT: E 84 MET cc_start: 0.8396 (mtm) cc_final: 0.8149 (mmm) REVERT: E 111 LYS cc_start: 0.7770 (mttp) cc_final: 0.7150 (mttt) REVERT: E 215 ARG cc_start: 0.9093 (ttt90) cc_final: 0.8818 (ttt90) REVERT: E 267 ASN cc_start: 0.9484 (t0) cc_final: 0.9182 (t0) REVERT: E 285 LYS cc_start: 0.9102 (ptmm) cc_final: 0.8809 (ptmm) REVERT: E 330 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (m110) REVERT: F 42 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 50 GLU cc_start: 0.7849 (mp0) cc_final: 0.7445 (mp0) REVERT: F 70 LYS cc_start: 0.5947 (mmtt) cc_final: 0.5338 (mtpp) REVERT: F 108 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: F 210 MET cc_start: 0.8610 (mtp) cc_final: 0.8117 (mtp) REVERT: F 213 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7251 (mp0) REVERT: F 214 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8226 (t) REVERT: F 253 LEU cc_start: 0.8826 (tp) cc_final: 0.8602 (tp) REVERT: F 296 SER cc_start: 0.8430 (m) cc_final: 0.8156 (p) REVERT: F 326 MET cc_start: 0.7896 (ttt) cc_final: 0.7652 (tmm) outliers start: 35 outliers final: 20 residues processed: 269 average time/residue: 0.7524 time to fit residues: 216.3066 Evaluate side-chains 260 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 285 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 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 223 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN 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 108 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN C 290 ASN D 202 GLN E 202 GLN F 200 GLN 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 = 0.3400 r_free = 0.3400 target = 0.134242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.097197 restraints weight = 72694.926| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.29 r_work: 0.2525 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15768 Z= 0.109 Angle : 0.468 6.241 21488 Z= 0.253 Chirality : 0.039 0.128 2434 Planarity : 0.004 0.045 2632 Dihedral : 14.964 87.796 2702 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 24.83 % 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 aren not related in a simple way. whole: 0.33 (0.20), residues: 1878 helix: 1.04 (0.18), residues: 906 sheet: 0.81 (0.39), residues: 210 loop : -0.93 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.009 0.001 TYR B 315 PHE 0.010 0.001 PHE F 46 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00244 (15768) covalent geometry : angle 0.46781 (21488) hydrogen bonds : bond 0.02343 ( 761) hydrogen bonds : angle 3.77407 ( 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 271 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6653 (ttm-80) REVERT: A 42 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7216 (tp30) REVERT: A 57 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6466 (mttp) REVERT: A 266 THR cc_start: 0.9198 (m) cc_final: 0.8861 (m) REVERT: A 326 MET cc_start: 0.8727 (ttp) cc_final: 0.8418 (mtp) REVERT: B 43 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7192 (mm-30) REVERT: B 161 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8611 (t70) REVERT: B 165 THR cc_start: 0.9063 (m) cc_final: 0.8713 (p) REVERT: B 196 ASN cc_start: 0.9362 (p0) cc_final: 0.9114 (p0) REVERT: B 202 GLN cc_start: 0.8476 (tp40) cc_final: 0.8251 (mm-40) REVERT: B 285 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8445 (ptpt) REVERT: C 39 LYS cc_start: 0.7596 (mttt) cc_final: 0.7033 (ttpt) REVERT: C 68 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7126 (mp0) REVERT: C 70 LYS cc_start: 0.6507 (mmtm) cc_final: 0.6273 (mmmm) REVERT: C 169 GLU cc_start: 0.8635 (pm20) cc_final: 0.8359 (mm-30) REVERT: C 176 GLU cc_start: 0.8562 (tp30) cc_final: 0.8133 (tp30) REVERT: C 205 TYR cc_start: 0.8826 (m-80) cc_final: 0.8480 (m-80) REVERT: C 306 ARG cc_start: 0.7763 (tmm160) cc_final: 0.7442 (tmm-80) REVERT: D 43 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7132 (mp0) REVERT: D 64 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7349 (ptmt) REVERT: E 39 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7163 (ptmt) REVERT: E 40 LYS cc_start: 0.6917 (mmtt) cc_final: 0.6661 (mmtp) REVERT: E 84 MET cc_start: 0.8376 (mtm) cc_final: 0.8138 (mmm) REVERT: E 111 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7153 (mttt) REVERT: E 215 ARG cc_start: 0.9141 (ttt90) cc_final: 0.8880 (ttt90) REVERT: E 267 ASN cc_start: 0.9465 (t0) cc_final: 0.9138 (t0) REVERT: E 285 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8818 (ptmm) REVERT: E 330 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8474 (m110) REVERT: F 70 LYS cc_start: 0.5795 (mmtt) cc_final: 0.5237 (mtpp) REVERT: F 210 MET cc_start: 0.8580 (mtp) cc_final: 0.8002 (mtp) REVERT: F 213 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7365 (mp0) REVERT: F 214 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (t) REVERT: F 296 SER cc_start: 0.8416 (m) cc_final: 0.8160 (p) REVERT: F 326 MET cc_start: 0.7885 (ttt) cc_final: 0.7636 (tmm) outliers start: 29 outliers final: 11 residues processed: 259 average time/residue: 0.7604 time to fit residues: 210.5233 Evaluate side-chains 249 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 330 ASN 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 111 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 214 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 50 optimal weight: 0.0980 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 272 GLN E 202 GLN F 196 ASN F 200 GLN 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 = 0.3352 r_free = 0.3352 target = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.091595 restraints weight = 77020.792| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.99 r_work: 0.2471 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2455 r_free = 0.2455 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15768 Z= 0.238 Angle : 0.572 9.401 21488 Z= 0.305 Chirality : 0.044 0.146 2434 Planarity : 0.005 0.046 2632 Dihedral : 15.060 87.633 2702 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.05 % Allowed : 23.97 % Favored : 72.97 % 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 aren not related in a simple way. whole: 0.08 (0.19), residues: 1878 helix: 0.81 (0.18), residues: 900 sheet: 0.59 (0.38), residues: 210 loop : -0.96 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 27 TYR 0.017 0.002 TYR B 159 PHE 0.016 0.002 PHE A 92 HIS 0.007 0.002 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00564 (15768) covalent geometry : angle 0.57214 (21488) hydrogen bonds : bond 0.03414 ( 761) hydrogen bonds : angle 4.20838 ( 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 274 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7054 (tp30) REVERT: A 57 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6686 (tttt) REVERT: A 243 MET cc_start: 0.9062 (mtp) cc_final: 0.8608 (mtt) REVERT: A 326 MET cc_start: 0.8705 (ttp) cc_final: 0.8347 (mtp) REVERT: B 43 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7246 (mm-30) REVERT: B 66 ILE cc_start: 0.7892 (mm) cc_final: 0.7456 (mp) REVERT: B 161 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8674 (t70) REVERT: B 165 THR cc_start: 0.9157 (m) cc_final: 0.8795 (p) REVERT: B 202 GLN cc_start: 0.8520 (tp40) cc_final: 0.8222 (mm-40) REVERT: B 326 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8329 (tmm) REVERT: C 39 LYS cc_start: 0.7747 (mttt) cc_final: 0.7136 (ttpt) REVERT: C 68 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7064 (mp0) REVERT: C 176 GLU cc_start: 0.8652 (tp30) cc_final: 0.8229 (tp30) REVERT: C 205 TYR cc_start: 0.8868 (m-80) cc_final: 0.8427 (m-80) REVERT: C 306 ARG cc_start: 0.7930 (tmm160) cc_final: 0.7381 (tmm-80) REVERT: D 43 GLU cc_start: 0.7979 (mt-10) cc_final: 0.6903 (mp0) REVERT: D 57 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7749 (ttmt) REVERT: D 64 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7308 (pttt) REVERT: D 111 LYS cc_start: 0.8367 (mttp) cc_final: 0.7856 (mtmt) REVERT: D 215 ARG cc_start: 0.8764 (ttt90) cc_final: 0.8480 (ttt90) REVERT: E 39 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7148 (ptmt) REVERT: E 40 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6550 (mmtp) REVERT: E 84 MET cc_start: 0.8438 (mtm) cc_final: 0.8198 (mmm) REVERT: E 111 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7250 (mttt) REVERT: E 285 LYS cc_start: 0.9099 (ptmm) cc_final: 0.8711 (ptmm) REVERT: E 330 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8578 (m110) REVERT: F 70 LYS cc_start: 0.6108 (mmtt) cc_final: 0.5388 (mtpp) REVERT: F 210 MET cc_start: 0.8663 (mtp) cc_final: 0.8225 (mtp) REVERT: F 213 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7266 (mp0) REVERT: F 214 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8239 (t) REVERT: F 326 MET cc_start: 0.8230 (ttt) cc_final: 0.7870 (tmm) outliers start: 37 outliers final: 19 residues processed: 258 average time/residue: 0.6952 time to fit residues: 192.2325 Evaluate side-chains 252 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 285 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 326 MET Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN 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 E residue 111 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN 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: 0.8980 chunk 111 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN E 202 GLN F 200 GLN 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 = 0.3401 r_free = 0.3401 target = 0.134365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.097110 restraints weight = 68814.172| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 5.15 r_work: 0.2537 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15768 Z= 0.105 Angle : 0.473 6.989 21488 Z= 0.255 Chirality : 0.039 0.127 2434 Planarity : 0.004 0.045 2632 Dihedral : 14.952 88.159 2702 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.06 % Allowed : 25.30 % 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 aren not related in a simple way. whole: 0.36 (0.20), residues: 1878 helix: 1.11 (0.18), residues: 900 sheet: 0.77 (0.39), residues: 210 loop : -0.93 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.009 0.001 TYR A 315 PHE 0.009 0.001 PHE F 46 HIS 0.002 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00232 (15768) covalent geometry : angle 0.47263 (21488) hydrogen bonds : bond 0.02250 ( 761) hydrogen bonds : angle 3.80213 ( 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 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7267 (mtt90) cc_final: 0.6718 (mtp-110) REVERT: A 42 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7041 (tp30) REVERT: A 57 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6370 (mttp) REVERT: A 251 MET cc_start: 0.8756 (mtp) cc_final: 0.8242 (mmm) REVERT: A 326 MET cc_start: 0.8689 (ttp) cc_final: 0.8376 (mtp) REVERT: B 43 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7439 (tm-30) REVERT: B 161 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8568 (t70) REVERT: B 165 THR cc_start: 0.9079 (m) cc_final: 0.8728 (p) REVERT: B 196 ASN cc_start: 0.9366 (p0) cc_final: 0.9113 (p0) REVERT: B 202 GLN cc_start: 0.8471 (tp40) cc_final: 0.8165 (mm110) REVERT: B 326 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8285 (tmm) REVERT: C 39 LYS cc_start: 0.7574 (mttt) cc_final: 0.7039 (ttpt) REVERT: C 68 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7059 (mp0) REVERT: C 169 GLU cc_start: 0.8551 (pm20) cc_final: 0.8308 (mm-30) REVERT: C 176 GLU cc_start: 0.8532 (tp30) cc_final: 0.8105 (tp30) REVERT: C 205 TYR cc_start: 0.8836 (m-80) cc_final: 0.8409 (m-80) REVERT: C 306 ARG cc_start: 0.7853 (tmm160) cc_final: 0.7336 (tmm-80) REVERT: D 43 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7126 (mp0) REVERT: D 57 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7641 (ttmt) REVERT: D 64 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7184 (ptmm) REVERT: E 39 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7120 (ptmt) REVERT: E 40 LYS cc_start: 0.6902 (mmtt) cc_final: 0.6624 (mmtp) REVERT: E 84 MET cc_start: 0.8387 (mtm) cc_final: 0.8022 (mmm) REVERT: E 111 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (mttt) REVERT: E 267 ASN cc_start: 0.9465 (t0) cc_final: 0.9147 (t0) REVERT: E 285 LYS cc_start: 0.9079 (ptmm) cc_final: 0.8809 (ptmm) REVERT: E 330 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8333 (m110) REVERT: F 70 LYS cc_start: 0.5796 (mmtt) cc_final: 0.5216 (mtpp) REVERT: F 210 MET cc_start: 0.8570 (mtp) cc_final: 0.8001 (mtp) REVERT: F 213 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7284 (mp0) REVERT: F 326 MET cc_start: 0.7997 (ttt) cc_final: 0.7708 (tmm) outliers start: 22 outliers final: 6 residues processed: 243 average time/residue: 0.6951 time to fit residues: 181.4355 Evaluate side-chains 230 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 330 ASN 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 330 ASN 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: 2.9990 chunk 188 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 196 ASN E 202 GLN F 196 ASN F 200 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.130385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.091165 restraints weight = 71531.452| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 4.87 r_work: 0.2484 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15768 Z= 0.222 Angle : 0.561 8.352 21488 Z= 0.299 Chirality : 0.043 0.145 2434 Planarity : 0.005 0.046 2632 Dihedral : 15.015 86.779 2702 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.93 % Allowed : 25.17 % Favored : 72.91 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 1878 helix: 0.92 (0.18), residues: 894 sheet: 0.27 (0.31), residues: 300 loop : -0.67 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 27 TYR 0.014 0.002 TYR B 216 PHE 0.016 0.002 PHE A 92 HIS 0.007 0.002 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00525 (15768) covalent geometry : angle 0.56108 (21488) hydrogen bonds : bond 0.03241 ( 761) hydrogen bonds : angle 4.16648 ( 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 248 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7266 (mtt90) cc_final: 0.6972 (mmm-85) REVERT: A 42 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7056 (tp30) REVERT: A 243 MET cc_start: 0.9051 (mtp) cc_final: 0.8594 (mtt) REVERT: A 326 MET cc_start: 0.8695 (ttp) cc_final: 0.8354 (mtp) REVERT: B 57 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7656 (tttp) REVERT: B 66 ILE cc_start: 0.7913 (mm) cc_final: 0.7482 (mp) REVERT: B 161 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (t70) REVERT: B 165 THR cc_start: 0.9158 (m) cc_final: 0.8794 (p) REVERT: B 251 MET cc_start: 0.8788 (mtp) cc_final: 0.8404 (mtp) REVERT: B 322 GLU cc_start: 0.8795 (tt0) cc_final: 0.8516 (tt0) REVERT: B 326 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8252 (tmm) REVERT: C 39 LYS cc_start: 0.7718 (mttt) cc_final: 0.7124 (ttpt) REVERT: C 68 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7102 (mp0) REVERT: C 176 GLU cc_start: 0.8626 (tp30) cc_final: 0.8195 (tp30) REVERT: C 205 TYR cc_start: 0.8850 (m-80) cc_final: 0.8406 (m-80) REVERT: C 306 ARG cc_start: 0.7909 (tmm160) cc_final: 0.7369 (tmm-80) REVERT: D 43 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7127 (mp0) REVERT: D 57 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7712 (ttmt) REVERT: D 64 LYS cc_start: 0.7532 (mmtm) cc_final: 0.7291 (ptmt) REVERT: D 111 LYS cc_start: 0.8367 (mttp) cc_final: 0.7848 (mtmt) REVERT: E 39 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7178 (ptmt) REVERT: E 40 LYS cc_start: 0.6874 (mmtt) cc_final: 0.6566 (mmtp) REVERT: E 84 MET cc_start: 0.8419 (mtm) cc_final: 0.8179 (mmm) REVERT: E 111 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7238 (mttt) REVERT: E 285 LYS cc_start: 0.9091 (ptmm) cc_final: 0.8729 (ptmm) REVERT: F 70 LYS cc_start: 0.6137 (mmtt) cc_final: 0.5405 (mtpp) REVERT: F 210 MET cc_start: 0.8646 (mtp) cc_final: 0.8088 (mtp) REVERT: F 213 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7276 (mp0) REVERT: F 214 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8187 (t) REVERT: F 326 MET cc_start: 0.8208 (ttt) cc_final: 0.7897 (tmm) outliers start: 20 outliers final: 11 residues processed: 241 average time/residue: 0.7541 time to fit residues: 194.6031 Evaluate side-chains 239 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 B residue 161 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE 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 F residue 214 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 94 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 202 GLN F 200 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.095240 restraints weight = 72203.707| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 5.05 r_work: 0.2546 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3920 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= 0.104 Angle : 0.473 7.065 21488 Z= 0.256 Chirality : 0.039 0.127 2434 Planarity : 0.004 0.044 2632 Dihedral : 14.940 87.878 2702 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.59 % Allowed : 25.70 % 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 aren not related in a simple way. whole: 0.57 (0.20), residues: 1878 helix: 1.15 (0.18), residues: 900 sheet: 0.43 (0.31), residues: 300 loop : -0.61 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.012 0.001 TYR B 216 PHE 0.009 0.001 PHE F 46 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00231 (15768) covalent geometry : angle 0.47316 (21488) hydrogen bonds : bond 0.02222 ( 761) hydrogen bonds : angle 3.80053 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5783.72 seconds wall clock time: 98 minutes 56.03 seconds (5936.03 seconds total)