Starting phenix.real_space_refine on Sat Jun 14 00:36:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.map" model { file = "/net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8br2_16197/06_2025/8br2_16197.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.82, per 1000 atoms: 1.14 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: 4.25 Conformation dependent library (CDL) restraints added in 4.0 seconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 18 sheets defined 52.5% alpha, 17.0% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.64 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: 5.50 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2549 1.31 - 1.43: 4095 1.43 - 1.56: 8890 1.56 - 1.68: 108 1.68 - 1.80: 126 Bond restraints: 15768 Sorted by residual: bond pdb=" C5 DA H 20 " pdb=" C6 DA H 20 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" N1 DT H 17 " pdb=" C6 DT H 17 " ideal model delta sigma weight residual 1.380 1.460 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" N9 DA H 14 " pdb=" C8 DA H 14 " ideal model delta sigma weight residual 1.367 1.446 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N1 DC H 8 " pdb=" C6 DC H 8 " ideal model delta sigma weight residual 1.364 1.440 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" SD MET D 251 " pdb=" CE MET D 251 " ideal model delta sigma weight residual 1.791 1.706 0.085 2.50e-02 1.60e+03 1.16e+01 ... (remaining 15763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20742 1.28 - 2.55: 596 2.55 - 3.83: 119 3.83 - 5.10: 19 5.10 - 6.38: 12 Bond angle restraints: 21488 Sorted by residual: angle pdb=" CA BARG F 130 " pdb=" CB BARG F 130 " pdb=" CG BARG F 130 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA BARG C 130 " pdb=" CB BARG C 130 " pdb=" CG BARG C 130 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG E 130 " pdb=" CB BARG E 130 " pdb=" CG BARG E 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG D 130 " pdb=" CB BARG D 130 " pdb=" CG BARG D 130 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA BARG A 130 " pdb=" CB BARG A 130 " pdb=" CG BARG A 130 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 ... (remaining 21483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8212 17.90 - 35.81: 967 35.81 - 53.71: 272 53.71 - 71.61: 101 71.61 - 89.51: 38 Dihedral angle restraints: 9590 sinusoidal: 4220 harmonic: 5370 Sorted by residual: dihedral pdb=" CD ARG A 303 " pdb=" NE ARG A 303 " pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.87 -86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CD ARG E 303 " pdb=" NE ARG E 303 " pdb=" CZ ARG E 303 " pdb=" NH1 ARG E 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CD ARG C 303 " pdb=" NE ARG C 303 " pdb=" CZ ARG C 303 " pdb=" NH1 ARG C 303 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 9587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1418 0.033 - 0.066: 715 0.066 - 0.099: 201 0.099 - 0.132: 87 0.132 - 0.165: 13 Chirality restraints: 2434 Sorted by residual: chirality pdb=" CA BARG A 130 " pdb=" N BARG A 130 " pdb=" C BARG A 130 " pdb=" CB BARG A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA BARG C 130 " pdb=" N BARG C 130 " pdb=" C BARG C 130 " pdb=" CB BARG C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA BARG E 130 " pdb=" N BARG E 130 " pdb=" C BARG E 130 " pdb=" CB BARG E 130 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 2431 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 303 " -1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 303 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 303 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 303 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG B 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 303 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 303 " 1.094 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG F 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG F 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG F 303 " 0.016 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 482 2.67 - 3.23: 14595 3.23 - 3.79: 24938 3.79 - 4.34: 37527 4.34 - 4.90: 58002 Nonbonded interactions: 135544 Sorted by model distance: nonbonded pdb=" OG1 THR F 134 " pdb="CA CA F 401 " model vdw 2.117 2.510 nonbonded pdb=" OG1 THR A 134 " pdb="CA CA A 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR C 134 " pdb="CA CA C 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR E 134 " pdb="CA CA E 401 " model vdw 2.118 2.510 nonbonded pdb=" OG1 THR B 134 " pdb="CA CA B 401 " model vdw 2.118 2.510 ... (remaining 135539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'B' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'C' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'D' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'E' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 401)) selection = (chain 'F' and (resid 21 through 129 or resid 131 through 253 or resid 255 throu \ gh 339 or resid 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: 5.000 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 52.150 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 15768 Z= 0.344 Angle : 0.556 6.377 21488 Z= 0.311 Chirality : 0.045 0.165 2434 Planarity : 0.024 0.490 2632 Dihedral : 18.028 89.513 6158 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.80 % Allowed : 22.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS B 294 PHE 0.008 0.002 PHE D 129 TYR 0.010 0.002 TYR A 159 ARG 0.005 0.001 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.21623 ( 761) hydrogen bonds : angle 7.78207 ( 2142) covalent geometry : bond 0.00778 (15768) covalent geometry : angle 0.55650 (21488) *********************** 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 : 1.471 Fit side-chains REVERT: A 176 GLU cc_start: 0.7387 (tp30) cc_final: 0.7038 (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: 0.7272 (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: 0.7682 (ttpt) REVERT: C 70 LYS cc_start: 0.6855 (mmtt) cc_final: 0.6555 (mmmm) REVERT: C 176 GLU cc_start: 0.7955 (tp30) cc_final: 0.7551 (tp30) REVERT: C 205 TYR cc_start: 0.8273 (m-80) cc_final: 0.8024 (m-80) REVERT: C 235 ARG cc_start: 0.9057 (ttp-170) cc_final: 0.8533 (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: 0.8798 (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: 0.8216 (m110) outliers start: 6 outliers final: 5 residues processed: 450 average time/residue: 1.6500 time to fit residues: 800.4118 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 : 1.285 ------------------------------------------------------------------------------- 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 160 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 196 ASN A 206 GLN A 290 ASN B 23 GLN B 145 GLN B 202 GLN B 330 ASN C 23 GLN C 101 GLN C 138 HIS C 145 GLN C 202 GLN C 206 GLN D 114 GLN D 145 GLN D 196 ASN D 202 GLN D 290 ASN E 206 GLN E 290 ASN F 202 GLN F 206 GLN F 290 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.099227 restraints weight = 81867.287| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 5.22 r_work: 0.2525 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15768 Z= 0.139 Angle : 0.532 7.025 21488 Z= 0.291 Chirality : 0.040 0.139 2434 Planarity : 0.005 0.050 2632 Dihedral : 15.581 89.728 2707 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.25 % Allowed : 23.37 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 1878 helix: -0.49 (0.16), residues: 900 sheet: 0.12 (0.30), residues: 342 loop : -1.18 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 93 PHE 0.014 0.001 PHE F 46 TYR 0.014 0.001 TYR E 301 ARG 0.007 0.001 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 761) hydrogen bonds : angle 4.53195 ( 2142) covalent geometry : bond 0.00305 (15768) covalent geometry : angle 0.53224 (21488) *********************** 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 304 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 3.111 Fit side-chains REVERT: A 37 ASP cc_start: 0.6592 (m-30) cc_final: 0.6192 (m-30) REVERT: A 42 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7114 (tp30) REVERT: A 57 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6590 (tttp) REVERT: A 94 GLN cc_start: 0.8352 (tp40) cc_final: 0.8129 (tp-100) REVERT: A 107 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7723 (mtpt) REVERT: A 202 GLN cc_start: 0.7337 (tm-30) cc_final: 0.7120 (tt0) REVERT: A 206 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: A 266 THR cc_start: 0.9137 (m) cc_final: 0.8779 (m) REVERT: B 43 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7267 (mm-30) REVERT: B 94 GLN cc_start: 0.8074 (mt0) cc_final: 0.7857 (mt0) REVERT: B 161 ASP cc_start: 0.8885 (t70) cc_final: 0.8637 (t70) REVERT: B 165 THR cc_start: 0.8785 (m) cc_final: 0.8500 (p) REVERT: B 210 MET cc_start: 0.8863 (mtp) cc_final: 0.8499 (mtp) REVERT: C 39 LYS cc_start: 0.7545 (mttt) cc_final: 0.6958 (ttpt) REVERT: C 70 LYS cc_start: 0.6732 (mmtt) cc_final: 0.6073 (mmmm) REVERT: C 169 GLU cc_start: 0.8577 (pm20) cc_final: 0.8229 (mm-30) REVERT: C 176 GLU cc_start: 0.8651 (tp30) cc_final: 0.8166 (tp30) REVERT: C 205 TYR cc_start: 0.8741 (m-80) cc_final: 0.8383 (m-80) REVERT: C 306 ARG cc_start: 0.7445 (tmm160) cc_final: 0.7227 (tmm160) REVERT: C 326 MET cc_start: 0.9134 (ttm) cc_final: 0.8855 (ttm) REVERT: D 43 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7045 (mm-30) REVERT: D 64 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7301 (pttt) REVERT: D 111 LYS cc_start: 0.8478 (mttp) cc_final: 0.7944 (mtmt) REVERT: D 176 GLU cc_start: 0.7941 (tp30) cc_final: 0.7586 (tm-30) REVERT: E 27 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6734 (mtt-85) REVERT: E 39 LYS cc_start: 0.7693 (mmmm) cc_final: 0.6947 (ptmt) REVERT: E 40 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6387 (mmtp) REVERT: E 43 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7073 (mt-10) REVERT: E 70 LYS cc_start: 0.6639 (tptt) cc_final: 0.6391 (tppt) REVERT: E 111 LYS cc_start: 0.7390 (mttp) cc_final: 0.6870 (mttt) REVERT: E 267 ASN cc_start: 0.9481 (t0) cc_final: 0.9209 (t0) REVERT: E 285 LYS cc_start: 0.9021 (ptmm) cc_final: 0.8770 (ptmm) REVERT: F 42 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7374 (mt-10) REVERT: F 70 LYS cc_start: 0.5994 (mmtt) cc_final: 0.5356 (mtpp) REVERT: F 177 ARG cc_start: 0.7512 (ttt-90) cc_final: 0.7009 (ttt180) REVERT: F 210 MET cc_start: 0.8677 (mtp) cc_final: 0.8287 (mtp) REVERT: F 211 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8262 (mtt) REVERT: F 213 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7436 (mp0) REVERT: F 253 LEU cc_start: 0.8423 (tp) cc_final: 0.8185 (tp) outliers start: 43 outliers final: 10 residues processed: 293 average time/residue: 1.7730 time to fit residues: 563.5071 Evaluate side-chains 250 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 202 GLN B 272 GLN C 23 GLN C 30 GLN C 202 GLN D 196 ASN D 202 GLN E 206 GLN E 272 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.134134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.095784 restraints weight = 72282.278| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 5.02 r_work: 0.2536 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15768 Z= 0.137 Angle : 0.503 7.159 21488 Z= 0.272 Chirality : 0.040 0.137 2434 Planarity : 0.004 0.049 2632 Dihedral : 15.191 88.678 2704 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.52 % Allowed : 22.84 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1878 helix: 0.43 (0.17), residues: 900 sheet: 0.19 (0.36), residues: 252 loop : -1.21 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 244 PHE 0.013 0.001 PHE F 46 TYR 0.014 0.001 TYR B 159 ARG 0.006 0.000 ARG F 250 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 761) hydrogen bonds : angle 4.03107 ( 2142) covalent geometry : bond 0.00307 (15768) covalent geometry : angle 0.50290 (21488) *********************** 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 310 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 1.556 Fit side-chains REVERT: A 37 ASP cc_start: 0.6575 (m-30) cc_final: 0.6331 (m-30) REVERT: A 42 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7086 (tp30) REVERT: A 57 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6577 (mmtt) REVERT: A 107 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7661 (mtpt) REVERT: A 202 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7206 (tt0) REVERT: A 251 MET cc_start: 0.8637 (mtp) cc_final: 0.8042 (mmm) REVERT: A 266 THR cc_start: 0.9161 (m) cc_final: 0.8822 (m) REVERT: A 326 MET cc_start: 0.8576 (ttp) cc_final: 0.8246 (mtp) REVERT: B 43 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7451 (tp30) REVERT: B 94 GLN cc_start: 0.8100 (mt0) cc_final: 0.7856 (mt0) REVERT: B 154 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7972 (mt-10) REVERT: B 161 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8596 (t70) REVERT: B 165 THR cc_start: 0.8908 (m) cc_final: 0.8629 (p) REVERT: B 202 GLN cc_start: 0.8488 (tp40) cc_final: 0.8286 (mm-40) REVERT: C 39 LYS cc_start: 0.7643 (mttt) cc_final: 0.7079 (ttpt) REVERT: C 114 GLN cc_start: 0.8870 (mt0) cc_final: 0.8632 (mt0) REVERT: C 169 GLU cc_start: 0.8572 (pm20) cc_final: 0.8286 (mm-30) REVERT: C 176 GLU cc_start: 0.8649 (tp30) cc_final: 0.8136 (tp30) REVERT: C 177 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8390 (ttt-90) REVERT: C 205 TYR cc_start: 0.8756 (m-80) cc_final: 0.8373 (m-80) REVERT: C 303 ARG cc_start: 0.9141 (ptt-90) cc_final: 0.8739 (ptt-90) REVERT: C 306 ARG cc_start: 0.7485 (tmm160) cc_final: 0.7211 (tmm160) REVERT: D 43 GLU cc_start: 0.7933 (mt-10) cc_final: 0.6951 (mp0) REVERT: D 64 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7337 (pttt) REVERT: D 80 LYS cc_start: 0.7748 (pttp) cc_final: 0.7539 (pttp) REVERT: D 111 LYS cc_start: 0.8524 (mttp) cc_final: 0.7995 (mtmt) REVERT: D 176 GLU cc_start: 0.7898 (tp30) cc_final: 0.7571 (tm-30) REVERT: E 39 LYS cc_start: 0.7746 (mmmm) cc_final: 0.7055 (ptmt) REVERT: E 40 LYS cc_start: 0.6795 (mmtt) cc_final: 0.6521 (mmtp) REVERT: E 43 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7081 (mt-10) REVERT: E 80 LYS cc_start: 0.6969 (pptt) cc_final: 0.6762 (pptt) REVERT: E 84 MET cc_start: 0.8417 (mtm) cc_final: 0.8035 (mmm) REVERT: E 111 LYS cc_start: 0.7660 (mttp) cc_final: 0.7184 (mttt) REVERT: E 215 ARG cc_start: 0.8958 (ttt90) cc_final: 0.8610 (ttt90) REVERT: E 267 ASN cc_start: 0.9470 (t0) cc_final: 0.9166 (t0) REVERT: E 285 LYS cc_start: 0.9085 (ptmm) cc_final: 0.8836 (ptmm) REVERT: E 330 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8518 (m110) REVERT: F 42 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7510 (mt-10) REVERT: F 58 LYS cc_start: 0.7485 (mtpt) cc_final: 0.6751 (mtpt) REVERT: F 70 LYS cc_start: 0.5957 (mmtt) cc_final: 0.5269 (mtpp) REVERT: F 108 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: F 210 MET cc_start: 0.8517 (mtp) cc_final: 0.8041 (mtp) REVERT: F 213 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7473 (mp0) REVERT: F 253 LEU cc_start: 0.8626 (tp) cc_final: 0.8229 (tp) REVERT: F 272 GLN cc_start: 0.8162 (mt0) cc_final: 0.7888 (mt0) REVERT: F 326 MET cc_start: 0.8394 (ttm) cc_final: 0.7977 (tpp) outliers start: 41 outliers final: 11 residues processed: 296 average time/residue: 1.7886 time to fit residues: 568.5176 Evaluate side-chains 261 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 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 181 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 129 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 34 ASN E 206 GLN 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 = 0.3357 r_free = 0.3357 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.092309 restraints weight = 73061.811| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.92 r_work: 0.2482 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15768 Z= 0.212 Angle : 0.573 8.860 21488 Z= 0.305 Chirality : 0.043 0.137 2434 Planarity : 0.005 0.048 2632 Dihedral : 15.178 88.978 2703 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.85 % Allowed : 22.71 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1878 helix: 0.49 (0.17), residues: 900 sheet: 0.17 (0.34), residues: 252 loop : -1.13 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 93 PHE 0.016 0.002 PHE A 92 TYR 0.017 0.002 TYR B 159 ARG 0.006 0.001 ARG F 250 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 761) hydrogen bonds : angle 4.25160 ( 2142) covalent geometry : bond 0.00498 (15768) covalent geometry : angle 0.57285 (21488) *********************** 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 295 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 247 time to evaluate : 1.613 Fit side-chains REVERT: A 42 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7214 (tp30) REVERT: A 57 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6589 (mmtt) REVERT: A 326 MET cc_start: 0.8594 (ttp) cc_final: 0.8262 (mtp) REVERT: B 43 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7428 (tp30) REVERT: B 68 GLU cc_start: 0.7198 (mp0) cc_final: 0.6937 (mp0) REVERT: B 94 GLN cc_start: 0.8143 (mt0) cc_final: 0.7888 (mt0) REVERT: B 161 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8654 (t70) REVERT: B 165 THR cc_start: 0.8990 (m) cc_final: 0.8674 (p) REVERT: C 39 LYS cc_start: 0.7773 (mttt) cc_final: 0.7143 (ttpt) REVERT: C 70 LYS cc_start: 0.6577 (mmtm) cc_final: 0.6158 (mmmm) REVERT: C 176 GLU cc_start: 0.8704 (tp30) cc_final: 0.8206 (tp30) REVERT: C 177 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (ttt180) REVERT: C 205 TYR cc_start: 0.8759 (m-80) cc_final: 0.8292 (m-80) REVERT: C 306 ARG cc_start: 0.7665 (tmm160) cc_final: 0.7204 (tmm160) REVERT: D 43 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7075 (mp0) REVERT: D 64 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7315 (pttt) REVERT: E 39 LYS cc_start: 0.7830 (mmmm) cc_final: 0.7047 (ptmt) REVERT: E 40 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6736 (mmtp) REVERT: E 43 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 84 MET cc_start: 0.8448 (mtm) cc_final: 0.8195 (mmm) REVERT: E 111 LYS cc_start: 0.7841 (mttp) cc_final: 0.7217 (mttt) REVERT: E 330 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8522 (m110) REVERT: F 42 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7522 (mt-10) REVERT: F 70 LYS cc_start: 0.5954 (mmtt) cc_final: 0.5389 (mtpp) REVERT: F 108 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: F 210 MET cc_start: 0.8649 (mtp) cc_final: 0.8176 (mtp) REVERT: F 213 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7283 (mp0) REVERT: F 253 LEU cc_start: 0.8828 (tp) cc_final: 0.8608 (tp) REVERT: F 324 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7720 (mt-10) outliers start: 48 outliers final: 21 residues processed: 277 average time/residue: 2.5894 time to fit residues: 773.6782 Evaluate side-chains 259 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 27 ARG 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 332 ASP Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 155 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 206 GLN B 30 GLN C 202 GLN C 290 ASN D 202 GLN E 206 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 = 0.3375 r_free = 0.3375 target = 0.132290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094054 restraints weight = 78451.394| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 5.20 r_work: 0.2498 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 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 = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3573 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= 0.152 Angle : 0.506 7.310 21488 Z= 0.272 Chirality : 0.041 0.129 2434 Planarity : 0.004 0.047 2632 Dihedral : 15.125 87.604 2702 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.19 % Allowed : 23.44 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1878 helix: 0.75 (0.18), residues: 900 sheet: 0.33 (0.35), residues: 246 loop : -1.12 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 93 PHE 0.011 0.001 PHE F 46 TYR 0.012 0.001 TYR B 159 ARG 0.006 0.000 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 761) hydrogen bonds : angle 4.03415 ( 2142) covalent geometry : bond 0.00354 (15768) covalent geometry : angle 0.50614 (21488) *********************** 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 284 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 1.587 Fit side-chains REVERT: A 42 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7195 (tp30) REVERT: A 57 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6609 (mttp) REVERT: A 70 LYS cc_start: 0.5284 (mmtt) cc_final: 0.5042 (mmtp) REVERT: A 202 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7195 (tt0) REVERT: A 326 MET cc_start: 0.8603 (ttp) cc_final: 0.8285 (mtp) REVERT: B 43 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7415 (tp30) REVERT: B 68 GLU cc_start: 0.7175 (mp0) cc_final: 0.6867 (mp0) REVERT: B 94 GLN cc_start: 0.8061 (mt0) cc_final: 0.7732 (mt0) REVERT: B 154 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8083 (mt-10) REVERT: B 161 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8616 (t70) REVERT: B 165 THR cc_start: 0.9035 (m) cc_final: 0.8717 (p) REVERT: B 326 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8297 (tmm) REVERT: C 39 LYS cc_start: 0.7742 (mttt) cc_final: 0.7167 (ttpt) REVERT: C 176 GLU cc_start: 0.8681 (tp30) cc_final: 0.8212 (tp30) REVERT: C 177 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (ttt180) REVERT: C 205 TYR cc_start: 0.8837 (m-80) cc_final: 0.8425 (m-80) REVERT: C 306 ARG cc_start: 0.7865 (tmm160) cc_final: 0.7423 (tmm160) REVERT: D 43 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6999 (mp0) REVERT: D 64 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7315 (pttt) REVERT: D 98 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7003 (mt-10) REVERT: E 39 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7063 (ptmt) REVERT: E 40 LYS cc_start: 0.6880 (mmtt) cc_final: 0.6603 (mmtp) REVERT: E 43 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7271 (mt-10) REVERT: E 84 MET cc_start: 0.8432 (mtm) cc_final: 0.8188 (mmm) REVERT: E 111 LYS cc_start: 0.7766 (mttp) cc_final: 0.7185 (mttt) REVERT: E 285 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8802 (ptmm) REVERT: E 330 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (m110) REVERT: F 42 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 58 LYS cc_start: 0.7369 (mtpt) cc_final: 0.6695 (mtpt) REVERT: F 70 LYS cc_start: 0.5802 (mmtt) cc_final: 0.5264 (mtpp) REVERT: F 108 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: F 210 MET cc_start: 0.8624 (mtp) cc_final: 0.8175 (mtp) REVERT: F 213 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7286 (mp0) REVERT: F 253 LEU cc_start: 0.8865 (tp) cc_final: 0.8620 (tp) outliers start: 39 outliers final: 17 residues processed: 267 average time/residue: 2.0328 time to fit residues: 582.9430 Evaluate side-chains 259 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 156 optimal weight: 0.0270 chunk 141 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 202 GLN D 202 GLN F 196 ASN F 200 GLN 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 = 0.3403 r_free = 0.3403 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.096225 restraints weight = 75319.176| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 5.15 r_work: 0.2534 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 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 = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15768 Z= 0.112 Angle : 0.472 6.248 21488 Z= 0.255 Chirality : 0.039 0.128 2434 Planarity : 0.004 0.046 2632 Dihedral : 14.995 87.547 2702 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.52 % Allowed : 24.70 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1878 helix: 0.93 (0.18), residues: 906 sheet: 0.33 (0.35), residues: 252 loop : -0.98 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 93 PHE 0.010 0.001 PHE F 46 TYR 0.009 0.001 TYR F 178 ARG 0.009 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.02391 ( 761) hydrogen bonds : angle 3.82426 ( 2142) covalent geometry : bond 0.00251 (15768) covalent geometry : angle 0.47167 (21488) *********************** 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 268 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.721 Fit side-chains REVERT: A 27 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6609 (ttm-80) REVERT: A 42 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7163 (tp30) REVERT: A 57 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6557 (mttp) REVERT: A 243 MET cc_start: 0.8951 (mtp) cc_final: 0.8504 (mtt) REVERT: A 326 MET cc_start: 0.8584 (ttp) cc_final: 0.8230 (mtp) REVERT: B 43 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7357 (tp30) REVERT: B 94 GLN cc_start: 0.8025 (mt0) cc_final: 0.7734 (mt0) REVERT: B 154 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8066 (mt-10) REVERT: B 161 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8584 (t70) REVERT: B 165 THR cc_start: 0.9099 (m) cc_final: 0.8739 (p) REVERT: B 326 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8129 (tmm) REVERT: C 39 LYS cc_start: 0.7581 (mttt) cc_final: 0.6970 (ttpt) REVERT: C 70 LYS cc_start: 0.6706 (mmtm) cc_final: 0.6467 (mmmm) REVERT: C 169 GLU cc_start: 0.8546 (pm20) cc_final: 0.8299 (mm-30) REVERT: C 176 GLU cc_start: 0.8570 (tp30) cc_final: 0.8098 (tp30) REVERT: C 177 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8454 (ttt-90) REVERT: C 205 TYR cc_start: 0.8849 (m-80) cc_final: 0.8452 (m-80) REVERT: C 306 ARG cc_start: 0.7841 (tmm160) cc_final: 0.7215 (tmm160) REVERT: D 43 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7019 (mp0) REVERT: D 64 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7274 (pttt) REVERT: E 39 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7144 (ptmt) REVERT: E 40 LYS cc_start: 0.6910 (mmtt) cc_final: 0.6642 (mmtp) REVERT: E 84 MET cc_start: 0.8393 (mtm) cc_final: 0.8159 (mmm) REVERT: E 111 LYS cc_start: 0.7775 (mttp) cc_final: 0.7123 (mttt) REVERT: E 267 ASN cc_start: 0.9475 (t0) cc_final: 0.9142 (t0) REVERT: E 285 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8635 (ptmm) REVERT: E 330 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8322 (m110) REVERT: F 42 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7471 (mt-10) REVERT: F 50 GLU cc_start: 0.7983 (mp0) cc_final: 0.7432 (mp0) REVERT: F 58 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6738 (mtpt) REVERT: F 70 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5263 (mtpp) REVERT: F 210 MET cc_start: 0.8588 (mtp) cc_final: 0.8052 (mtp) REVERT: F 213 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7251 (mp0) REVERT: F 214 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8209 (t) outliers start: 29 outliers final: 8 residues processed: 256 average time/residue: 2.0654 time to fit residues: 565.8958 Evaluate side-chains 244 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 177 ARG 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 E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 48 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN B 202 GLN C 202 GLN D 202 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094041 restraints weight = 65721.448| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.63 r_work: 0.2523 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15768 Z= 0.147 Angle : 0.502 7.697 21488 Z= 0.270 Chirality : 0.040 0.131 2434 Planarity : 0.004 0.045 2632 Dihedral : 15.009 89.525 2702 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.52 % Allowed : 24.70 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1878 helix: 0.94 (0.18), residues: 900 sheet: 0.40 (0.34), residues: 264 loop : -0.96 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 93 PHE 0.012 0.001 PHE F 46 TYR 0.011 0.001 TYR B 315 ARG 0.007 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.02707 ( 761) hydrogen bonds : angle 3.92093 ( 2142) covalent geometry : bond 0.00342 (15768) covalent geometry : angle 0.50199 (21488) *********************** 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 260 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6860 (mtt-85) REVERT: A 37 ASP cc_start: 0.6374 (m-30) cc_final: 0.6083 (m-30) REVERT: A 42 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7018 (tp30) REVERT: A 57 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6460 (mttp) REVERT: A 243 MET cc_start: 0.9032 (mtp) cc_final: 0.8582 (mtt) REVERT: A 326 MET cc_start: 0.8636 (ttp) cc_final: 0.8258 (mtp) REVERT: B 43 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7434 (tm-30) REVERT: B 94 GLN cc_start: 0.8028 (mt0) cc_final: 0.7748 (mt0) REVERT: B 154 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8077 (mt-10) REVERT: B 161 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8583 (t70) REVERT: B 165 THR cc_start: 0.9075 (m) cc_final: 0.8706 (p) REVERT: B 326 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8229 (tmm) REVERT: C 39 LYS cc_start: 0.7590 (mttt) cc_final: 0.7045 (ttpt) REVERT: C 70 LYS cc_start: 0.6701 (mmtm) cc_final: 0.6476 (mmmm) REVERT: C 176 GLU cc_start: 0.8590 (tp30) cc_final: 0.8132 (tp30) REVERT: C 177 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (ttt180) REVERT: C 205 TYR cc_start: 0.8821 (m-80) cc_final: 0.8365 (m-80) REVERT: C 306 ARG cc_start: 0.7810 (tmm160) cc_final: 0.7148 (tmm160) REVERT: D 43 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7103 (mp0) REVERT: D 64 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7306 (pttt) REVERT: E 39 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7133 (ptmt) REVERT: E 40 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6640 (mmtp) REVERT: E 84 MET cc_start: 0.8395 (mtm) cc_final: 0.8159 (mmm) REVERT: E 111 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7147 (mttt) REVERT: E 267 ASN cc_start: 0.9463 (t0) cc_final: 0.9157 (t0) REVERT: E 285 LYS cc_start: 0.9083 (ptmm) cc_final: 0.8577 (ptmm) REVERT: E 330 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8473 (m110) REVERT: F 42 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7460 (mt-10) REVERT: F 50 GLU cc_start: 0.7783 (mp0) cc_final: 0.7453 (mp0) REVERT: F 70 LYS cc_start: 0.5960 (mmtt) cc_final: 0.5345 (mtpp) REVERT: F 210 MET cc_start: 0.8609 (mtp) cc_final: 0.8099 (mtp) REVERT: F 213 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7236 (mp0) REVERT: F 214 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8175 (t) outliers start: 29 outliers final: 17 residues processed: 250 average time/residue: 2.1233 time to fit residues: 568.3145 Evaluate side-chains 254 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 202 GLN D 202 GLN D 272 GLN F 196 ASN F 200 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.130111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.093724 restraints weight = 66225.841| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.81 r_work: 0.2477 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15768 Z= 0.237 Angle : 0.581 9.699 21488 Z= 0.309 Chirality : 0.044 0.133 2434 Planarity : 0.005 0.046 2632 Dihedral : 15.106 88.160 2702 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.99 % Allowed : 24.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1878 helix: 0.71 (0.17), residues: 900 sheet: 0.23 (0.30), residues: 306 loop : -0.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 93 PHE 0.017 0.002 PHE A 92 TYR 0.016 0.002 TYR B 159 ARG 0.007 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 761) hydrogen bonds : angle 4.27203 ( 2142) covalent geometry : bond 0.00563 (15768) covalent geometry : angle 0.58061 (21488) *********************** 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 272 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7021 (tp30) REVERT: A 57 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6452 (mttp) REVERT: A 243 MET cc_start: 0.9062 (mtp) cc_final: 0.8614 (mtt) REVERT: A 326 MET cc_start: 0.8617 (ttp) cc_final: 0.8265 (mtp) REVERT: B 43 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7315 (tm-30) REVERT: B 57 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7695 (tttp) REVERT: B 94 GLN cc_start: 0.8092 (mt0) cc_final: 0.7757 (mt0) REVERT: B 161 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8678 (t70) REVERT: B 165 THR cc_start: 0.9080 (m) cc_final: 0.8746 (p) REVERT: B 169 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: B 322 GLU cc_start: 0.8779 (tt0) cc_final: 0.8429 (tt0) REVERT: B 326 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8525 (tmm) REVERT: C 39 LYS cc_start: 0.7741 (mttt) cc_final: 0.7123 (ttpt) REVERT: C 70 LYS cc_start: 0.6512 (mmtm) cc_final: 0.6291 (mmmm) REVERT: C 176 GLU cc_start: 0.8688 (tp30) cc_final: 0.8263 (tp30) REVERT: C 177 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8521 (ttt180) REVERT: C 205 TYR cc_start: 0.8804 (m-80) cc_final: 0.8332 (m-80) REVERT: C 306 ARG cc_start: 0.7955 (tmm160) cc_final: 0.7409 (tmm-80) REVERT: D 43 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7178 (mp0) REVERT: D 64 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7334 (pttt) REVERT: D 111 LYS cc_start: 0.8353 (mttp) cc_final: 0.7834 (mtmt) REVERT: E 39 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7167 (ptmt) REVERT: E 40 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6563 (mmtp) REVERT: E 84 MET cc_start: 0.8439 (mtm) cc_final: 0.8204 (mmm) REVERT: E 111 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7253 (mttt) REVERT: E 285 LYS cc_start: 0.9100 (ptmm) cc_final: 0.8702 (ptmm) REVERT: E 330 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8561 (m110) REVERT: F 42 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7563 (mt-10) REVERT: F 70 LYS cc_start: 0.6137 (mmtt) cc_final: 0.5414 (mtpp) REVERT: F 210 MET cc_start: 0.8684 (mtp) cc_final: 0.8249 (mtp) REVERT: F 213 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7285 (mp0) REVERT: F 214 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8205 (t) outliers start: 38 outliers final: 19 residues processed: 258 average time/residue: 1.9411 time to fit residues: 535.8578 Evaluate side-chains 262 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 211 MET 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 237 GLU Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 80 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN B 202 GLN C 202 GLN D 202 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.130626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.093290 restraints weight = 65941.937| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.86 r_work: 0.2487 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2473 r_free = 0.2473 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15768 Z= 0.210 Angle : 0.565 8.726 21488 Z= 0.300 Chirality : 0.043 0.135 2434 Planarity : 0.005 0.046 2632 Dihedral : 15.118 87.336 2702 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.46 % Allowed : 25.03 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1878 helix: 0.70 (0.17), residues: 900 sheet: 0.25 (0.30), residues: 300 loop : -0.77 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 93 PHE 0.013 0.002 PHE A 92 TYR 0.014 0.002 TYR B 159 ARG 0.007 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 761) hydrogen bonds : angle 4.22545 ( 2142) covalent geometry : bond 0.00498 (15768) covalent geometry : angle 0.56469 (21488) *********************** 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 259 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7020 (tp30) REVERT: A 57 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6490 (mttp) REVERT: A 243 MET cc_start: 0.9059 (mtp) cc_final: 0.8607 (mtt) REVERT: A 326 MET cc_start: 0.8604 (ttp) cc_final: 0.8250 (mtp) REVERT: B 57 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7590 (tttp) REVERT: B 94 GLN cc_start: 0.8109 (mt0) cc_final: 0.7778 (mt0) REVERT: B 161 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8650 (t70) REVERT: B 165 THR cc_start: 0.9079 (m) cc_final: 0.8750 (p) REVERT: B 322 GLU cc_start: 0.8764 (tt0) cc_final: 0.8416 (tt0) REVERT: B 326 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8528 (tmm) REVERT: C 39 LYS cc_start: 0.7869 (mttt) cc_final: 0.7342 (ttpt) REVERT: C 176 GLU cc_start: 0.8678 (tp30) cc_final: 0.8255 (tp30) REVERT: C 177 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8512 (ttt180) REVERT: C 205 TYR cc_start: 0.8815 (m-80) cc_final: 0.8345 (m-80) REVERT: C 306 ARG cc_start: 0.7975 (tmm160) cc_final: 0.7399 (tmm-80) REVERT: D 43 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7187 (mp0) REVERT: D 64 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7339 (pttt) REVERT: D 111 LYS cc_start: 0.8360 (mttp) cc_final: 0.7837 (mtmt) REVERT: E 39 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7114 (ptmt) REVERT: E 40 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6452 (mmtp) REVERT: E 84 MET cc_start: 0.8422 (mtm) cc_final: 0.8057 (mmm) REVERT: E 111 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7291 (mttt) REVERT: E 285 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8691 (ptmm) REVERT: F 42 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7508 (mt-10) REVERT: F 50 GLU cc_start: 0.8002 (mp0) cc_final: 0.7559 (mp0) REVERT: F 70 LYS cc_start: 0.5995 (mmtt) cc_final: 0.5329 (mtpp) REVERT: F 210 MET cc_start: 0.8659 (mtp) cc_final: 0.8114 (mtp) REVERT: F 213 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7255 (mp0) REVERT: F 214 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8190 (t) outliers start: 30 outliers final: 19 residues processed: 251 average time/residue: 2.6125 time to fit residues: 705.2872 Evaluate side-chains 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 82 VAL 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 29 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 96 optimal weight: 0.0010 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 173 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 202 GLN D 202 GLN F 47 HIS F 196 ASN F 200 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.135177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097591 restraints weight = 82173.727| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 5.55 r_work: 0.2539 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15768 Z= 0.103 Angle : 0.477 7.035 21488 Z= 0.257 Chirality : 0.039 0.128 2434 Planarity : 0.004 0.044 2632 Dihedral : 14.961 86.502 2702 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.79 % Allowed : 25.63 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1878 helix: 1.01 (0.18), residues: 906 sheet: 0.21 (0.38), residues: 228 loop : -0.92 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 294 PHE 0.010 0.001 PHE F 46 TYR 0.009 0.001 TYR E 205 ARG 0.008 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.02217 ( 761) hydrogen bonds : angle 3.82099 ( 2142) covalent geometry : bond 0.00228 (15768) covalent geometry : angle 0.47661 (21488) ********************** 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 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7029 (tp30) REVERT: A 57 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6512 (mttp) REVERT: A 243 MET cc_start: 0.8997 (mtp) cc_final: 0.8570 (mtt) REVERT: A 326 MET cc_start: 0.8655 (ttp) cc_final: 0.8298 (mtp) REVERT: B 57 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7475 (tttp) REVERT: B 94 GLN cc_start: 0.8039 (mt0) cc_final: 0.7755 (mt0) REVERT: B 161 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8570 (t70) REVERT: B 165 THR cc_start: 0.9126 (m) cc_final: 0.8762 (p) REVERT: B 202 GLN cc_start: 0.8503 (tp40) cc_final: 0.8286 (mm-40) REVERT: B 251 MET cc_start: 0.8804 (mtp) cc_final: 0.8431 (mtp) REVERT: B 322 GLU cc_start: 0.8811 (tt0) cc_final: 0.8487 (tt0) REVERT: B 326 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: C 39 LYS cc_start: 0.7575 (mttt) cc_final: 0.6986 (ttpt) REVERT: C 70 LYS cc_start: 0.6560 (mmtm) cc_final: 0.6246 (mmmm) REVERT: C 169 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8295 (mm-30) REVERT: C 176 GLU cc_start: 0.8560 (tp30) cc_final: 0.8138 (tp30) REVERT: C 205 TYR cc_start: 0.8860 (m-80) cc_final: 0.8475 (m-80) REVERT: C 306 ARG cc_start: 0.7808 (tmm160) cc_final: 0.7291 (tmm-80) REVERT: D 43 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7132 (mp0) REVERT: D 64 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7221 (ptmm) REVERT: E 39 LYS cc_start: 0.7806 (mmmm) cc_final: 0.7131 (ptmt) REVERT: E 40 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6516 (mmtp) REVERT: E 84 MET cc_start: 0.8371 (mtm) cc_final: 0.7999 (mmm) REVERT: E 111 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7209 (mttt) REVERT: E 267 ASN cc_start: 0.9473 (t0) cc_final: 0.9175 (t0) REVERT: E 285 LYS cc_start: 0.9077 (ptmm) cc_final: 0.8810 (ptmm) REVERT: F 50 GLU cc_start: 0.7986 (mp0) cc_final: 0.7440 (mp0) REVERT: F 70 LYS cc_start: 0.5964 (mmtt) cc_final: 0.5371 (mtpp) REVERT: F 210 MET cc_start: 0.8574 (mtp) cc_final: 0.7975 (mtp) REVERT: F 213 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7295 (mp0) outliers start: 20 outliers final: 5 residues processed: 244 average time/residue: 1.9250 time to fit residues: 507.2931 Evaluate side-chains 231 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain F residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 188 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 127 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 202 GLN D 202 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.095506 restraints weight = 61250.482| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.50 r_work: 0.2555 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15768 Z= 0.117 Angle : 0.483 6.454 21488 Z= 0.260 Chirality : 0.039 0.133 2434 Planarity : 0.004 0.044 2632 Dihedral : 14.908 85.914 2702 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.39 % Allowed : 26.43 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1878 helix: 1.06 (0.18), residues: 906 sheet: 0.12 (0.29), residues: 360 loop : -0.58 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.009 0.001 PHE F 46 TYR 0.010 0.001 TYR B 315 ARG 0.009 0.000 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.02391 ( 761) hydrogen bonds : angle 3.81173 ( 2142) covalent geometry : bond 0.00266 (15768) covalent geometry : angle 0.48330 (21488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15616.22 seconds wall clock time: 275 minutes 3.82 seconds (16503.82 seconds total)