Starting phenix.real_space_refine on Thu Aug 6 17:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnc_53243/08_2026/9qnc_53243.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.160 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: 7 Type Number sf(0) Gaussians K 5 8.98 5 P 41 5.49 5 Mg 5 5.21 5 S 81 5.16 5 C 9954 2.51 5 N 2877 2.21 5 O 3133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16096 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 305} Chain breaks: 1 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 143 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "C" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2452 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 142 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2452 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Chain: "F" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 151 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "G" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2452 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "I" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2443 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 142 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "K" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2443 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 309} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "Z" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' K': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, '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: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.22, per 1000 atoms: 0.20 Number of scatterers: 16096 At special positions: 0 Unit cell: (125.28, 127.44, 162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 5 19.00 S 81 16.00 P 41 15.00 Mg 5 11.99 O 3133 8.00 N 2877 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 659.1 milliseconds 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3698 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 18 sheets defined 48.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.575A pdb=" N CYS A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 32 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.817A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.767A pdb=" N LYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.939A 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 213 removed outlier: 3.709A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.853A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.837A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.284A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.515A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.966A 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 212 removed outlier: 3.748A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 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: 3.790A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 removed outlier: 4.011A pdb=" N GLN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 26 through 31' Processing helix chain 'E' and resid 35 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.686A pdb=" N LYS E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.623A 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: 4.085A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 removed outlier: 3.528A pdb=" N ASN E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.952A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.583A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.818A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 removed outlier: 4.095A pdb=" N GLY G 32 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.561A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.599A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 169 through 179 Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 212 removed outlier: 4.150A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.763A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.860A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 Processing helix chain 'I' and resid 34 through 45 removed outlier: 3.519A pdb=" N VAL I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.572A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.851A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.638A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.502A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 289 through 296 removed outlier: 3.503A pdb=" N SER I 296 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.829A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 removed outlier: 3.537A pdb=" N VAL K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.533A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.658A pdb=" N GLU K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.910A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'K' and resid 196 through 213 removed outlier: 3.915A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.699A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 259 Processing helix chain 'K' and resid 289 through 296 removed outlier: 3.897A pdb=" N ALA K 293 " --> pdb=" O GLY K 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 5.770A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN C 267 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET C 125 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR C 301 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE C 314 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ARG C 303 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N CYS C 312 " --> pdb=" O ARG C 303 " (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: 5.798A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 123 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN A 267 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.580A 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 'C' and resid 87 through 88 removed outlier: 5.788A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR E 123 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN E 267 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET E 125 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.395A pdb=" N ALA G 157 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ALA G 192 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR G 159 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.497A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA I 217 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.525A pdb=" N ALA K 157 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ALA K 192 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N TYR K 159 " --> pdb=" O ALA K 192 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR K 123 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN K 267 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET K 125 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'K' and resid 269 through 271 745 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5406 1.34 - 1.46: 3026 1.46 - 1.58: 7741 1.58 - 1.69: 74 1.69 - 1.81: 132 Bond restraints: 16379 Sorted by residual: bond pdb=" C3' DC Z 7 " pdb=" C2' DC Z 7 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.24e+00 bond pdb=" C3' DC Z 4 " pdb=" C2' DC Z 4 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.46e+00 bond pdb=" C3' DC Z 19 " pdb=" C2' DC Z 19 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.20e+00 bond pdb=" C3' DA Z 6 " pdb=" C2' DA Z 6 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.47e+00 bond pdb=" C2' DC Z 7 " pdb=" C1' DC Z 7 " ideal model delta sigma weight residual 1.518 1.536 -0.018 1.00e-02 1.00e+04 3.08e+00 ... (remaining 16374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 21973 1.88 - 3.76: 224 3.76 - 5.63: 20 5.63 - 7.51: 4 7.51 - 9.39: 4 Bond angle restraints: 22225 Sorted by residual: angle pdb=" C ALA G 276 " pdb=" CA ALA G 276 " pdb=" CB ALA G 276 " ideal model delta sigma weight residual 115.89 110.08 5.81 1.32e+00 5.74e-01 1.94e+01 angle pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " pdb=" CD GLU A 308 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" CB MET E 278 " pdb=" CG MET E 278 " pdb=" SD MET E 278 " ideal model delta sigma weight residual 112.70 122.09 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" CA GLU C 176 " pdb=" CB GLU C 176 " pdb=" CG GLU C 176 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 ... (remaining 22220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8423 17.67 - 35.35: 1135 35.35 - 53.02: 390 53.02 - 70.70: 91 70.70 - 88.37: 31 Dihedral angle restraints: 10070 sinusoidal: 4302 harmonic: 5768 Sorted by residual: dihedral pdb=" CA ALA E 277 " pdb=" C ALA E 277 " pdb=" N MET E 278 " pdb=" CA MET E 278 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CG ARG L 333 " pdb=" CD ARG L 333 " pdb=" NE ARG L 333 " pdb=" CZ ARG L 333 " ideal model delta sinusoidal sigma weight residual 90.00 40.66 49.34 2 1.50e+01 4.44e-03 1.23e+01 dihedral pdb=" CA ARG K 27 " pdb=" C ARG K 27 " pdb=" N LEU K 28 " pdb=" CA LEU K 28 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 10067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1482 0.026 - 0.051: 638 0.051 - 0.077: 230 0.077 - 0.103: 106 0.103 - 0.128: 69 Chirality restraints: 2525 Sorted by residual: chirality pdb=" P DC Z 1 " pdb=" OP1 DC Z 1 " pdb=" OP2 DC Z 1 " pdb=" O5' DC Z 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.46 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ARG K 130 " pdb=" N ARG K 130 " pdb=" C ARG K 130 " pdb=" CB ARG K 130 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE K 265 " pdb=" N ILE K 265 " pdb=" C ILE K 265 " pdb=" CB ILE K 265 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2522 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 303 " 0.145 9.50e-02 1.11e+02 6.52e-02 3.30e+00 pdb=" NE ARG A 303 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 303 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 303 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 248 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C PHE K 248 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE K 248 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU K 249 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 282 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO E 283 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 283 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 283 " 0.020 5.00e-02 4.00e+02 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 4 2.54 - 3.19: 13416 3.19 - 3.84: 29507 3.84 - 4.49: 41869 4.49 - 5.14: 69341 Nonbonded interactions: 154137 Sorted by model distance: nonbonded pdb="MG MG I 401 " pdb=" O1G ATP I 402 " model vdw 1.891 2.170 nonbonded pdb="MG MG E 401 " pdb=" O1G ATP E 402 " model vdw 2.030 2.170 nonbonded pdb=" O5' DC Z 7 " pdb=" O4' DC Z 7 " model vdw 2.515 2.432 nonbonded pdb=" O GLU C 176 " pdb=" OE1 GLU C 176 " model vdw 2.527 3.040 nonbonded pdb=" O2' ATP C 402 " pdb=" O3' ATP C 402 " model vdw 2.559 2.432 ... (remaining 154132 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 19 through 339) selection = (chain 'C' and (resid 19 through 277 or resid 282 through 339)) selection = (chain 'E' and (resid 19 through 277 or resid 282 through 339)) selection = (chain 'G' and (resid 19 through 277 or resid 282 through 339)) selection = (chain 'I' and (resid 19 through 277 or resid 282 through 339)) selection = (chain 'K' and (resid 19 through 277 or resid 282 through 339)) } ncs_group { reference = (chain 'B' and resid 331 through 347) selection = (chain 'D' and resid 331 through 347) selection = (chain 'F' and resid 331 through 347) selection = (chain 'H' and resid 331 through 347) selection = (chain 'J' and resid 331 through 347) } 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=1.00 max=1.00 mean=1.00 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: 1.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.003 0.044 16379 Z= 0.156 Angle : 0.480 9.390 22225 Z= 0.270 Chirality : 0.039 0.128 2525 Planarity : 0.003 0.065 2793 Dihedral : 18.643 88.372 6372 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 0.50 % Allowed : 32.61 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1997 helix: 1.19 (0.18), residues: 840 sheet: 1.03 (0.31), residues: 309 loop : -0.80 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 303 TYR 0.010 0.001 TYR E 191 PHE 0.007 0.001 PHE E 327 HIS 0.003 0.000 HIS I 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (16379) covalent geometry : angle 0.48042 / 0.27 (22225) hydrogen bonds : bond 0.12773 / 8.15 ( 745) hydrogen bonds : angle 5.57007 / 3.93 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.585 Fit side-chains REVERT: A 91 GLU cc_start: 0.6772 (mp0) cc_final: 0.6530 (mp0) REVERT: A 257 ASP cc_start: 0.8076 (m-30) cc_final: 0.7726 (m-30) REVERT: A 308 GLU cc_start: 0.5971 (tm-30) cc_final: 0.5385 (tt0) REVERT: C 247 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7528 (mtp-110) REVERT: C 251 MET cc_start: 0.8478 (tpp) cc_final: 0.8132 (tpt) REVERT: E 278 MET cc_start: 0.5367 (pmm) cc_final: 0.4537 (mmt) REVERT: F 341 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7042 (pmt170) REVERT: G 99 ILE cc_start: 0.8442 (tt) cc_final: 0.8111 (tt) REVERT: G 247 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7431 (mtm180) REVERT: G 278 MET cc_start: 0.5801 (mmm) cc_final: 0.5017 (mtm) REVERT: I 118 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7370 (pm20) REVERT: K 27 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7174 (ptt180) REVERT: K 30 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: K 94 GLN cc_start: 0.6225 (tm-30) cc_final: 0.5948 (tp40) REVERT: K 216 TYR cc_start: 0.8015 (m-80) cc_final: 0.7653 (m-80) outliers start: 8 outliers final: 4 residues processed: 166 average time/residue: 0.6090 time to fit residues: 111.5049 Evaluate side-chains 162 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain I residue 63 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain K residue 30 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 202 GLN C 188 ASN D 346 HIS K 272 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102194 restraints weight = 20564.353| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.69 r_work: 0.3081 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16379 Z= 0.129 Angle : 0.445 7.513 22225 Z= 0.240 Chirality : 0.039 0.136 2525 Planarity : 0.003 0.035 2793 Dihedral : 11.691 81.356 2709 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 3.86 % Allowed : 27.75 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1997 helix: 1.42 (0.18), residues: 849 sheet: 1.13 (0.31), residues: 310 loop : -0.81 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.007 0.001 TYR A 315 PHE 0.009 0.001 PHE G 126 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16379) covalent geometry : angle 0.44486 / 0.24 (22225) hydrogen bonds : bond 0.04081 / 2.69 ( 745) hydrogen bonds : angle 4.44620 / 3.14 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 0.615 Fit side-chains REVERT: A 91 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: A 257 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: A 336 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: C 247 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7512 (mtp-110) REVERT: C 251 MET cc_start: 0.8496 (tpp) cc_final: 0.8129 (tpt) REVERT: E 133 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7185 (mttp) REVERT: F 341 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7117 (pmt170) REVERT: G 99 ILE cc_start: 0.8458 (tt) cc_final: 0.8132 (tt) REVERT: G 247 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7422 (mtm180) REVERT: G 278 MET cc_start: 0.5909 (mmm) cc_final: 0.5603 (mpp) REVERT: I 118 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7334 (pm20) REVERT: K 27 ARG cc_start: 0.7688 (ptm160) cc_final: 0.7092 (ptt180) REVERT: K 30 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.5750 (pm20) REVERT: K 94 GLN cc_start: 0.6318 (tm-30) cc_final: 0.5954 (tp40) REVERT: K 98 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: K 216 TYR cc_start: 0.8001 (m-80) cc_final: 0.7604 (m-80) outliers start: 62 outliers final: 23 residues processed: 206 average time/residue: 0.5529 time to fit residues: 125.9205 Evaluate side-chains 183 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097530 restraints weight = 20947.666| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.69 r_work: 0.3032 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16379 Z= 0.207 Angle : 0.511 7.328 22225 Z= 0.271 Chirality : 0.041 0.140 2525 Planarity : 0.004 0.055 2793 Dihedral : 12.123 84.651 2705 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 5.54 % Allowed : 26.01 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1997 helix: 1.32 (0.18), residues: 848 sheet: 0.94 (0.30), residues: 311 loop : -0.95 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 303 TYR 0.015 0.001 TYR C 228 PHE 0.013 0.001 PHE A 248 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (16379) covalent geometry : angle 0.51087 / 0.27 (22225) hydrogen bonds : bond 0.04894 / 3.29 ( 745) hydrogen bonds : angle 4.48883 / 3.17 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 154 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6794 (tttm) REVERT: A 91 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: A 158 MET cc_start: 0.8059 (mtp) cc_final: 0.7593 (ttm) REVERT: C 91 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: C 206 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: C 247 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7603 (mtp-110) REVERT: C 251 MET cc_start: 0.8399 (tpp) cc_final: 0.8032 (tpt) REVERT: E 202 GLN cc_start: 0.8205 (tp40) cc_final: 0.7406 (tm-30) REVERT: E 278 MET cc_start: 0.6081 (pmm) cc_final: 0.4960 (mmt) REVERT: F 341 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7152 (pmt170) REVERT: G 80 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8589 (mtpt) REVERT: G 99 ILE cc_start: 0.8536 (tt) cc_final: 0.8213 (tt) REVERT: G 202 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 247 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7417 (mtm180) REVERT: G 278 MET cc_start: 0.6034 (mmm) cc_final: 0.5712 (mpp) REVERT: H 341 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6102 (pmm-80) REVERT: I 118 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7343 (pm20) REVERT: K 27 ARG cc_start: 0.7646 (ptm160) cc_final: 0.7318 (ptm160) REVERT: K 30 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.5642 (pm20) REVERT: K 94 GLN cc_start: 0.6313 (tm-30) cc_final: 0.5969 (tp40) REVERT: K 98 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: K 216 TYR cc_start: 0.8072 (m-80) cc_final: 0.7811 (m-80) REVERT: K 235 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.4546 (tpp-160) outliers start: 89 outliers final: 42 residues processed: 221 average time/residue: 0.5162 time to fit residues: 126.7637 Evaluate side-chains 201 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 341 ARG Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 235 ARG Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 119 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 110 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS I 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101366 restraints weight = 20727.719| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.67 r_work: 0.3070 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16379 Z= 0.119 Angle : 0.436 7.072 22225 Z= 0.235 Chirality : 0.038 0.133 2525 Planarity : 0.003 0.038 2793 Dihedral : 11.933 88.770 2705 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 4.23 % Allowed : 27.32 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1997 helix: 1.45 (0.18), residues: 848 sheet: 0.91 (0.31), residues: 310 loop : -0.90 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 247 TYR 0.008 0.001 TYR E 191 PHE 0.011 0.001 PHE G 126 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16379) covalent geometry : angle 0.43589 / 0.23 (22225) hydrogen bonds : bond 0.03774 / 2.54 ( 745) hydrogen bonds : angle 4.24067 / 3.00 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 159 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6934 (tttm) REVERT: A 91 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: A 158 MET cc_start: 0.7972 (mtp) cc_final: 0.7486 (mtm) REVERT: A 257 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: A 303 ARG cc_start: 0.8276 (mtm110) cc_final: 0.8069 (mtm110) REVERT: C 43 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 91 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 247 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7605 (mtp-110) REVERT: C 251 MET cc_start: 0.8405 (tpp) cc_final: 0.8038 (tpt) REVERT: E 202 GLN cc_start: 0.8175 (tp40) cc_final: 0.7421 (tm-30) REVERT: F 341 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7146 (pmt170) REVERT: G 80 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: G 99 ILE cc_start: 0.8499 (tt) cc_final: 0.8177 (tt) REVERT: G 202 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7683 (tm-30) REVERT: G 247 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7456 (mtm180) REVERT: G 278 MET cc_start: 0.6014 (mmm) cc_final: 0.5691 (mpp) REVERT: H 341 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6022 (pmm-80) REVERT: I 99 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mm) REVERT: I 118 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7233 (pm20) REVERT: K 30 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.5712 (pm20) REVERT: K 94 GLN cc_start: 0.6330 (tm-30) cc_final: 0.5982 (tp40) REVERT: K 98 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: K 216 TYR cc_start: 0.8016 (m-80) cc_final: 0.7715 (m-80) REVERT: K 235 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.4520 (tpp-160) REVERT: K 243 MET cc_start: 0.8316 (mtm) cc_final: 0.8052 (mtp) outliers start: 68 outliers final: 35 residues processed: 210 average time/residue: 0.6254 time to fit residues: 144.1475 Evaluate side-chains 199 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 341 ARG Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 235 ARG Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS J 346 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099871 restraints weight = 20758.816| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.69 r_work: 0.3049 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16379 Z= 0.154 Angle : 0.457 7.295 22225 Z= 0.245 Chirality : 0.039 0.134 2525 Planarity : 0.003 0.039 2793 Dihedral : 12.013 88.787 2705 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 4.42 % Allowed : 27.69 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1997 helix: 1.44 (0.18), residues: 848 sheet: 0.85 (0.30), residues: 311 loop : -0.92 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 247 TYR 0.011 0.001 TYR C 228 PHE 0.010 0.001 PHE A 248 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (16379) covalent geometry : angle 0.45681 / 0.25 (22225) hydrogen bonds : bond 0.04059 / 2.74 ( 745) hydrogen bonds : angle 4.25830 / 3.01 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: A 158 MET cc_start: 0.8008 (mtp) cc_final: 0.7506 (mtm) REVERT: C 91 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: C 206 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: C 247 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7602 (mtp-110) REVERT: C 251 MET cc_start: 0.8415 (tpp) cc_final: 0.8049 (tpt) REVERT: E 202 GLN cc_start: 0.8184 (tp40) cc_final: 0.7430 (tm-30) REVERT: E 278 MET cc_start: 0.6014 (pmm) cc_final: 0.4819 (mmt) REVERT: F 341 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7203 (pmt170) REVERT: G 99 ILE cc_start: 0.8523 (tt) cc_final: 0.8210 (tt) REVERT: G 202 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7677 (tm-30) REVERT: G 247 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7460 (mtm180) REVERT: G 278 MET cc_start: 0.5973 (mmm) cc_final: 0.5653 (mpp) REVERT: H 341 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6021 (pmm-80) REVERT: I 99 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7624 (mm) REVERT: I 118 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7203 (pm20) REVERT: K 30 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: K 94 GLN cc_start: 0.6331 (tm-30) cc_final: 0.5986 (tp40) REVERT: K 98 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6717 (mt-10) REVERT: K 216 TYR cc_start: 0.8035 (m-80) cc_final: 0.7808 (m-80) REVERT: K 235 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.4498 (tpp-160) REVERT: K 243 MET cc_start: 0.8337 (mtm) cc_final: 0.8056 (mtp) outliers start: 71 outliers final: 41 residues processed: 208 average time/residue: 0.5553 time to fit residues: 128.0971 Evaluate side-chains 200 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 341 ARG Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 215 ARG Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 235 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 192 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 96 optimal weight: 0.0040 chunk 26 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102696 restraints weight = 20572.917| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.69 r_work: 0.3090 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16379 Z= 0.090 Angle : 0.411 6.423 22225 Z= 0.223 Chirality : 0.037 0.129 2525 Planarity : 0.003 0.040 2793 Dihedral : 11.718 84.263 2705 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 4.17 % Allowed : 28.25 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1997 helix: 1.61 (0.18), residues: 846 sheet: 0.85 (0.30), residues: 312 loop : -0.83 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.007 0.001 TYR A 216 PHE 0.009 0.001 PHE G 126 HIS 0.004 0.000 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (16379) covalent geometry : angle 0.41097 / 0.22 (22225) hydrogen bonds : bond 0.03114 / 2.10 ( 745) hydrogen bonds : angle 4.03201 / 2.85 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6867 (tttm) REVERT: A 84 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7475 (mmp) REVERT: A 91 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: A 158 MET cc_start: 0.7907 (mtp) cc_final: 0.7408 (mtm) REVERT: A 257 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: C 27 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7566 (mmm160) REVERT: C 91 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: C 212 VAL cc_start: 0.8376 (p) cc_final: 0.8147 (p) REVERT: C 247 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7528 (mtp-110) REVERT: C 251 MET cc_start: 0.8434 (tpp) cc_final: 0.8071 (tpt) REVERT: F 341 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7190 (pmt170) REVERT: G 80 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: G 99 ILE cc_start: 0.8431 (tt) cc_final: 0.8118 (tt) REVERT: G 202 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 247 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7473 (mtm180) REVERT: G 278 MET cc_start: 0.5984 (mmm) cc_final: 0.5674 (mpp) REVERT: I 99 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7662 (mm) REVERT: I 118 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7202 (pm20) REVERT: K 30 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: K 94 GLN cc_start: 0.6361 (tm-30) cc_final: 0.5896 (tp40) REVERT: K 95 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7801 (tpp80) REVERT: K 98 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: K 243 MET cc_start: 0.8350 (mtm) cc_final: 0.8078 (mtp) outliers start: 67 outliers final: 30 residues processed: 216 average time/residue: 0.5920 time to fit residues: 141.0585 Evaluate side-chains 192 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 193 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100094 restraints weight = 20669.811| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.66 r_work: 0.3054 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16379 Z= 0.170 Angle : 0.468 7.636 22225 Z= 0.251 Chirality : 0.039 0.137 2525 Planarity : 0.004 0.058 2793 Dihedral : 11.961 81.568 2705 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 4.60 % Allowed : 27.82 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1997 helix: 1.51 (0.18), residues: 848 sheet: 0.75 (0.30), residues: 326 loop : -0.88 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 303 TYR 0.012 0.001 TYR C 228 PHE 0.012 0.001 PHE E 279 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (16379) covalent geometry : angle 0.46777 / 0.25 (22225) hydrogen bonds : bond 0.04031 / 2.73 ( 745) hydrogen bonds : angle 4.17667 / 2.96 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 152 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: A 158 MET cc_start: 0.7985 (mtp) cc_final: 0.7468 (mtm) REVERT: A 257 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: C 91 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: C 247 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7549 (mtp-110) REVERT: C 251 MET cc_start: 0.8381 (tpp) cc_final: 0.8008 (tpt) REVERT: E 202 GLN cc_start: 0.8132 (tp40) cc_final: 0.7410 (tm-30) REVERT: F 341 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7150 (pmt170) REVERT: G 80 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: G 99 ILE cc_start: 0.8502 (tt) cc_final: 0.8191 (tt) REVERT: G 202 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7671 (tm-30) REVERT: G 247 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7422 (mtm180) REVERT: G 278 MET cc_start: 0.6039 (mmm) cc_final: 0.5726 (mpp) REVERT: I 99 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7627 (mm) REVERT: I 118 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7292 (pm20) REVERT: K 30 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.5576 (pm20) REVERT: K 94 GLN cc_start: 0.6335 (tm-30) cc_final: 0.5862 (tp40) REVERT: K 95 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7726 (tpp80) REVERT: K 98 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: K 243 MET cc_start: 0.8373 (mtm) cc_final: 0.8058 (mtp) outliers start: 74 outliers final: 45 residues processed: 209 average time/residue: 0.6264 time to fit residues: 144.7538 Evaluate side-chains 201 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 336 ASP Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100814 restraints weight = 20658.457| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.67 r_work: 0.3064 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16379 Z= 0.134 Angle : 0.445 8.656 22225 Z= 0.239 Chirality : 0.038 0.133 2525 Planarity : 0.003 0.047 2793 Dihedral : 11.918 79.300 2705 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 4.04 % Allowed : 28.62 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1997 helix: 1.55 (0.18), residues: 846 sheet: 0.68 (0.30), residues: 327 loop : -0.88 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 303 TYR 0.009 0.001 TYR A 315 PHE 0.009 0.001 PHE E 279 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (16379) covalent geometry : angle 0.44487 / 0.24 (22225) hydrogen bonds : bond 0.03717 / 2.52 ( 745) hydrogen bonds : angle 4.12767 / 2.92 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6849 (tttm) REVERT: A 91 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 158 MET cc_start: 0.7964 (mtp) cc_final: 0.7446 (mtm) REVERT: A 257 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: C 91 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: C 206 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7296 (mt0) REVERT: C 247 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7555 (mtp-110) REVERT: C 251 MET cc_start: 0.8380 (tpp) cc_final: 0.8009 (tpt) REVERT: E 202 GLN cc_start: 0.8113 (tp40) cc_final: 0.7425 (tm-30) REVERT: E 278 MET cc_start: 0.5722 (pmm) cc_final: 0.4522 (mmt) REVERT: F 341 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7138 (pmt170) REVERT: G 29 GLU cc_start: 0.8158 (tp30) cc_final: 0.7532 (pp20) REVERT: G 80 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8592 (mtpt) REVERT: G 99 ILE cc_start: 0.8479 (tt) cc_final: 0.8158 (tt) REVERT: G 202 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7619 (tm-30) REVERT: G 247 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7391 (mtm180) REVERT: G 278 MET cc_start: 0.6028 (mmm) cc_final: 0.5712 (mpp) REVERT: I 99 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7611 (mm) REVERT: I 118 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7189 (pm20) REVERT: K 30 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.6505 (pp30) REVERT: K 94 GLN cc_start: 0.6337 (tm-30) cc_final: 0.5859 (tp40) REVERT: K 95 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7691 (tpp80) REVERT: K 98 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6521 (mt-10) outliers start: 65 outliers final: 41 residues processed: 204 average time/residue: 0.5744 time to fit residues: 130.4163 Evaluate side-chains 200 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 24 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100070 restraints weight = 20716.901| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.67 r_work: 0.3049 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16379 Z= 0.159 Angle : 0.461 8.058 22225 Z= 0.247 Chirality : 0.039 0.135 2525 Planarity : 0.003 0.044 2793 Dihedral : 12.002 80.872 2705 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 28.62 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1997 helix: 1.50 (0.18), residues: 848 sheet: 0.69 (0.30), residues: 326 loop : -0.91 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 303 TYR 0.010 0.001 TYR C 228 PHE 0.010 0.001 PHE A 248 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (16379) covalent geometry : angle 0.46061 / 0.25 (22225) hydrogen bonds : bond 0.03974 / 2.69 ( 745) hydrogen bonds : angle 4.16715 / 2.95 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: A 158 MET cc_start: 0.7990 (mtp) cc_final: 0.7478 (mtm) REVERT: A 176 GLU cc_start: 0.8530 (tp30) cc_final: 0.8144 (tp30) REVERT: A 257 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: C 91 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 206 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: C 247 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7565 (mtp-110) REVERT: C 251 MET cc_start: 0.8391 (tpp) cc_final: 0.8021 (tpt) REVERT: E 64 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7597 (mtpt) REVERT: E 202 GLN cc_start: 0.8126 (tp40) cc_final: 0.7439 (tm-30) REVERT: F 341 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7135 (pmt170) REVERT: G 80 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8579 (mtpt) REVERT: G 99 ILE cc_start: 0.8500 (tt) cc_final: 0.8187 (tt) REVERT: G 202 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7646 (tm-30) REVERT: G 247 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7409 (mtm180) REVERT: G 278 MET cc_start: 0.5977 (mmm) cc_final: 0.5669 (mpp) REVERT: I 99 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7588 (mm) REVERT: I 118 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7221 (pm20) REVERT: K 30 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6666 (pp30) REVERT: K 94 GLN cc_start: 0.6325 (tm-30) cc_final: 0.5850 (tp40) REVERT: K 95 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7689 (tpp80) REVERT: K 98 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6533 (mt-10) outliers start: 64 outliers final: 46 residues processed: 199 average time/residue: 0.5712 time to fit residues: 125.7590 Evaluate side-chains 204 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100984 restraints weight = 20607.978| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.67 r_work: 0.3066 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16379 Z= 0.124 Angle : 0.445 9.506 22225 Z= 0.239 Chirality : 0.038 0.133 2525 Planarity : 0.003 0.041 2793 Dihedral : 11.924 79.608 2705 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 3.67 % Allowed : 28.94 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1997 helix: 1.56 (0.18), residues: 846 sheet: 0.66 (0.30), residues: 327 loop : -0.88 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 247 TYR 0.009 0.001 TYR A 315 PHE 0.009 0.001 PHE E 279 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (16379) covalent geometry : angle 0.44523 / 0.24 (22225) hydrogen bonds : bond 0.03657 / 2.48 ( 745) hydrogen bonds : angle 4.09901 / 2.90 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3994 Ramachandran restraints generated. 1997 Oldfield, 0 Emsley, 1997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: A 158 MET cc_start: 0.7957 (mtp) cc_final: 0.7440 (mtm) REVERT: A 176 GLU cc_start: 0.8465 (tp30) cc_final: 0.8065 (tp30) REVERT: A 257 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 91 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: C 206 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: C 247 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7556 (mtp-110) REVERT: C 251 MET cc_start: 0.8380 (tpp) cc_final: 0.8013 (tpt) REVERT: E 64 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7585 (mtpt) REVERT: E 202 GLN cc_start: 0.8102 (tp40) cc_final: 0.7432 (tm-30) REVERT: F 341 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7126 (pmt170) REVERT: G 80 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8592 (mtpt) REVERT: G 99 ILE cc_start: 0.8475 (tt) cc_final: 0.8150 (tt) REVERT: G 247 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7388 (mtm180) REVERT: G 278 MET cc_start: 0.5962 (mmm) cc_final: 0.5675 (mpp) REVERT: I 118 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7156 (pm20) REVERT: K 27 ARG cc_start: 0.7506 (ptm160) cc_final: 0.7126 (ptt180) REVERT: K 30 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6715 (pp30) REVERT: K 94 GLN cc_start: 0.6331 (tm-30) cc_final: 0.5856 (tp40) REVERT: K 95 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7687 (tpp80) REVERT: K 98 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6537 (mt-10) outliers start: 59 outliers final: 47 residues processed: 200 average time/residue: 0.5538 time to fit residues: 122.6270 Evaluate side-chains 205 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 330 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 326 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098768 restraints weight = 20691.121| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.67 r_work: 0.3035 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16379 Z= 0.195 Angle : 0.488 8.428 22225 Z= 0.261 Chirality : 0.040 0.139 2525 Planarity : 0.004 0.043 2793 Dihedral : 12.122 83.106 2705 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 4.23 % Allowed : 28.38 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1997 helix: 1.47 (0.18), residues: 848 sheet: 0.62 (0.30), residues: 326 loop : -0.96 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.013 0.001 TYR C 228 PHE 0.011 0.001 PHE A 248 HIS 0.003 0.001 HIS K 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (16379) covalent geometry : angle 0.48796 / 0.26 (22225) hydrogen bonds : bond 0.04335 / 2.94 ( 745) hydrogen bonds : angle 4.24520 / 3.01 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5663.36 seconds wall clock time: 96 minutes 54.97 seconds (5814.97 seconds total)