Starting phenix.real_space_refine on Fri Jul 3 18:39:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.map" model { file = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8br2_16197/07_2026/8br2_16197.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 58 5.49 5 S 78 5.16 5 C 9477 2.51 5 N 2757 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15574 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "B" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "C" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "D" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "E" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "F" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2394 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "H" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 residue: pdb=" N AARG A 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 254 " occ=0.50 residue: pdb=" N AARG B 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 130 " occ=0.50 residue: pdb=" N AARG B 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 254 " occ=0.50 residue: pdb=" N AARG C 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 130 " occ=0.50 residue: pdb=" N AARG C 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 254 " occ=0.50 residue: pdb=" N AARG D 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 130 " occ=0.50 residue: pdb=" N AARG D 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 254 " occ=0.50 residue: pdb=" N AARG E 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 130 " occ=0.50 residue: pdb=" N AARG E 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 254 " occ=0.50 residue: pdb=" N AARG F 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 130 " occ=0.50 residue: pdb=" N AARG F 254 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 254 " occ=0.50 Time building chain proxies: 4.90, per 1000 atoms: 0.31 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: 1.13 Conformation dependent library (CDL) restraints added in 707.3 milliseconds 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: 1.69 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: 2.47 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2549 1.31 - 1.43: 4095 1.43 - 1.56: 8890 1.56 - 1.68: 108 1.68 - 1.80: 126 Bond restraints: 15768 Sorted by residual: bond pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " ideal model delta sigma weight residual 1.367 1.440 -0.073 6.00e-03 2.78e+04 1.47e+02 bond pdb=" N1 DT H 17 " pdb=" C6 DT H 17 " ideal model delta sigma weight residual 1.378 1.460 -0.082 7.00e-03 2.04e+04 1.36e+02 bond pdb=" N1 DT H 11 " pdb=" C6 DT H 11 " ideal model delta sigma weight residual 1.378 1.446 -0.068 7.00e-03 2.04e+04 9.45e+01 bond pdb=" C5 DA H 20 " pdb=" C6 DA H 20 " ideal model delta sigma weight residual 1.406 1.492 -0.086 9.00e-03 1.23e+04 9.03e+01 bond pdb=" C5 DT H 11 " pdb=" C6 DT H 11 " ideal model delta sigma weight residual 1.339 1.403 -0.064 7.00e-03 2.04e+04 8.32e+01 ... (remaining 15763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20622 1.28 - 2.55: 703 2.55 - 3.83: 131 3.83 - 5.10: 20 5.10 - 6.38: 12 Bond angle restraints: 21488 Sorted by residual: angle pdb=" N9 DA H 20 " pdb=" C4 DA H 20 " pdb=" C5 DA H 20 " ideal model delta sigma weight residual 105.80 101.99 3.81 4.00e-01 6.25e+00 9.08e+01 angle pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " pdb=" C5 DC H 8 " ideal model delta sigma weight residual 121.00 117.54 3.46 5.00e-01 4.00e+00 4.80e+01 angle pdb=" C6 DA H 20 " pdb=" C5 DA H 20 " pdb=" C4 DA H 20 " ideal model delta sigma weight residual 117.00 113.56 3.44 5.00e-01 4.00e+00 4.74e+01 angle pdb=" N9 DA H 14 " pdb=" C8 DA H 14 " pdb=" N7 DA H 14 " ideal model delta sigma weight residual 113.80 110.51 3.29 5.00e-01 4.00e+00 4.32e+01 angle pdb=" N7 DA H 20 " pdb=" C5 DA H 20 " pdb=" C4 DA H 20 " ideal model delta sigma weight residual 110.70 113.98 -3.28 5.00e-01 4.00e+00 4.30e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8076 17.38 - 34.75: 931 34.75 - 52.12: 256 52.12 - 69.50: 115 69.50 - 86.87: 26 Dihedral angle restraints: 9404 sinusoidal: 4034 harmonic: 5370 Sorted by residual: dihedral pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CD ARG E 303 " pdb=" NE ARG E 303 " pdb=" CZ ARG E 303 " pdb=" NH1 ARG E 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CD ARG C 303 " pdb=" NE ARG C 303 " pdb=" CZ ARG C 303 " pdb=" NH1 ARG C 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 9401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1526 0.037 - 0.074: 618 0.074 - 0.112: 237 0.112 - 0.149: 40 0.149 - 0.186: 13 Chirality restraints: 2434 Sorted by residual: chirality pdb=" C3' DT G 7 " pdb=" C4' DT G 7 " pdb=" O3' DT G 7 " pdb=" C2' DT G 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA BARG A 130 " pdb=" N BARG A 130 " pdb=" C BARG A 130 " pdb=" CB BARG A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA BARG C 130 " pdb=" N BARG C 130 " pdb=" C BARG C 130 " pdb=" CB BARG C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2431 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 303 " -1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 303 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 303 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 303 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG B 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 303 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG F 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG F 303 " 0.016 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 482 2.67 - 3.23: 14595 3.23 - 3.79: 24938 3.79 - 4.34: 37527 4.34 - 4.90: 58002 Nonbonded interactions: 135544 Sorted by model distance: nonbonded pdb=" OG1 THR F 134 " pdb="CA CA F 401 " model vdw 2.117 2.510 nonbonded pdb=" OG1 THR A 134 " pdb="CA CA A 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR E 134 " pdb="CA CA E 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR B 134 " pdb="CA CA B 401 " model vdw 2.118 2.510 ... (remaining 135539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'B' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'C' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'D' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'E' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) selection = (chain 'F' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.590 Find NCS groups from input model: 0.240 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:5.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 15768 Z= 0.468 Angle : 0.581 6.377 21488 Z= 0.399 Chirality : 0.046 0.186 2434 Planarity : 0.024 0.490 2632 Dihedral : 17.500 86.872 5972 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.80 % Allowed : 22.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.17), residues: 1878 helix: -2.43 (0.13), residues: 894 sheet: 0.23 (0.30), residues: 306 loop : -1.87 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 247 TYR 0.010 0.002 TYR A 159 PHE 0.008 0.002 PHE D 129 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.47 (15768) covalent geometry : angle 0.58115 / 0.40 (21488) hydrogen bonds : bond 0.21623 / 14.40 ( 761) hydrogen bonds : angle 7.78207 / 5.53 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 444 time to evaluate : 0.466 Fit side-chains REVERT: A 176 GLU cc_start: 0.7387 (tp30) cc_final: 0.7039 (tp30) REVERT: A 243 MET cc_start: 0.8725 (mtp) cc_final: 0.8365 (mtt) REVERT: A 266 THR cc_start: 0.8968 (m) cc_final: 0.8599 (m) REVERT: A 268 GLN cc_start: 0.9032 (mt0) cc_final: 0.8641 (mt0) REVERT: B 40 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7273 (mttt) REVERT: B 95 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7879 (mtm110) REVERT: B 187 ASP cc_start: 0.8264 (m-30) cc_final: 0.7922 (m-30) REVERT: C 39 LYS cc_start: 0.8098 (mttt) cc_final: 0.7681 (ttpt) REVERT: C 70 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6556 (mmmm) REVERT: C 176 GLU cc_start: 0.7955 (tp30) cc_final: 0.7549 (tp30) REVERT: C 205 TYR cc_start: 0.8273 (m-80) cc_final: 0.8024 (m-80) REVERT: C 211 MET cc_start: 0.8173 (mtt) cc_final: 0.7794 (mtt) REVERT: C 235 ARG cc_start: 0.9057 (ttp-170) cc_final: 0.8532 (ttp-170) REVERT: D 43 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7339 (mm-30) REVERT: D 108 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7637 (tp30) REVERT: D 111 LYS cc_start: 0.8070 (mttp) cc_final: 0.7812 (mtmt) REVERT: D 210 MET cc_start: 0.9015 (mtp) cc_final: 0.8799 (mtm) REVERT: E 40 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6882 (mmtp) REVERT: E 111 LYS cc_start: 0.7993 (mttp) cc_final: 0.7712 (mttt) REVERT: E 200 GLN cc_start: 0.9231 (tt0) cc_final: 0.8999 (tt0) REVERT: E 284 LYS cc_start: 0.8046 (pttm) cc_final: 0.7673 (ptmt) REVERT: F 70 LYS cc_start: 0.5470 (mmtt) cc_final: 0.5072 (mmtt) REVERT: F 210 MET cc_start: 0.8417 (mtp) cc_final: 0.7983 (mtp) REVERT: F 330 ASN cc_start: 0.8432 (m-40) cc_final: 0.8217 (m110) outliers start: 6 outliers final: 5 residues processed: 450 average time/residue: 0.6886 time to fit residues: 333.7475 Evaluate side-chains 246 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain E residue 31 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 206 GLN A 290 ASN B 23 GLN B 145 GLN B 202 GLN B 330 ASN C 23 GLN C 101 GLN C 138 HIS C 145 GLN C 202 GLN C 206 GLN D 114 GLN D 145 GLN D 196 ASN D 202 GLN E 206 GLN E 290 ASN F 202 GLN F 206 GLN F 290 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.135032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098729 restraints weight = 77525.020| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 5.18 r_work: 0.2517 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 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 = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15768 Z= 0.164 Angle : 0.582 6.618 21488 Z= 0.322 Chirality : 0.043 0.178 2434 Planarity : 0.005 0.105 2632 Dihedral : 14.302 81.409 2521 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.72 % Allowed : 23.11 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 1878 helix: -0.57 (0.16), residues: 894 sheet: -0.00 (0.29), residues: 348 loop : -1.24 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 303 TYR 0.019 0.001 TYR F 178 PHE 0.014 0.002 PHE F 46 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15768) covalent geometry : angle 0.58167 / 0.32 (21488) hydrogen bonds : bond 0.05101 / 3.46 ( 761) hydrogen bonds : angle 4.83071 / 3.43 ( 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 310 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.484 Fit side-chains REVERT: A 42 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7028 (tp30) REVERT: A 57 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6520 (tttp) REVERT: A 107 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7828 (mtpt) REVERT: A 206 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: A 266 THR cc_start: 0.9175 (m) cc_final: 0.8821 (m) REVERT: B 43 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7276 (mm-30) REVERT: B 94 GLN cc_start: 0.7995 (mt0) cc_final: 0.7746 (mt0) REVERT: B 165 THR cc_start: 0.8954 (m) cc_final: 0.8670 (p) REVERT: B 210 MET cc_start: 0.8884 (mtp) cc_final: 0.8528 (mtp) REVERT: C 39 LYS cc_start: 0.7624 (mttt) cc_final: 0.7019 (ttpt) REVERT: C 70 LYS cc_start: 0.6933 (mmtt) cc_final: 0.6310 (mmmm) REVERT: C 176 GLU cc_start: 0.8557 (tp30) cc_final: 0.8056 (tp30) REVERT: C 205 TYR cc_start: 0.8748 (m-80) cc_final: 0.8411 (m-80) REVERT: C 235 ARG cc_start: 0.8950 (ttp-170) cc_final: 0.8480 (ttp-170) REVERT: C 326 MET cc_start: 0.9221 (ttm) cc_final: 0.8882 (ttm) REVERT: D 43 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7177 (mm-30) REVERT: D 64 LYS cc_start: 0.7970 (mmtm) cc_final: 0.7363 (pttt) REVERT: D 108 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8131 (mm-30) REVERT: D 111 LYS cc_start: 0.8537 (mttp) cc_final: 0.8026 (mtmt) REVERT: D 176 GLU cc_start: 0.7974 (tp30) cc_final: 0.7745 (tm-30) REVERT: E 39 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7125 (ptmt) REVERT: E 40 LYS cc_start: 0.6743 (mmtt) cc_final: 0.6387 (mmtp) REVERT: E 43 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7130 (mt-10) REVERT: E 70 LYS cc_start: 0.6613 (tptt) cc_final: 0.6358 (tppt) REVERT: E 111 LYS cc_start: 0.7330 (mttp) cc_final: 0.6846 (mttt) REVERT: E 267 ASN cc_start: 0.9387 (t0) cc_final: 0.9091 (t0) REVERT: E 285 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8763 (ptmt) REVERT: E 310 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8375 (mtt-85) REVERT: F 70 LYS cc_start: 0.5986 (mmtt) cc_final: 0.5379 (mtpp) REVERT: F 108 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: F 210 MET cc_start: 0.8566 (mtp) cc_final: 0.8103 (mtp) REVERT: F 211 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8169 (mtt) outliers start: 51 outliers final: 13 residues processed: 291 average time/residue: 0.7567 time to fit residues: 236.7007 Evaluate side-chains 255 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 138 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 206 GLN B 202 GLN C 23 GLN C 202 GLN D 196 ASN D 202 GLN D 272 GLN D 290 ASN F 196 ASN 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 = 0.3372 r_free = 0.3372 target = 0.132113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094484 restraints weight = 78405.343| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 5.41 r_work: 0.2484 rms_B_bonded: 4.85 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 = 0.34 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15768 Z= 0.196 Angle : 0.561 6.592 21488 Z= 0.308 Chirality : 0.043 0.138 2434 Planarity : 0.005 0.049 2632 Dihedral : 14.227 81.082 2520 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.52 % Allowed : 23.64 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1878 helix: 0.16 (0.17), residues: 900 sheet: 0.01 (0.29), residues: 342 loop : -1.03 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.022 0.002 TYR B 159 PHE 0.015 0.002 PHE F 46 HIS 0.007 0.002 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (15768) covalent geometry : angle 0.56079 / 0.31 (21488) hydrogen bonds : bond 0.04155 / 2.85 ( 761) hydrogen bonds : angle 4.44447 / 3.15 ( 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 294 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.579 Fit side-chains REVERT: A 42 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7103 (tp30) REVERT: A 57 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6737 (tttp) REVERT: A 66 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7591 (mp) REVERT: A 206 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: A 266 THR cc_start: 0.9291 (m) cc_final: 0.8983 (m) REVERT: B 43 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7287 (mm-30) REVERT: B 94 GLN cc_start: 0.8032 (mt0) cc_final: 0.7829 (mt0) REVERT: B 98 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7219 (pp20) REVERT: B 161 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (t70) REVERT: B 165 THR cc_start: 0.8955 (m) cc_final: 0.8691 (p) REVERT: B 210 MET cc_start: 0.8873 (mtp) cc_final: 0.8604 (mtp) REVERT: C 39 LYS cc_start: 0.7676 (mttt) cc_final: 0.7041 (ttpt) REVERT: C 70 LYS cc_start: 0.6554 (mmtt) cc_final: 0.5912 (mmmm) REVERT: C 176 GLU cc_start: 0.8664 (tp30) cc_final: 0.8134 (tp30) REVERT: C 177 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8428 (ttt180) REVERT: C 205 TYR cc_start: 0.8802 (m-80) cc_final: 0.8382 (m-80) REVERT: C 235 ARG cc_start: 0.8942 (ttp-170) cc_final: 0.8596 (ttp-170) REVERT: D 43 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7163 (mm-30) REVERT: D 64 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7270 (pttt) REVERT: D 111 LYS cc_start: 0.8505 (mttp) cc_final: 0.8042 (mtmt) REVERT: E 39 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7041 (ptmt) REVERT: E 40 LYS cc_start: 0.6764 (mmtt) cc_final: 0.6373 (mmtp) REVERT: E 43 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7110 (mt-10) REVERT: E 70 LYS cc_start: 0.6567 (tptt) cc_final: 0.6335 (tppt) REVERT: E 111 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7039 (mttt) REVERT: E 310 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8179 (mtt-85) REVERT: F 70 LYS cc_start: 0.6010 (mmtt) cc_final: 0.5374 (mtpp) REVERT: F 108 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: F 210 MET cc_start: 0.8655 (mtp) cc_final: 0.8214 (mtp) REVERT: F 211 MET cc_start: 0.8683 (mtt) cc_final: 0.8417 (mtt) REVERT: F 213 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7380 (mp0) REVERT: F 253 LEU cc_start: 0.8502 (tp) cc_final: 0.8269 (tp) outliers start: 46 outliers final: 22 residues processed: 278 average time/residue: 0.8688 time to fit residues: 259.1322 Evaluate side-chains 261 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 310 ARG Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 183 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 290 ASN C 23 GLN C 30 GLN C 202 GLN D 202 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.134161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.096010 restraints weight = 71848.902| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 5.06 r_work: 0.2528 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- 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 = 0.31 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15768 Z= 0.115 Angle : 0.493 7.086 21488 Z= 0.272 Chirality : 0.040 0.140 2434 Planarity : 0.004 0.048 2632 Dihedral : 14.088 81.184 2519 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.65 % Allowed : 23.44 % 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 are not related in a simple way. whole: -0.08 (0.19), residues: 1878 helix: 0.60 (0.17), residues: 900 sheet: 0.14 (0.31), residues: 300 loop : -0.91 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 310 TYR 0.010 0.001 TYR A 205 PHE 0.011 0.001 PHE F 46 HIS 0.002 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (15768) covalent geometry : angle 0.49314 / 0.27 (21488) hydrogen bonds : bond 0.03076 / 2.10 ( 761) hydrogen bonds : angle 4.08992 / 2.89 ( 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 292 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.589 Fit side-chains REVERT: A 42 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7096 (tp30) REVERT: A 57 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6705 (mmtt) REVERT: A 66 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 202 GLN cc_start: 0.7215 (tm130) cc_final: 0.6990 (tt0) REVERT: A 266 THR cc_start: 0.9190 (m) cc_final: 0.8846 (m) REVERT: B 43 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7300 (tp30) REVERT: B 98 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7234 (pp20) REVERT: B 154 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8018 (mt-10) REVERT: B 161 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (t70) REVERT: B 165 THR cc_start: 0.8866 (m) cc_final: 0.8612 (p) REVERT: B 177 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7982 (ttt-90) REVERT: B 285 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8549 (ptpt) REVERT: C 39 LYS cc_start: 0.7630 (mttt) cc_final: 0.7032 (ttpt) REVERT: C 70 LYS cc_start: 0.6537 (mmtt) cc_final: 0.5908 (mmmm) REVERT: C 169 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: C 176 GLU cc_start: 0.8646 (tp30) cc_final: 0.8125 (tp30) REVERT: C 205 TYR cc_start: 0.8758 (m-80) cc_final: 0.8363 (m-80) REVERT: C 308 GLU cc_start: 0.8598 (pm20) cc_final: 0.8370 (pm20) REVERT: D 43 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7017 (mp0) REVERT: D 64 LYS cc_start: 0.7757 (mmtm) cc_final: 0.7246 (pttt) REVERT: D 72 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: D 111 LYS cc_start: 0.8490 (mttp) cc_final: 0.8041 (mtmt) REVERT: E 39 LYS cc_start: 0.7670 (mmmm) cc_final: 0.6920 (ptmt) REVERT: E 40 LYS cc_start: 0.6732 (mmtt) cc_final: 0.6373 (mmtp) REVERT: E 43 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7016 (mt-10) REVERT: E 70 LYS cc_start: 0.6603 (tptt) cc_final: 0.6310 (tppt) REVERT: E 111 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7215 (mttt) REVERT: E 215 ARG cc_start: 0.8987 (ttt90) cc_final: 0.8633 (ttt90) REVERT: E 267 ASN cc_start: 0.9460 (t0) cc_final: 0.9169 (t0) REVERT: E 285 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8629 (ptmm) REVERT: F 70 LYS cc_start: 0.5997 (mmtt) cc_final: 0.5270 (mtpp) REVERT: F 108 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: F 210 MET cc_start: 0.8577 (mtp) cc_final: 0.8108 (mtp) REVERT: F 211 MET cc_start: 0.8690 (mtt) cc_final: 0.8405 (mtt) REVERT: F 213 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7373 (mp0) REVERT: F 253 LEU cc_start: 0.8616 (tp) cc_final: 0.8288 (tp) REVERT: F 326 MET cc_start: 0.8372 (ttm) cc_final: 0.7939 (tpp) outliers start: 44 outliers final: 18 residues processed: 280 average time/residue: 0.8337 time to fit residues: 251.4806 Evaluate side-chains 266 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN B 94 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN 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 = 0.3377 r_free = 0.3377 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.093879 restraints weight = 69511.280| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.86 r_work: 0.2512 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 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 = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15768 Z= 0.153 Angle : 0.517 7.015 21488 Z= 0.282 Chirality : 0.041 0.150 2434 Planarity : 0.004 0.047 2632 Dihedral : 13.930 81.033 2519 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.92 % Allowed : 24.17 % 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 are not related in a simple way. whole: -0.10 (0.19), residues: 1878 helix: 0.73 (0.18), residues: 900 sheet: 0.28 (0.39), residues: 210 loop : -1.07 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 310 TYR 0.015 0.001 TYR B 159 PHE 0.013 0.002 PHE B 327 HIS 0.005 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15768) covalent geometry : angle 0.51692 / 0.28 (21488) hydrogen bonds : bond 0.03170 / 2.17 ( 761) hydrogen bonds : angle 4.06022 / 2.88 ( 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 278 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7218 (tp30) REVERT: A 66 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 184 ASP cc_start: 0.7720 (m-30) cc_final: 0.7507 (m-30) REVERT: A 202 GLN cc_start: 0.7507 (tm130) cc_final: 0.7043 (tt0) REVERT: A 266 THR cc_start: 0.9271 (m) cc_final: 0.8944 (m) REVERT: B 43 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7310 (tp30) REVERT: B 98 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7283 (pp20) REVERT: B 154 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8062 (mt-10) REVERT: B 161 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8606 (t70) REVERT: B 165 THR cc_start: 0.9008 (m) cc_final: 0.8711 (p) REVERT: B 202 GLN cc_start: 0.8470 (tp40) cc_final: 0.8249 (mm-40) REVERT: B 285 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8508 (ptpt) REVERT: C 39 LYS cc_start: 0.7719 (mttt) cc_final: 0.7129 (ttpt) REVERT: C 70 LYS cc_start: 0.6655 (mmtt) cc_final: 0.6013 (mmmm) REVERT: C 114 GLN cc_start: 0.8907 (mt0) cc_final: 0.8699 (mt0) REVERT: C 169 GLU cc_start: 0.8569 (pm20) cc_final: 0.8305 (mm-30) REVERT: C 176 GLU cc_start: 0.8683 (tp30) cc_final: 0.8153 (tp30) REVERT: C 205 TYR cc_start: 0.8783 (m-80) cc_final: 0.8361 (m-80) REVERT: C 308 GLU cc_start: 0.8627 (pm20) cc_final: 0.8405 (pm20) REVERT: D 43 GLU cc_start: 0.7955 (mt-10) cc_final: 0.6989 (mp0) REVERT: D 111 LYS cc_start: 0.8518 (mttp) cc_final: 0.8051 (mtmt) REVERT: E 39 LYS cc_start: 0.7777 (mmmm) cc_final: 0.7066 (ptmt) REVERT: E 40 LYS cc_start: 0.6865 (mmtt) cc_final: 0.6542 (mmtp) REVERT: E 43 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7040 (mt-10) REVERT: E 111 LYS cc_start: 0.7749 (mttp) cc_final: 0.7276 (mttt) REVERT: E 215 ARG cc_start: 0.8988 (ttt90) cc_final: 0.8653 (ttt90) REVERT: F 70 LYS cc_start: 0.5900 (mmtt) cc_final: 0.5179 (mtpp) REVERT: F 108 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: F 210 MET cc_start: 0.8617 (mtp) cc_final: 0.8096 (mtp) REVERT: F 213 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7405 (mp0) REVERT: F 253 LEU cc_start: 0.8656 (tp) cc_final: 0.8212 (tp) outliers start: 33 outliers final: 19 residues processed: 268 average time/residue: 0.8667 time to fit residues: 250.0349 Evaluate side-chains 257 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 5.9990 chunk 149 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 34 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.092405 restraints weight = 74894.530| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.90 r_work: 0.2484 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15768 Z= 0.174 Angle : 0.530 7.430 21488 Z= 0.288 Chirality : 0.042 0.146 2434 Planarity : 0.004 0.046 2632 Dihedral : 13.868 81.547 2517 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.59 % Allowed : 23.97 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1878 helix: 0.74 (0.17), residues: 900 sheet: 0.19 (0.39), residues: 210 loop : -1.06 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.013 0.001 TYR B 232 PHE 0.012 0.002 PHE B 327 HIS 0.006 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (15768) covalent geometry : angle 0.53011 / 0.29 (21488) hydrogen bonds : bond 0.03203 / 2.20 ( 761) hydrogen bonds : angle 4.11697 / 2.91 ( 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 288 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.460 Fit side-chains REVERT: A 42 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7238 (tp30) REVERT: A 57 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6776 (mttp) REVERT: A 66 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 184 ASP cc_start: 0.7745 (m-30) cc_final: 0.7486 (m-30) REVERT: A 202 GLN cc_start: 0.7748 (tm130) cc_final: 0.7230 (tt0) REVERT: A 266 THR cc_start: 0.9350 (m) cc_final: 0.9074 (m) REVERT: B 43 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7478 (tp30) REVERT: B 98 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7266 (pp20) REVERT: B 161 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8650 (t70) REVERT: B 165 THR cc_start: 0.9032 (m) cc_final: 0.8725 (p) REVERT: B 202 GLN cc_start: 0.8497 (tp40) cc_final: 0.8266 (mm-40) REVERT: B 326 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8468 (tmm) REVERT: C 39 LYS cc_start: 0.7737 (mttt) cc_final: 0.7192 (ttpt) REVERT: C 114 GLN cc_start: 0.8915 (mt0) cc_final: 0.8689 (mt0) REVERT: C 169 GLU cc_start: 0.8604 (pm20) cc_final: 0.8307 (mm-30) REVERT: C 176 GLU cc_start: 0.8719 (tp30) cc_final: 0.8213 (tp30) REVERT: C 205 TYR cc_start: 0.8801 (m-80) cc_final: 0.8368 (m-80) REVERT: D 43 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7080 (mp0) REVERT: D 64 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7246 (pttt) REVERT: D 111 LYS cc_start: 0.8606 (mttp) cc_final: 0.8065 (mtmt) REVERT: E 39 LYS cc_start: 0.7788 (mmmm) cc_final: 0.7012 (ptmt) REVERT: E 40 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6732 (mmtp) REVERT: E 43 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7094 (mt-10) REVERT: E 72 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: E 111 LYS cc_start: 0.7829 (mttp) cc_final: 0.7282 (mttt) REVERT: E 285 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8664 (ptmm) REVERT: F 70 LYS cc_start: 0.5775 (mmtt) cc_final: 0.5072 (mtpp) REVERT: F 108 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: F 210 MET cc_start: 0.8637 (mtp) cc_final: 0.8177 (mtp) REVERT: F 213 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7427 (mp0) REVERT: F 214 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8211 (t) REVERT: F 253 LEU cc_start: 0.8665 (tp) cc_final: 0.8172 (tp) outliers start: 43 outliers final: 23 residues processed: 277 average time/residue: 0.8844 time to fit residues: 262.9202 Evaluate side-chains 263 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 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 67 SER Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 89 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 94 GLN C 202 GLN D 202 GLN D 272 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.094300 restraints weight = 72715.634| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.99 r_work: 0.2511 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 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 = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3433 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= 0.127 Angle : 0.496 6.822 21488 Z= 0.271 Chirality : 0.040 0.138 2434 Planarity : 0.004 0.045 2632 Dihedral : 13.850 81.426 2517 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.99 % Allowed : 25.03 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1878 helix: 0.88 (0.18), residues: 900 sheet: 0.30 (0.40), residues: 210 loop : -1.02 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 310 TYR 0.010 0.001 TYR B 315 PHE 0.009 0.001 PHE F 46 HIS 0.003 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15768) covalent geometry : angle 0.49607 / 0.27 (21488) hydrogen bonds : bond 0.02766 / 1.89 ( 761) hydrogen bonds : angle 3.96401 / 2.80 ( 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 268 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.561 Fit side-chains REVERT: A 42 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7231 (tp30) REVERT: A 57 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6767 (mttp) REVERT: A 184 ASP cc_start: 0.7708 (m-30) cc_final: 0.7450 (m-30) REVERT: A 202 GLN cc_start: 0.7742 (tm130) cc_final: 0.7170 (tt0) REVERT: A 266 THR cc_start: 0.9263 (m) cc_final: 0.8966 (m) REVERT: B 43 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7502 (tp30) REVERT: B 98 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7309 (pp20) REVERT: B 161 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8620 (t70) REVERT: B 165 THR cc_start: 0.9078 (m) cc_final: 0.8726 (p) REVERT: B 202 GLN cc_start: 0.8475 (tp40) cc_final: 0.8245 (mm-40) REVERT: C 39 LYS cc_start: 0.7704 (mttt) cc_final: 0.7150 (ttpt) REVERT: C 169 GLU cc_start: 0.8583 (pm20) cc_final: 0.8314 (mm-30) REVERT: C 176 GLU cc_start: 0.8673 (tp30) cc_final: 0.8168 (tp30) REVERT: C 205 TYR cc_start: 0.8782 (m-80) cc_final: 0.8346 (m-80) REVERT: D 43 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7066 (mp0) REVERT: D 64 LYS cc_start: 0.7748 (mmtm) cc_final: 0.7243 (pttt) REVERT: D 111 LYS cc_start: 0.8608 (mttp) cc_final: 0.8059 (mtmt) REVERT: E 39 LYS cc_start: 0.7737 (mmmm) cc_final: 0.7037 (ptmt) REVERT: E 40 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6702 (mmtp) REVERT: E 43 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7117 (mt-10) REVERT: E 84 MET cc_start: 0.8414 (mtm) cc_final: 0.8181 (mmm) REVERT: E 107 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7679 (mtmt) REVERT: E 111 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7221 (mttt) REVERT: E 267 ASN cc_start: 0.9487 (t0) cc_final: 0.9205 (t0) REVERT: F 70 LYS cc_start: 0.5717 (mmtt) cc_final: 0.5088 (mtpp) REVERT: F 210 MET cc_start: 0.8617 (mtp) cc_final: 0.8145 (mtp) REVERT: F 213 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7434 (mp0) REVERT: F 214 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8186 (t) REVERT: F 253 LEU cc_start: 0.8654 (tp) cc_final: 0.8199 (tp) outliers start: 34 outliers final: 20 residues processed: 257 average time/residue: 0.8170 time to fit residues: 225.5285 Evaluate side-chains 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain 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 111 LYS Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN F 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097706 restraints weight = 77231.749| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 5.60 r_work: 0.2515 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 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 = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15768 Z= 0.116 Angle : 0.482 6.577 21488 Z= 0.264 Chirality : 0.040 0.135 2434 Planarity : 0.004 0.044 2632 Dihedral : 13.827 81.265 2517 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.92 % Allowed : 25.17 % Favored : 71.91 % 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 are not related in a simple way. whole: 0.15 (0.20), residues: 1878 helix: 0.93 (0.18), residues: 906 sheet: 0.38 (0.40), residues: 210 loop : -0.95 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 250 TYR 0.009 0.001 TYR D 315 PHE 0.009 0.001 PHE F 46 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15768) covalent geometry : angle 0.48186 / 0.26 (21488) hydrogen bonds : bond 0.02588 / 1.77 ( 761) hydrogen bonds : angle 3.88571 / 2.74 ( 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 275 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.640 Fit side-chains REVERT: A 27 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.7079 (mtt90) REVERT: A 42 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7209 (tp30) REVERT: A 57 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6506 (mttp) REVERT: A 184 ASP cc_start: 0.7747 (m-30) cc_final: 0.7494 (m-30) REVERT: A 202 GLN cc_start: 0.7765 (tm130) cc_final: 0.7016 (tt0) REVERT: A 206 GLN cc_start: 0.8305 (mp10) cc_final: 0.8057 (mp-120) REVERT: A 266 THR cc_start: 0.9231 (m) cc_final: 0.8910 (m) REVERT: B 43 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7503 (tp30) REVERT: B 98 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7338 (pp20) REVERT: B 161 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8619 (t70) REVERT: B 165 THR cc_start: 0.9081 (m) cc_final: 0.8738 (p) REVERT: B 202 GLN cc_start: 0.8505 (tp40) cc_final: 0.8271 (mm-40) REVERT: B 326 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: C 39 LYS cc_start: 0.7686 (mttt) cc_final: 0.7164 (ttpt) REVERT: C 169 GLU cc_start: 0.8590 (pm20) cc_final: 0.8304 (mm-30) REVERT: C 176 GLU cc_start: 0.8638 (tp30) cc_final: 0.8187 (tp30) REVERT: C 205 TYR cc_start: 0.8773 (m-80) cc_final: 0.8394 (m-80) REVERT: C 306 ARG cc_start: 0.7788 (tmm-80) cc_final: 0.7104 (tmm160) REVERT: D 43 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7068 (mp0) REVERT: D 111 LYS cc_start: 0.8619 (mttp) cc_final: 0.8065 (mtmt) REVERT: E 39 LYS cc_start: 0.7711 (mmmm) cc_final: 0.7026 (ptmt) REVERT: E 40 LYS cc_start: 0.6919 (mmtt) cc_final: 0.6650 (mmtp) REVERT: E 43 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7114 (mt-10) REVERT: E 84 MET cc_start: 0.8398 (mtm) cc_final: 0.8170 (mmm) REVERT: E 111 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7204 (mttt) REVERT: E 267 ASN cc_start: 0.9482 (t0) cc_final: 0.9171 (t0) REVERT: E 285 LYS cc_start: 0.8968 (ptmt) cc_final: 0.8686 (ptmm) REVERT: F 70 LYS cc_start: 0.5745 (mmtt) cc_final: 0.5274 (mtpp) REVERT: F 210 MET cc_start: 0.8604 (mtp) cc_final: 0.8083 (mtp) REVERT: F 213 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7255 (mp0) REVERT: F 214 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8173 (t) REVERT: F 253 LEU cc_start: 0.8835 (tp) cc_final: 0.8374 (tp) outliers start: 34 outliers final: 20 residues processed: 263 average time/residue: 0.7991 time to fit residues: 226.0947 Evaluate side-chains 256 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 61 ILE 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 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN F 196 ASN F 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.131959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.093447 restraints weight = 69020.283| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.82 r_work: 0.2504 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15768 Z= 0.165 Angle : 0.515 7.329 21488 Z= 0.279 Chirality : 0.041 0.142 2434 Planarity : 0.004 0.045 2632 Dihedral : 13.806 80.898 2517 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.86 % Allowed : 25.10 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1878 helix: 0.87 (0.18), residues: 906 sheet: 0.93 (0.41), residues: 192 loop : -0.99 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.012 0.001 TYR B 315 PHE 0.012 0.002 PHE B 327 HIS 0.006 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (15768) covalent geometry : angle 0.51483 / 0.28 (21488) hydrogen bonds : bond 0.02937 / 2.01 ( 761) hydrogen bonds : angle 4.01505 / 2.84 ( 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 269 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.420 Fit side-chains REVERT: A 42 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7249 (tp30) REVERT: A 57 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6629 (mttp) REVERT: A 184 ASP cc_start: 0.7793 (m-30) cc_final: 0.7546 (m-30) REVERT: A 202 GLN cc_start: 0.7796 (tm130) cc_final: 0.7055 (tt0) REVERT: A 206 GLN cc_start: 0.8348 (mp10) cc_final: 0.8080 (mp-120) REVERT: A 266 THR cc_start: 0.9305 (m) cc_final: 0.9010 (m) REVERT: B 43 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7456 (tp30) REVERT: B 70 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6308 (tppt) REVERT: B 98 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7335 (pp20) REVERT: B 161 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8632 (t70) REVERT: B 165 THR cc_start: 0.9020 (m) cc_final: 0.8720 (p) REVERT: B 202 GLN cc_start: 0.8454 (tp40) cc_final: 0.8215 (mm-40) REVERT: B 251 MET cc_start: 0.9081 (mtp) cc_final: 0.8833 (mtp) REVERT: B 326 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8283 (tmm) REVERT: C 39 LYS cc_start: 0.7737 (mttt) cc_final: 0.7136 (ttpt) REVERT: C 70 LYS cc_start: 0.6656 (mmtm) cc_final: 0.6446 (mmmm) REVERT: C 169 GLU cc_start: 0.8567 (pm20) cc_final: 0.8303 (mm-30) REVERT: C 176 GLU cc_start: 0.8707 (tp30) cc_final: 0.8209 (tp30) REVERT: C 205 TYR cc_start: 0.8802 (m-80) cc_final: 0.8378 (m-80) REVERT: C 306 ARG cc_start: 0.7847 (tmm-80) cc_final: 0.7150 (tmm160) REVERT: D 43 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7089 (mp0) REVERT: D 111 LYS cc_start: 0.8617 (mttp) cc_final: 0.8063 (mtmt) REVERT: E 39 LYS cc_start: 0.7824 (mmmm) cc_final: 0.7065 (ptmt) REVERT: E 40 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6769 (mmtp) REVERT: E 43 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7142 (mt-10) REVERT: E 84 MET cc_start: 0.8420 (mtm) cc_final: 0.8191 (mmm) REVERT: E 107 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7688 (mttt) REVERT: E 111 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7226 (mttt) REVERT: F 61 ILE cc_start: 0.7595 (mt) cc_final: 0.7288 (mt) REVERT: F 70 LYS cc_start: 0.5781 (mmtt) cc_final: 0.5302 (mtpp) REVERT: F 210 MET cc_start: 0.8649 (mtp) cc_final: 0.8155 (mtp) REVERT: F 213 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7283 (mp0) REVERT: F 214 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8177 (t) REVERT: F 253 LEU cc_start: 0.8851 (tp) cc_final: 0.8366 (tp) outliers start: 33 outliers final: 20 residues processed: 258 average time/residue: 0.7791 time to fit residues: 215.9617 Evaluate side-chains 256 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 61 ILE 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 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN F 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.132040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095726 restraints weight = 71704.840| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 5.21 r_work: 0.2497 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 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 = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15768 Z= 0.157 Angle : 0.512 7.526 21488 Z= 0.278 Chirality : 0.041 0.139 2434 Planarity : 0.004 0.045 2632 Dihedral : 13.805 81.186 2517 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.66 % Allowed : 25.37 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1878 helix: 0.92 (0.18), residues: 900 sheet: 0.90 (0.41), residues: 192 loop : -1.00 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 27 TYR 0.011 0.001 TYR B 315 PHE 0.010 0.001 PHE A 92 HIS 0.005 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (15768) covalent geometry : angle 0.51173 / 0.28 (21488) hydrogen bonds : bond 0.02892 / 1.98 ( 761) hydrogen bonds : angle 4.01759 / 2.84 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7273 (mtt90) cc_final: 0.6985 (mtt-85) REVERT: A 42 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7229 (tp30) REVERT: A 57 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6624 (mttp) REVERT: A 202 GLN cc_start: 0.7836 (tm130) cc_final: 0.7098 (tt0) REVERT: A 206 GLN cc_start: 0.8405 (mp10) cc_final: 0.8131 (mp-120) REVERT: A 266 THR cc_start: 0.9313 (m) cc_final: 0.9026 (m) REVERT: B 43 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7469 (tp30) REVERT: B 70 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6292 (tppt) REVERT: B 98 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7336 (pp20) REVERT: B 161 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (t70) REVERT: B 165 THR cc_start: 0.9092 (m) cc_final: 0.8745 (p) REVERT: B 202 GLN cc_start: 0.8496 (tp40) cc_final: 0.8251 (mm-40) REVERT: B 326 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8310 (tmm) REVERT: C 39 LYS cc_start: 0.7662 (mttt) cc_final: 0.7052 (ttpt) REVERT: C 169 GLU cc_start: 0.8583 (pm20) cc_final: 0.8311 (mm-30) REVERT: C 176 GLU cc_start: 0.8671 (tp30) cc_final: 0.8228 (tp30) REVERT: C 205 TYR cc_start: 0.8819 (m-80) cc_final: 0.8394 (m-80) REVERT: C 306 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7063 (tmm160) REVERT: D 43 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7085 (mp0) REVERT: D 64 LYS cc_start: 0.7713 (mmtm) cc_final: 0.6978 (ptmm) REVERT: D 111 LYS cc_start: 0.8631 (mttp) cc_final: 0.8081 (mtmt) REVERT: E 39 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7016 (ptmt) REVERT: E 40 LYS cc_start: 0.6962 (mmtt) cc_final: 0.6672 (mmtp) REVERT: E 43 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7131 (mt-10) REVERT: E 84 MET cc_start: 0.8415 (mtm) cc_final: 0.8183 (mmm) REVERT: E 111 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7235 (mttt) REVERT: E 285 LYS cc_start: 0.8961 (ptmt) cc_final: 0.8647 (ptmm) REVERT: F 61 ILE cc_start: 0.7523 (mt) cc_final: 0.7233 (mt) REVERT: F 70 LYS cc_start: 0.5784 (mmtt) cc_final: 0.5293 (mtpp) REVERT: F 210 MET cc_start: 0.8650 (mtp) cc_final: 0.8152 (mtp) REVERT: F 213 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7285 (mp0) REVERT: F 214 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8188 (t) REVERT: F 253 LEU cc_start: 0.8842 (tp) cc_final: 0.8344 (tp) outliers start: 30 outliers final: 19 residues processed: 255 average time/residue: 0.8125 time to fit residues: 222.7399 Evaluate side-chains 255 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 61 ILE 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 202 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN B 30 GLN C 23 GLN C 202 GLN C 290 ASN D 202 GLN F 196 ASN F 202 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.095808 restraints weight = 72264.977| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.96 r_work: 0.2532 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15768 Z= 0.109 Angle : 0.478 6.383 21488 Z= 0.262 Chirality : 0.039 0.129 2434 Planarity : 0.004 0.044 2632 Dihedral : 13.804 81.757 2517 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 25.76 % Favored : 71.91 % 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 are not related in a simple way. whole: 0.37 (0.20), residues: 1878 helix: 1.07 (0.18), residues: 900 sheet: 1.06 (0.42), residues: 192 loop : -0.91 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.008 0.001 TYR B 315 PHE 0.008 0.001 PHE F 327 HIS 0.002 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (15768) covalent geometry : angle 0.47796 / 0.26 (21488) hydrogen bonds : bond 0.02421 / 1.65 ( 761) hydrogen bonds : angle 3.84075 / 2.71 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.78 seconds wall clock time: 108 minutes 22.15 seconds (6502.15 seconds total)