Starting phenix.real_space_refine on Fri Jul 3 22:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnc_53243/07_2026/9qnc_53243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnc_53243/07_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_53243/07_2026/9qnc_53243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnc_53243/07_2026/9qnc_53243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qnc_53243/07_2026/9qnc_53243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnc_53243/07_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-dev-6108/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, 31 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 3.08, per 1000 atoms: 0.19 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: 0.94 Conformation dependent library (CDL) restraints added in 528.4 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: 0.50 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: 2.29 Time building geometry restraints manager: 1.27 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- 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 0.48007 / 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 : 0.394 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: 0.5725 time to fit residues: 104.5473 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 : 0.593 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.145695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102260 restraints weight = 20560.319| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.69 r_work: 0.3082 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16379 Z= 0.128 Angle : 0.444 7.275 22225 Z= 0.240 Chirality : 0.038 0.136 2525 Planarity : 0.003 0.035 2793 Dihedral : 11.656 87.831 2709 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 3.73 % Allowed : 27.82 % 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: 0.68 (0.19), residues: 1997 helix: 1.41 (0.18), residues: 847 sheet: 1.12 (0.31), residues: 310 loop : -0.80 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 303 TYR 0.008 0.001 TYR A 315 PHE 0.009 0.001 PHE G 126 HIS 0.003 0.001 HIS I 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16379) covalent geometry : angle 0.44398 / 0.24 (22225) hydrogen bonds : bond 0.04186 / 2.75 ( 745) hydrogen bonds : angle 4.46869 / 3.16 ( 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 219 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.599 Fit side-chains REVERT: A 91 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: A 257 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 336 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: C 247 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7511 (mtp-110) REVERT: C 251 MET cc_start: 0.8497 (tpp) cc_final: 0.8129 (tpt) REVERT: E 133 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7186 (mttp) REVERT: F 341 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7116 (pmt170) REVERT: G 99 ILE cc_start: 0.8460 (tt) cc_final: 0.8134 (tt) REVERT: G 247 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7418 (mtm180) REVERT: G 278 MET cc_start: 0.5911 (mmm) cc_final: 0.5604 (mpp) REVERT: I 118 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7342 (pm20) REVERT: K 27 ARG cc_start: 0.7692 (ptm160) cc_final: 0.7386 (ptm160) REVERT: K 30 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.5751 (pm20) REVERT: K 94 GLN cc_start: 0.6323 (tm-30) cc_final: 0.5959 (tp40) REVERT: K 98 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: K 216 TYR cc_start: 0.8011 (m-80) cc_final: 0.7616 (m-80) outliers start: 60 outliers final: 22 residues processed: 203 average time/residue: 0.5217 time to fit residues: 117.2731 Evaluate side-chains 181 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 12 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096049 restraints weight = 21040.135| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.69 r_work: 0.3013 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 16379 Z= 0.289 Angle : 0.571 7.377 22225 Z= 0.302 Chirality : 0.043 0.150 2525 Planarity : 0.004 0.049 2793 Dihedral : 12.199 83.908 2705 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 5.72 % Allowed : 26.26 % Favored : 68.01 % 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: 0.32 (0.19), residues: 1997 helix: 1.15 (0.18), residues: 848 sheet: 0.87 (0.30), residues: 311 loop : -1.02 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 303 TYR 0.019 0.002 TYR C 228 PHE 0.015 0.002 PHE A 248 HIS 0.003 0.001 HIS K 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.29 (16379) covalent geometry : angle 0.57088 / 0.30 (22225) hydrogen bonds : bond 0.05596 / 3.76 ( 745) hydrogen bonds : angle 4.67660 / 3.31 ( 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 244 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 152 time to evaluate : 0.548 Fit side-chains REVERT: A 91 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: C 91 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: C 206 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: C 247 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7633 (mtp-110) REVERT: C 251 MET cc_start: 0.8565 (tpp) cc_final: 0.8208 (tpt) REVERT: E 133 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7489 (mttp) REVERT: E 202 GLN cc_start: 0.8241 (tp40) cc_final: 0.7423 (tm-30) REVERT: E 278 MET cc_start: 0.5876 (pmm) cc_final: 0.4590 (mmt) REVERT: F 341 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7196 (pmt170) REVERT: G 80 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8592 (mtpt) REVERT: G 99 ILE cc_start: 0.8592 (tt) cc_final: 0.8261 (tt) REVERT: G 181 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7842 (p) REVERT: G 247 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7445 (mtm180) REVERT: G 278 MET cc_start: 0.5958 (mmm) cc_final: 0.5640 (mpp) REVERT: H 341 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6112 (pmm-80) REVERT: I 118 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7345 (pm20) REVERT: K 27 ARG cc_start: 0.7663 (ptm160) cc_final: 0.7327 (ptm160) REVERT: K 30 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.5642 (pm20) REVERT: K 94 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5934 (tp40) REVERT: K 98 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: K 235 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.4711 (tpp-160) outliers start: 92 outliers final: 42 residues processed: 222 average time/residue: 0.5495 time to fit residues: 135.1744 Evaluate side-chains 202 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain A residue 162 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 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 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 133 LYS Chi-restraints excluded: chain E residue 162 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 181 SER 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 63 ILE Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 104 THR 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 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: 3.9990 chunk 28 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 0.0030 chunk 183 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN D 346 HIS I 94 GLN J 346 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102439 restraints weight = 20664.148| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.70 r_work: 0.3082 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16379 Z= 0.096 Angle : 0.432 6.767 22225 Z= 0.233 Chirality : 0.038 0.136 2525 Planarity : 0.003 0.039 2793 Dihedral : 11.804 89.086 2705 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.75 % Favored : 98.20 % Rotamer: Outliers : 3.42 % Allowed : 28.19 % 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: 0.59 (0.19), residues: 1997 helix: 1.44 (0.18), residues: 846 sheet: 0.87 (0.31), residues: 312 loop : -0.88 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 247 TYR 0.007 0.001 TYR E 191 PHE 0.011 0.001 PHE G 126 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (16379) covalent geometry : angle 0.43180 / 0.23 (22225) hydrogen bonds : bond 0.03416 / 2.30 ( 745) hydrogen bonds : angle 4.20786 / 2.98 ( 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 215 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6906 (tttm) REVERT: A 91 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: A 158 MET cc_start: 0.7893 (mtp) cc_final: 0.7429 (ttm) REVERT: A 176 GLU cc_start: 0.8574 (tp30) cc_final: 0.8252 (tp30) REVERT: C 247 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7538 (mtp-110) REVERT: C 251 MET cc_start: 0.8392 (tpp) cc_final: 0.8033 (tpt) REVERT: F 341 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7147 (pmt170) REVERT: G 80 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8608 (mtpt) REVERT: G 99 ILE cc_start: 0.8461 (tt) cc_final: 0.8146 (tt) REVERT: G 202 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 247 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7441 (mtm180) REVERT: G 278 MET cc_start: 0.6003 (mmm) cc_final: 0.5681 (mpp) REVERT: I 118 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7188 (pm20) REVERT: K 30 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.5733 (pm20) REVERT: K 94 GLN cc_start: 0.6333 (tm-30) cc_final: 0.6021 (tp40) REVERT: K 98 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: K 235 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.4480 (tpp-160) outliers start: 55 outliers final: 29 residues processed: 203 average time/residue: 0.5660 time to fit residues: 126.6796 Evaluate side-chains 186 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 187 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 326 MET 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 266 THR 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 142 VAL Chi-restraints excluded: chain I residue 212 VAL 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 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: 9.9990 chunk 44 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101134 restraints weight = 20730.952| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.70 r_work: 0.3066 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16379 Z= 0.124 Angle : 0.438 7.227 22225 Z= 0.235 Chirality : 0.038 0.131 2525 Planarity : 0.003 0.056 2793 Dihedral : 11.828 88.782 2705 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 4.36 % Allowed : 28.00 % Favored : 67.64 % 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: 0.64 (0.19), residues: 1997 helix: 1.50 (0.18), residues: 846 sheet: 0.85 (0.31), residues: 312 loop : -0.86 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 303 TYR 0.008 0.001 TYR C 228 PHE 0.008 0.001 PHE A 248 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 0.43755 / 0.23 (22225) hydrogen bonds : bond 0.03652 / 2.46 ( 745) hydrogen bonds : angle 4.16885 / 2.95 ( 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: 70 poor density : 154 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6902 (tttm) REVERT: A 91 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: A 158 MET cc_start: 0.7929 (mtp) cc_final: 0.7491 (ttm) REVERT: C 91 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: C 247 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7601 (mtp-110) REVERT: C 251 MET cc_start: 0.8423 (tpp) cc_final: 0.8062 (tpt) REVERT: E 133 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7325 (mttp) REVERT: E 202 GLN cc_start: 0.8166 (tp40) cc_final: 0.7432 (tm-30) REVERT: E 278 MET cc_start: 0.5663 (pmm) cc_final: 0.4417 (mmt) REVERT: F 341 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7152 (pmt170) REVERT: G 99 ILE cc_start: 0.8482 (tt) cc_final: 0.8162 (tt) REVERT: G 184 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: G 202 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 247 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7466 (mtm180) REVERT: G 278 MET cc_start: 0.6019 (mmm) cc_final: 0.5693 (mpp) REVERT: I 99 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7725 (mm) REVERT: I 118 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7223 (pm20) REVERT: K 30 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.5949 (pm20) REVERT: K 94 GLN cc_start: 0.6332 (tm-30) cc_final: 0.5977 (tp40) REVERT: K 98 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: K 235 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4449 (tpp-160) outliers start: 70 outliers final: 37 residues processed: 207 average time/residue: 0.5503 time to fit residues: 126.4101 Evaluate side-chains 198 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 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 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 61 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 336 ASP 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 339 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 192 optimal weight: 9.9990 chunk 57 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 244 HIS J 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103532 restraints weight = 20585.925| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.67 r_work: 0.3099 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16379 Z= 0.090 Angle : 0.410 6.461 22225 Z= 0.223 Chirality : 0.038 0.138 2525 Planarity : 0.003 0.041 2793 Dihedral : 11.641 88.927 2705 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 3.80 % Allowed : 28.62 % 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: 1.59 (0.18), residues: 847 sheet: 0.88 (0.31), residues: 312 loop : -0.81 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 303 TYR 0.007 0.001 TYR E 178 PHE 0.007 0.001 PHE G 126 HIS 0.004 0.000 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (16379) covalent geometry : angle 0.41049 / 0.22 (22225) hydrogen bonds : bond 0.03058 / 2.07 ( 745) hydrogen bonds : angle 3.99780 / 2.83 ( 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 222 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 161 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6861 (tttm) REVERT: A 84 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7415 (mmp) REVERT: A 91 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: A 158 MET cc_start: 0.7859 (mtp) cc_final: 0.7389 (ttm) REVERT: A 176 GLU cc_start: 0.8507 (tp30) cc_final: 0.8174 (tp30) REVERT: C 43 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 91 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: C 212 VAL cc_start: 0.8321 (p) cc_final: 0.8098 (p) REVERT: C 247 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7484 (mtp-110) REVERT: C 251 MET cc_start: 0.8411 (tpp) cc_final: 0.8048 (tpt) REVERT: F 341 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7137 (pmt170) REVERT: G 99 ILE cc_start: 0.8401 (tt) cc_final: 0.8091 (tt) REVERT: G 202 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7658 (tm-30) REVERT: G 247 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7413 (mtm180) REVERT: G 278 MET cc_start: 0.5977 (mmm) cc_final: 0.5664 (mpp) REVERT: I 99 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7686 (mm) REVERT: I 118 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7182 (pm20) REVERT: I 338 LYS cc_start: 0.6641 (mmmt) cc_final: 0.6418 (mmmt) REVERT: K 30 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: K 94 GLN cc_start: 0.6339 (tm-30) cc_final: 0.5874 (tp40) REVERT: K 95 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7766 (tpp80) REVERT: K 98 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6601 (mt-10) outliers start: 61 outliers final: 28 residues processed: 211 average time/residue: 0.6645 time to fit residues: 154.4359 Evaluate side-chains 193 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 330 ASN Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 GLU 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 E residue 266 THR 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 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 269 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 230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 193 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101452 restraints weight = 20643.525| |-----------------------------------------------------------------------------| r_work (start): 0.3207 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: 4.81 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1023 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= 0.136 Angle : 0.441 7.920 22225 Z= 0.237 Chirality : 0.039 0.133 2525 Planarity : 0.003 0.063 2793 Dihedral : 11.739 85.998 2705 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 4.11 % Allowed : 28.44 % Favored : 67.45 % 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: 0.70 (0.19), residues: 1997 helix: 1.58 (0.18), residues: 845 sheet: 0.88 (0.31), residues: 312 loop : -0.85 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 303 TYR 0.009 0.001 TYR C 228 PHE 0.009 0.001 PHE A 248 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16379) covalent geometry : angle 0.44125 / 0.24 (22225) hydrogen bonds : bond 0.03617 / 2.45 ( 745) hydrogen bonds : angle 4.07464 / 2.89 ( 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 222 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6881 (tttm) REVERT: A 91 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: A 158 MET cc_start: 0.7910 (mtp) cc_final: 0.7432 (ttm) REVERT: A 257 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: C 43 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: C 91 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: C 247 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7563 (mtp-110) REVERT: C 251 MET cc_start: 0.8395 (tpp) cc_final: 0.8026 (tpt) REVERT: E 202 GLN cc_start: 0.8117 (tp40) cc_final: 0.7425 (tm-30) REVERT: E 278 MET cc_start: 0.5965 (pmm) cc_final: 0.4747 (mmt) REVERT: F 341 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7175 (pmt170) REVERT: G 80 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8587 (mtpt) REVERT: G 99 ILE cc_start: 0.8428 (tt) cc_final: 0.8106 (tt) REVERT: G 202 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 247 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7423 (mtm180) REVERT: G 278 MET cc_start: 0.6011 (mmm) cc_final: 0.5698 (mpp) REVERT: I 99 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7708 (mm) REVERT: I 118 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7252 (pm20) REVERT: K 30 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: K 94 GLN cc_start: 0.6328 (tm-30) cc_final: 0.5856 (tp40) REVERT: K 95 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7723 (tpp80) REVERT: K 98 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6594 (mt-10) outliers start: 66 outliers final: 38 residues processed: 207 average time/residue: 0.6203 time to fit residues: 142.2292 Evaluate side-chains 202 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 109 LEU 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 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 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 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 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 215 ARG 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 339 LEU 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 326 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 44 optimal weight: 6.9990 chunk 144 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102093 restraints weight = 20650.368| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.68 r_work: 0.3080 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1068 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= 0.113 Angle : 0.426 7.048 22225 Z= 0.230 Chirality : 0.038 0.136 2525 Planarity : 0.003 0.047 2793 Dihedral : 11.688 86.169 2705 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 3.92 % Allowed : 28.56 % Favored : 67.52 % 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: 0.71 (0.19), residues: 1997 helix: 1.61 (0.18), residues: 846 sheet: 0.87 (0.31), residues: 312 loop : -0.86 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 303 TYR 0.007 0.001 TYR A 315 PHE 0.008 0.001 PHE A 129 HIS 0.003 0.000 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16379) covalent geometry : angle 0.42626 / 0.23 (22225) hydrogen bonds : bond 0.03369 / 2.28 ( 745) hydrogen bonds : angle 4.02587 / 2.85 ( 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 220 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6856 (tttm) REVERT: A 91 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: A 158 MET cc_start: 0.7890 (mtp) cc_final: 0.7400 (ttm) REVERT: A 176 GLU cc_start: 0.8471 (tp30) cc_final: 0.8079 (tp30) REVERT: A 257 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: C 43 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: C 91 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: C 206 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: C 247 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7552 (mtp-110) REVERT: C 251 MET cc_start: 0.8390 (tpp) cc_final: 0.8025 (tpt) REVERT: E 202 GLN cc_start: 0.8091 (tp40) cc_final: 0.7420 (tm-30) REVERT: F 341 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7143 (pmt170) REVERT: G 80 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8608 (mtpt) REVERT: G 99 ILE cc_start: 0.8427 (tt) cc_final: 0.8107 (tt) REVERT: G 184 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: G 202 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7663 (tm-30) REVERT: G 247 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7431 (mtm180) REVERT: G 278 MET cc_start: 0.6029 (mmm) cc_final: 0.5706 (mpp) REVERT: I 99 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7739 (mm) REVERT: I 118 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7233 (pm20) REVERT: I 338 LYS cc_start: 0.6806 (mmmt) cc_final: 0.6505 (mmmt) REVERT: K 30 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: K 94 GLN cc_start: 0.6331 (tm-30) cc_final: 0.5853 (tp40) REVERT: K 95 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7689 (tpp80) REVERT: K 98 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6606 (mt-10) outliers start: 63 outliers final: 37 residues processed: 205 average time/residue: 0.5946 time to fit residues: 134.8098 Evaluate side-chains 200 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 257 ASP 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 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 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 D residue 338 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 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 184 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 273 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 24 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098101 restraints weight = 20795.479| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.69 r_work: 0.3030 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16379 Z= 0.222 Angle : 0.520 10.428 22225 Z= 0.276 Chirality : 0.041 0.143 2525 Planarity : 0.004 0.050 2793 Dihedral : 12.027 80.767 2705 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 4.17 % Allowed : 28.56 % Favored : 67.27 % 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: 0.51 (0.19), residues: 1997 helix: 1.43 (0.18), residues: 848 sheet: 0.68 (0.30), residues: 326 loop : -0.97 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 27 TYR 0.016 0.002 TYR C 228 PHE 0.013 0.001 PHE A 248 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (16379) covalent geometry : angle 0.51957 / 0.28 (22225) hydrogen bonds : bond 0.04624 / 3.13 ( 745) hydrogen bonds : angle 4.30754 / 3.05 ( 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 222 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 155 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: A 158 MET cc_start: 0.8011 (mtp) cc_final: 0.7491 (mtm) REVERT: A 176 GLU cc_start: 0.8505 (tp30) cc_final: 0.8134 (tp30) REVERT: C 91 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: C 247 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7625 (mtp-110) REVERT: C 251 MET cc_start: 0.8442 (tpp) cc_final: 0.8064 (tpt) REVERT: E 43 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: E 64 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7633 (mtpt) REVERT: E 202 GLN cc_start: 0.8182 (tp40) cc_final: 0.7436 (tm-30) REVERT: E 278 MET cc_start: 0.5696 (pmm) cc_final: 0.4714 (mmt) REVERT: F 341 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7172 (pmt170) REVERT: G 80 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8637 (mtpt) REVERT: G 99 ILE cc_start: 0.8557 (tt) cc_final: 0.8241 (tt) REVERT: G 202 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 247 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7503 (mtm180) REVERT: G 278 MET cc_start: 0.6021 (mmm) cc_final: 0.5719 (mpp) REVERT: I 118 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7334 (pm20) REVERT: K 30 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6674 (pp30) REVERT: K 94 GLN cc_start: 0.6369 (tm-30) cc_final: 0.5900 (tp40) REVERT: K 95 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7716 (tpp80) REVERT: K 98 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6599 (mt-10) outliers start: 67 outliers final: 40 residues processed: 205 average time/residue: 0.6451 time to fit residues: 146.5590 Evaluate side-chains 201 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain A residue 218 LEU 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 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 E residue 43 GLU 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 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 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 185 VAL Chi-restraints excluded: chain I residue 212 VAL 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 339 LEU 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: 9.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101326 restraints weight = 20584.765| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.69 r_work: 0.3073 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16379 Z= 0.108 Angle : 0.442 9.220 22225 Z= 0.238 Chirality : 0.038 0.133 2525 Planarity : 0.003 0.042 2793 Dihedral : 11.792 85.006 2705 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 2.68 % Allowed : 29.99 % 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: 1.57 (0.18), residues: 846 sheet: 0.75 (0.31), residues: 312 loop : -0.93 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 247 TYR 0.008 0.001 TYR A 315 PHE 0.008 0.001 PHE G 126 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16379) covalent geometry : angle 0.44243 / 0.24 (22225) hydrogen bonds : bond 0.03468 / 2.35 ( 745) hydrogen bonds : angle 4.07711 / 2.89 ( 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 198 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: A 158 MET cc_start: 0.7919 (mtp) cc_final: 0.7404 (mtm) REVERT: A 176 GLU cc_start: 0.8501 (tp30) cc_final: 0.8135 (tp30) REVERT: C 91 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: C 206 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: C 247 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7599 (mtp-110) REVERT: C 251 MET cc_start: 0.8428 (tpp) cc_final: 0.8066 (tpt) REVERT: E 64 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7602 (mtpt) REVERT: E 202 GLN cc_start: 0.8116 (tp40) cc_final: 0.7458 (tm-30) REVERT: E 278 MET cc_start: 0.5709 (pmm) cc_final: 0.4493 (mmt) REVERT: F 341 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7167 (pmt170) REVERT: G 99 ILE cc_start: 0.8457 (tt) cc_final: 0.8134 (tt) REVERT: G 247 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7458 (mtm180) REVERT: G 278 MET cc_start: 0.5970 (mmm) cc_final: 0.5688 (mpp) REVERT: I 84 MET cc_start: 0.7756 (mtm) cc_final: 0.7376 (mmm) REVERT: I 99 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (mm) REVERT: I 118 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7214 (pm20) REVERT: I 338 LYS cc_start: 0.6790 (mmmt) cc_final: 0.6539 (mmmt) REVERT: K 27 ARG cc_start: 0.7533 (ptm160) cc_final: 0.7190 (ptt180) REVERT: K 30 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6667 (pp30) REVERT: K 94 GLN cc_start: 0.6368 (tm-30) cc_final: 0.5894 (tp40) REVERT: K 95 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7729 (tpp80) REVERT: K 98 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6576 (mt-10) outliers start: 43 outliers final: 34 residues processed: 192 average time/residue: 0.6044 time to fit residues: 128.8890 Evaluate side-chains 193 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 239 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain E residue 43 GLU 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 G residue 103 THR Chi-restraints excluded: chain G residue 154 GLU 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 185 VAL Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 269 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 100 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 346 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096291 restraints weight = 20788.643| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.68 r_work: 0.3021 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16379 Z= 0.268 Angle : 0.549 9.001 22225 Z= 0.292 Chirality : 0.043 0.144 2525 Planarity : 0.004 0.047 2793 Dihedral : 12.181 81.869 2705 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 3.42 % Allowed : 29.31 % Favored : 67.27 % 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: 0.36 (0.19), residues: 1997 helix: 1.35 (0.18), residues: 848 sheet: 0.55 (0.30), residues: 326 loop : -1.06 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 338 TYR 0.018 0.002 TYR C 228 PHE 0.014 0.002 PHE A 248 HIS 0.003 0.001 HIS K 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.27 (16379) covalent geometry : angle 0.54945 / 0.29 (22225) hydrogen bonds : bond 0.04986 / 3.38 ( 745) hydrogen bonds : angle 4.40278 / 3.12 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5735.18 seconds wall clock time: 98 minutes 21.79 seconds (5901.79 seconds total)