Starting phenix.real_space_refine on Fri Sep 27 09:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_16197.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_16197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_16197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_16197.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8br2_16197/09_2024/8br2_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-5461/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: 16.32, per 1000 atoms: 1.05 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: 4.24 Conformation dependent library (CDL) restraints added in 3.6 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: 6.54 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: 6.56 Time building geometry restraints manager: 4.79 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: 0.580 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 51.600 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:15.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.860 ------------------------------------------------------------------------------- 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= 0.500 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 444 time to evaluate : 1.699 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: 1.6168 time to fit residues: 784.1849 Evaluate side-chains 246 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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= 0.198 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 *********************** 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 fitting. rotamer outliers: 43 poor density : 261 time to evaluate : 1.595 Fit side-chains REVERT: A 57 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7055 (tttp) REVERT: A 94 GLN cc_start: 0.8136 (tp40) cc_final: 0.7913 (tp-100) REVERT: A 107 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8070 (mtpt) REVERT: A 202 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7214 (tt0) REVERT: A 206 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: A 266 THR cc_start: 0.8932 (m) cc_final: 0.8581 (m) REVERT: B 94 GLN cc_start: 0.7964 (mt0) cc_final: 0.7760 (mt0) REVERT: B 161 ASP cc_start: 0.8597 (t70) cc_final: 0.8381 (t70) REVERT: B 165 THR cc_start: 0.8284 (m) cc_final: 0.8036 (p) REVERT: B 210 MET cc_start: 0.8705 (mtp) cc_final: 0.8387 (mtp) REVERT: C 39 LYS cc_start: 0.7567 (mttt) cc_final: 0.7359 (ttpt) REVERT: C 70 LYS cc_start: 0.6839 (mmtt) cc_final: 0.6520 (mmmm) REVERT: C 176 GLU cc_start: 0.7816 (tp30) cc_final: 0.7355 (tp30) REVERT: C 205 TYR cc_start: 0.8371 (m-80) cc_final: 0.8129 (m-80) REVERT: C 326 MET cc_start: 0.8804 (ttm) cc_final: 0.8467 (ttm) REVERT: D 43 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7009 (mm-30) REVERT: D 111 LYS cc_start: 0.8143 (mttp) cc_final: 0.7696 (mtmt) REVERT: E 27 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7153 (mtt-85) REVERT: E 39 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7679 (ptmt) REVERT: E 40 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6947 (mmtp) REVERT: E 111 LYS cc_start: 0.7531 (mttp) cc_final: 0.7242 (mttt) REVERT: E 267 ASN cc_start: 0.9275 (t0) cc_final: 0.9049 (t0) REVERT: E 285 LYS cc_start: 0.8982 (ptmm) cc_final: 0.8745 (ptmm) REVERT: F 177 ARG cc_start: 0.7719 (ttt-90) cc_final: 0.7487 (ttt180) REVERT: F 210 MET cc_start: 0.8388 (mtp) cc_final: 0.8151 (mtp) REVERT: F 211 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (mtt) outliers start: 43 outliers final: 10 residues processed: 293 average time/residue: 1.7121 time to fit residues: 539.6934 Evaluate side-chains 247 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 233 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 30 GLN B 202 GLN B 272 GLN C 23 GLN C 202 GLN D 196 ASN D 202 GLN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15768 Z= 0.296 Angle : 0.559 7.632 21488 Z= 0.301 Chirality : 0.042 0.143 2434 Planarity : 0.005 0.050 2632 Dihedral : 15.288 89.567 2704 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.92 % Allowed : 22.91 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.19), residues: 1878 helix: 0.26 (0.17), residues: 900 sheet: 0.24 (0.35), residues: 246 loop : -1.26 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 93 PHE 0.016 0.002 PHE A 92 TYR 0.015 0.002 TYR B 232 ARG 0.005 0.001 ARG F 250 *********************** 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 305 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8062 (mtpt) REVERT: A 202 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7323 (tt0) REVERT: A 206 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: A 266 THR cc_start: 0.9117 (m) cc_final: 0.8888 (m) REVERT: A 326 MET cc_start: 0.8169 (ttp) cc_final: 0.7891 (mtp) REVERT: B 73 LYS cc_start: 0.7964 (tttp) cc_final: 0.7636 (ttpt) REVERT: B 94 GLN cc_start: 0.8025 (mt0) cc_final: 0.7789 (mt0) REVERT: B 161 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8425 (t70) REVERT: B 165 THR cc_start: 0.8458 (m) cc_final: 0.8146 (p) REVERT: C 39 LYS cc_start: 0.7577 (mttt) cc_final: 0.7372 (ttpt) REVERT: C 70 LYS cc_start: 0.6680 (mmtt) cc_final: 0.6340 (mmmm) REVERT: C 176 GLU cc_start: 0.7899 (tp30) cc_final: 0.7415 (tp30) REVERT: C 205 TYR cc_start: 0.8474 (m-80) cc_final: 0.8119 (m-80) REVERT: C 303 ARG cc_start: 0.8936 (ptt-90) cc_final: 0.8593 (ptt-90) REVERT: C 306 ARG cc_start: 0.7315 (tmm160) cc_final: 0.6950 (tmm160) REVERT: C 326 MET cc_start: 0.8890 (ttm) cc_final: 0.8684 (ttm) REVERT: D 43 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7115 (mp0) REVERT: D 111 LYS cc_start: 0.8223 (mttp) cc_final: 0.7766 (mtmt) REVERT: E 39 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7646 (ptmt) REVERT: E 111 LYS cc_start: 0.7814 (mttp) cc_final: 0.7452 (mttt) REVERT: E 215 ARG cc_start: 0.8795 (ttt90) cc_final: 0.8506 (ttt90) REVERT: F 108 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: F 210 MET cc_start: 0.8421 (mtp) cc_final: 0.8103 (mtp) outliers start: 47 outliers final: 21 residues processed: 288 average time/residue: 1.8471 time to fit residues: 573.3564 Evaluate side-chains 269 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 23 GLN C 30 GLN C 202 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15768 Z= 0.190 Angle : 0.493 6.978 21488 Z= 0.267 Chirality : 0.040 0.130 2434 Planarity : 0.004 0.048 2632 Dihedral : 15.157 89.842 2704 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.92 % Allowed : 23.84 % Favored : 73.24 % 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 (0.19), residues: 1878 helix: 0.64 (0.17), residues: 900 sheet: 0.23 (0.35), residues: 252 loop : -1.12 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.009 0.001 PHE B 327 TYR 0.011 0.001 TYR B 159 ARG 0.007 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 264 time to evaluate : 1.692 Fit side-chains REVERT: A 42 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 57 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7083 (mmtt) REVERT: A 202 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7268 (tt0) REVERT: A 206 GLN cc_start: 0.8320 (mt0) cc_final: 0.8061 (mt0) REVERT: A 266 THR cc_start: 0.9065 (m) cc_final: 0.8786 (m) REVERT: A 326 MET cc_start: 0.8149 (ttp) cc_final: 0.7882 (mtp) REVERT: B 94 GLN cc_start: 0.7915 (mt0) cc_final: 0.7641 (mt0) REVERT: B 161 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8358 (t70) REVERT: B 165 THR cc_start: 0.8327 (m) cc_final: 0.8087 (p) REVERT: B 285 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8428 (ptpt) REVERT: B 326 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7670 (tmm) REVERT: C 70 LYS cc_start: 0.6878 (mmtt) cc_final: 0.6614 (mmmm) REVERT: C 114 GLN cc_start: 0.8745 (mt0) cc_final: 0.8465 (mt0) REVERT: C 176 GLU cc_start: 0.7828 (tp30) cc_final: 0.7376 (tp30) REVERT: C 205 TYR cc_start: 0.8480 (m-80) cc_final: 0.8130 (m-80) REVERT: C 306 ARG cc_start: 0.7305 (tmm160) cc_final: 0.6874 (tmm160) REVERT: C 308 GLU cc_start: 0.8313 (pm20) cc_final: 0.8065 (pm20) REVERT: D 43 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7047 (mp0) REVERT: E 39 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7612 (ptmt) REVERT: E 111 LYS cc_start: 0.7822 (mttp) cc_final: 0.7462 (mttt) REVERT: E 215 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8451 (ttt90) REVERT: E 267 ASN cc_start: 0.9312 (t0) cc_final: 0.9043 (t0) REVERT: E 285 LYS cc_start: 0.9046 (ptmm) cc_final: 0.8818 (ptmm) REVERT: F 108 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: F 210 MET cc_start: 0.8445 (mtp) cc_final: 0.8136 (mtp) outliers start: 33 outliers final: 12 residues processed: 283 average time/residue: 1.8383 time to fit residues: 557.0185 Evaluate side-chains 257 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU 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 99 ILE Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 B 202 GLN C 23 GLN C 202 GLN D 202 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3564 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= 0.387 Angle : 0.602 9.526 21488 Z= 0.319 Chirality : 0.045 0.139 2434 Planarity : 0.005 0.048 2632 Dihedral : 15.190 88.971 2702 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.85 % Allowed : 22.58 % Favored : 73.57 % 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: -0.25 (0.19), residues: 1878 helix: 0.56 (0.17), residues: 894 sheet: 0.00 (0.33), residues: 270 loop : -1.07 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 93 PHE 0.018 0.002 PHE A 92 TYR 0.020 0.002 TYR B 159 ARG 0.005 0.001 ARG F 250 *********************** 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 307 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 257 time to evaluate : 1.576 Fit side-chains REVERT: A 57 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7084 (mttp) REVERT: A 202 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7208 (tt0) REVERT: A 206 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: A 243 MET cc_start: 0.8790 (mtp) cc_final: 0.8398 (mtt) REVERT: A 326 MET cc_start: 0.8213 (ttp) cc_final: 0.7891 (mtp) REVERT: B 94 GLN cc_start: 0.7958 (mt0) cc_final: 0.7653 (mt0) REVERT: B 161 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8457 (t70) REVERT: B 165 THR cc_start: 0.8470 (m) cc_final: 0.8194 (p) REVERT: B 326 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7906 (tmm) REVERT: C 176 GLU cc_start: 0.7933 (tp30) cc_final: 0.7472 (tp30) REVERT: C 205 TYR cc_start: 0.8563 (m-80) cc_final: 0.8145 (m-80) REVERT: C 306 ARG cc_start: 0.7439 (tmm160) cc_final: 0.6972 (tmm160) REVERT: D 43 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7030 (mp0) REVERT: D 111 LYS cc_start: 0.8155 (mttp) cc_final: 0.7652 (mtmt) REVERT: D 177 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8230 (ttt-90) REVERT: E 39 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7640 (ptmt) REVERT: E 111 LYS cc_start: 0.7902 (mttp) cc_final: 0.7588 (mttt) REVERT: F 210 MET cc_start: 0.8469 (mtp) cc_final: 0.8162 (mtp) outliers start: 50 outliers final: 27 residues processed: 286 average time/residue: 1.9100 time to fit residues: 583.6302 Evaluate side-chains 274 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 242 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 332 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 23 GLN C 202 GLN D 202 GLN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3712 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= 0.195 Angle : 0.499 6.578 21488 Z= 0.269 Chirality : 0.040 0.130 2434 Planarity : 0.004 0.046 2632 Dihedral : 15.112 88.843 2702 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.05 % Allowed : 23.97 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.19), residues: 1878 helix: 0.77 (0.18), residues: 906 sheet: 0.51 (0.32), residues: 282 loop : -0.84 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 93 PHE 0.009 0.001 PHE B 327 TYR 0.011 0.001 TYR B 315 ARG 0.006 0.000 ARG F 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7152 (mttp) REVERT: A 202 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7234 (tt0) REVERT: A 206 GLN cc_start: 0.8236 (mt0) cc_final: 0.7988 (mt0) REVERT: A 326 MET cc_start: 0.8139 (ttp) cc_final: 0.7839 (mtp) REVERT: B 161 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8389 (t70) REVERT: B 165 THR cc_start: 0.8557 (m) cc_final: 0.8208 (p) REVERT: C 70 LYS cc_start: 0.6813 (mmtm) cc_final: 0.6537 (mmmm) REVERT: C 176 GLU cc_start: 0.7762 (tp30) cc_final: 0.7346 (tp30) REVERT: C 205 TYR cc_start: 0.8560 (m-80) cc_final: 0.8166 (m-80) REVERT: C 306 ARG cc_start: 0.7437 (tmm160) cc_final: 0.6958 (tmm160) REVERT: D 43 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7008 (mp0) REVERT: D 111 LYS cc_start: 0.8148 (mttp) cc_final: 0.7672 (mtpt) REVERT: E 111 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7520 (mttt) REVERT: E 267 ASN cc_start: 0.9319 (t0) cc_final: 0.9064 (t0) REVERT: E 285 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8775 (ptmm) REVERT: F 210 MET cc_start: 0.8395 (mtp) cc_final: 0.7975 (mtp) outliers start: 37 outliers final: 15 residues processed: 272 average time/residue: 1.8473 time to fit residues: 538.7584 Evaluate side-chains 265 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 161 ASP Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 114 optimal weight: 0.0040 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.4910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 30 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15768 Z= 0.143 Angle : 0.467 6.302 21488 Z= 0.252 Chirality : 0.039 0.126 2434 Planarity : 0.004 0.048 2632 Dihedral : 14.873 84.702 2702 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.46 % Allowed : 24.90 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.20), residues: 1878 helix: 1.05 (0.18), residues: 900 sheet: 0.27 (0.29), residues: 342 loop : -0.60 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 294 PHE 0.008 0.001 PHE D 126 TYR 0.008 0.001 TYR B 315 ARG 0.007 0.000 ARG F 250 *********************** 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 294 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.6939 (mtt-85) REVERT: A 68 GLU cc_start: 0.7080 (mp0) cc_final: 0.6679 (mp0) REVERT: A 202 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7263 (tt0) REVERT: A 206 GLN cc_start: 0.8431 (mt0) cc_final: 0.8154 (mt0) REVERT: A 326 MET cc_start: 0.8186 (ttp) cc_final: 0.7859 (mtp) REVERT: B 161 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8282 (t70) REVERT: B 165 THR cc_start: 0.8540 (m) cc_final: 0.8201 (p) REVERT: B 326 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7453 (tmm) REVERT: C 161 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.7921 (t70) REVERT: C 176 GLU cc_start: 0.7716 (tp30) cc_final: 0.7321 (tp30) REVERT: C 205 TYR cc_start: 0.8533 (m-80) cc_final: 0.8236 (m-80) REVERT: C 306 ARG cc_start: 0.7447 (tmm160) cc_final: 0.6954 (tmm160) REVERT: D 43 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6996 (mp0) REVERT: D 57 LYS cc_start: 0.8381 (tttt) cc_final: 0.7940 (ttmt) REVERT: D 111 LYS cc_start: 0.8137 (mttp) cc_final: 0.7622 (mtmt) REVERT: E 39 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7146 (pptt) REVERT: E 111 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7462 (mttt) REVERT: E 267 ASN cc_start: 0.9289 (t0) cc_final: 0.9035 (t0) REVERT: E 285 LYS cc_start: 0.8999 (ptmm) cc_final: 0.8648 (ptmm) REVERT: F 210 MET cc_start: 0.8337 (mtp) cc_final: 0.7939 (mtp) outliers start: 28 outliers final: 6 residues processed: 282 average time/residue: 1.7409 time to fit residues: 528.4326 Evaluate side-chains 246 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 161 ASP 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 239 SER Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 111 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 196 ASN A 206 GLN B 30 GLN B 202 GLN C 23 GLN C 202 GLN D 202 GLN E 196 ASN E 206 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3877 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= 0.190 Angle : 0.489 6.922 21488 Z= 0.262 Chirality : 0.040 0.131 2434 Planarity : 0.004 0.046 2632 Dihedral : 14.916 87.407 2702 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.19 % Allowed : 25.37 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.20), residues: 1878 helix: 1.04 (0.18), residues: 900 sheet: 0.52 (0.34), residues: 264 loop : -0.87 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.009 0.001 PHE B 327 TYR 0.010 0.001 TYR B 315 ARG 0.006 0.000 ARG F 250 *********************** 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 256 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6907 (mtt-85) REVERT: A 202 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7286 (tt0) REVERT: A 326 MET cc_start: 0.8158 (ttp) cc_final: 0.7785 (mtp) REVERT: B 161 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8350 (t70) REVERT: B 165 THR cc_start: 0.8535 (m) cc_final: 0.8191 (p) REVERT: B 326 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7515 (tmm) REVERT: C 176 GLU cc_start: 0.7753 (tp30) cc_final: 0.7349 (tp30) REVERT: C 205 TYR cc_start: 0.8518 (m-80) cc_final: 0.8169 (m-80) REVERT: C 306 ARG cc_start: 0.7509 (tmm160) cc_final: 0.6964 (tmm160) REVERT: D 43 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7099 (mp0) REVERT: D 111 LYS cc_start: 0.8150 (mttp) cc_final: 0.7633 (mtmt) REVERT: E 39 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7372 (pptt) REVERT: E 111 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7473 (mttt) REVERT: E 267 ASN cc_start: 0.9293 (t0) cc_final: 0.9022 (t0) REVERT: E 285 LYS cc_start: 0.9013 (ptmm) cc_final: 0.8617 (ptmm) REVERT: F 50 GLU cc_start: 0.8003 (mp0) cc_final: 0.7797 (mp0) REVERT: F 210 MET cc_start: 0.8460 (mtp) cc_final: 0.8072 (mtp) outliers start: 24 outliers final: 12 residues processed: 244 average time/residue: 1.8529 time to fit residues: 483.7484 Evaluate side-chains 248 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 181 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 202 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN D 272 GLN E 196 ASN E 206 GLN F 202 GLN F 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15768 Z= 0.179 Angle : 0.484 6.731 21488 Z= 0.261 Chirality : 0.039 0.129 2434 Planarity : 0.004 0.046 2632 Dihedral : 14.896 87.355 2702 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.12 % Allowed : 25.37 % 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: 0.43 (0.20), residues: 1878 helix: 1.14 (0.18), residues: 894 sheet: 0.56 (0.34), residues: 264 loop : -0.85 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 244 PHE 0.008 0.001 PHE B 327 TYR 0.010 0.001 TYR B 315 ARG 0.007 0.000 ARG B 306 *********************** 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 262 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6875 (mtt-85) REVERT: A 202 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7330 (tt0) REVERT: A 326 MET cc_start: 0.8154 (ttp) cc_final: 0.7788 (mtp) REVERT: B 161 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8341 (t70) REVERT: B 165 THR cc_start: 0.8530 (m) cc_final: 0.8191 (p) REVERT: B 322 GLU cc_start: 0.8124 (tt0) cc_final: 0.7793 (tt0) REVERT: B 326 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: C 176 GLU cc_start: 0.7741 (tp30) cc_final: 0.7354 (tp30) REVERT: C 205 TYR cc_start: 0.8579 (m-80) cc_final: 0.8172 (m-80) REVERT: C 306 ARG cc_start: 0.7456 (tmm160) cc_final: 0.7045 (tmm-80) REVERT: D 43 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7101 (mp0) REVERT: D 57 LYS cc_start: 0.8361 (tttt) cc_final: 0.7967 (ttmt) REVERT: D 111 LYS cc_start: 0.8149 (mttp) cc_final: 0.7674 (mtpt) REVERT: E 39 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7400 (pptt) REVERT: E 111 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7520 (mttt) REVERT: E 267 ASN cc_start: 0.9300 (t0) cc_final: 0.9028 (t0) REVERT: E 285 LYS cc_start: 0.9005 (ptmm) cc_final: 0.8614 (ptmm) REVERT: F 210 MET cc_start: 0.8424 (mtp) cc_final: 0.8061 (mtp) outliers start: 23 outliers final: 12 residues processed: 249 average time/residue: 1.8244 time to fit residues: 486.8245 Evaluate side-chains 253 residues out of total 1482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 237 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP 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 239 SER Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 202 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 196 ASN A 206 GLN B 30 GLN C 23 GLN C 202 GLN D 202 GLN F 196 ASN F 202 GLN F 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3871 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: