Starting phenix.real_space_refine on Thu Feb 5 04:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.map" model { file = "/net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnb_53242/02_2026/9qnb_53242.cif" } resolution = 3.63 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= 0.005 sd= 0.098 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 6 8.98 5 P 12 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 9225 2.51 5 N 2609 2.21 5 O 2855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14791 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2438 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2438 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2438 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2438 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2438 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2427 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' K': 2, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.64, per 1000 atoms: 0.25 Number of scatterers: 14791 At special positions: 0 Unit cell: (117.72, 118.8, 172.8, 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 6 19.00 S 78 16.00 P 12 15.00 Mg 6 11.99 O 2855 8.00 N 2609 7.00 C 9225 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: 0.95 Conformation dependent library (CDL) restraints added in 769.5 milliseconds 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3502 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 14 sheets defined 49.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.536A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.508A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.696A pdb=" N GLU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.747A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.074A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.780A pdb=" N ILE C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.610A pdb=" N LYS C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 4.155A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.740A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.653A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.985A pdb=" N GLU E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 30' Processing helix chain 'E' and resid 34 through 45 removed outlier: 3.563A pdb=" N VAL E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.601A pdb=" N VAL E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.612A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 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 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 179 removed outlier: 4.166A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 189 removed outlier: 3.539A pdb=" N VAL E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.657A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.511A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 34 through 45 removed outlier: 3.735A pdb=" N VAL G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.940A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.717A pdb=" N GLU G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.603A pdb=" N GLU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 113 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 167 through 179 removed outlier: 4.041A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 187 Processing helix chain 'G' and resid 196 through 214 removed outlier: 4.028A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.615A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'I' and resid 24 through 32 Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 98 Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 169 through 179 Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 212 removed outlier: 3.622A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'K' and resid 24 through 31 Processing helix chain 'K' and resid 34 through 45 removed outlier: 3.688A pdb=" N VAL K 38 " --> pdb=" O ASN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.649A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 88 through 98 removed outlier: 3.582A pdb=" N GLU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 167 through 178 removed outlier: 3.976A 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 214 Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.719A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 292 through 296 removed outlier: 3.889A pdb=" N ALA K 295 " --> pdb=" O ILE K 292 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER K 296 " --> pdb=" O ALA K 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 292 through 296' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.591A pdb=" N ALA C 157 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ALA C 192 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR C 159 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 220 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP C 222 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 265 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 310 " --> pdb=" O PHE C 327 " (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: 6.812A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 217 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 264 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 266 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 221 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLN A 268 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 298 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 310 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.514A pdb=" N TYR E 159 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE E 220 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR E 266 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL E 221 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N GLN E 268 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 265 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 127 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.774A pdb=" N ALA G 190 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N GLN G 268 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG G 310 " --> pdb=" O PHE G 327 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE G 327 " --> pdb=" O ARG G 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.708A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I 220 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP I 222 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'I' and resid 87 through 88 removed outlier: 5.648A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP K 222 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG K 310 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE K 327 " --> pdb=" O ARG K 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'I' and resid 327 through 330 Processing sheet with id=AB5, first strand: chain 'K' and resid 101 through 102 697 hydrogen bonds defined for protein. 1944 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: 2.39 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5018 1.34 - 1.46: 2973 1.46 - 1.58: 6871 1.58 - 1.70: 24 1.70 - 1.81: 126 Bond restraints: 15012 Sorted by residual: bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C4 ADP K 402 " pdb=" C5 ADP K 402 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C4 ADP I 402 " pdb=" C5 ADP I 402 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C4 ADP E 402 " pdb=" C5 ADP E 402 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 15007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 20134 3.26 - 6.53: 109 6.53 - 9.79: 39 9.79 - 13.06: 6 13.06 - 16.32: 6 Bond angle restraints: 20294 Sorted by residual: angle pdb=" PA ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sigma weight residual 120.50 136.82 -16.32 3.00e+00 1.11e-01 2.96e+01 angle pdb=" PA ADP I 402 " pdb=" O3A ADP I 402 " pdb=" PB ADP I 402 " ideal model delta sigma weight residual 120.50 136.80 -16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" PA ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PB ADP A 402 " ideal model delta sigma weight residual 120.50 136.79 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" PA ADP K 402 " pdb=" O3A ADP K 402 " pdb=" PB ADP K 402 " ideal model delta sigma weight residual 120.50 136.72 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" PA ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sigma weight residual 120.50 136.71 -16.21 3.00e+00 1.11e-01 2.92e+01 ... (remaining 20289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 8105 23.18 - 46.37: 825 46.37 - 69.55: 125 69.55 - 92.73: 30 92.73 - 115.92: 6 Dihedral angle restraints: 9091 sinusoidal: 3616 harmonic: 5475 Sorted by residual: dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 -175.91 115.92 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O2A ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PA ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -169.24 109.24 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O1B ADP K 402 " pdb=" O3A ADP K 402 " pdb=" PB ADP K 402 " pdb=" PA ADP K 402 " ideal model delta sinusoidal sigma weight residual -60.00 46.84 -106.85 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 9088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1766 0.043 - 0.085: 374 0.085 - 0.127: 147 0.127 - 0.170: 15 0.170 - 0.212: 1 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CB THR G 225 " pdb=" CA THR G 225 " pdb=" OG1 THR G 225 " pdb=" CG2 THR G 225 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU C 203 " pdb=" CB LEU C 203 " pdb=" CD1 LEU C 203 " pdb=" CD2 LEU C 203 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C2' ADP G 402 " pdb=" C1' ADP G 402 " pdb=" C3' ADP G 402 " pdb=" O2' ADP G 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2300 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 167 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO I 168 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO I 168 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 168 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 161 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" CG ASP A 161 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 161 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 161 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 282 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO G 283 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 283 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 283 " -0.022 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.61: 24 2.61 - 3.24: 14500 3.24 - 3.88: 27472 3.88 - 4.51: 35751 4.51 - 5.14: 58606 Nonbonded interactions: 136353 Sorted by model distance: nonbonded pdb=" OG1 THR E 134 " pdb="MG MG E 401 " model vdw 1.981 2.170 nonbonded pdb="MG MG E 401 " pdb=" O3B ADP E 402 " model vdw 2.010 2.170 nonbonded pdb="MG MG G 401 " pdb=" O1B ADP G 402 " model vdw 2.017 2.170 nonbonded pdb="MG MG I 401 " pdb=" O3B ADP I 402 " model vdw 2.022 2.170 nonbonded pdb="MG MG A 401 " pdb=" O3B ADP A 402 " model vdw 2.024 2.170 ... (remaining 136348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 402) selection = (chain 'C' and resid 21 through 402) selection = (chain 'E' and resid 21 through 402) selection = (chain 'G' and resid 21 through 402) selection = (chain 'I' and resid 21 through 402) selection = chain 'K' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.004 0.105 15012 Z= 0.218 Angle : 0.749 16.321 20294 Z= 0.329 Chirality : 0.041 0.212 2303 Planarity : 0.003 0.043 2632 Dihedral : 18.491 115.915 5589 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 0.80 % Allowed : 31.82 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.03 (0.19), residues: 1907 helix: 1.29 (0.19), residues: 846 sheet: 0.43 (0.34), residues: 233 loop : -1.59 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 130 TYR 0.011 0.001 TYR E 216 PHE 0.013 0.001 PHE K 129 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00438 (15012) covalent geometry : angle 0.74861 (20294) hydrogen bonds : bond 0.15035 ( 697) hydrogen bonds : angle 5.92642 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: C 315 TYR cc_start: 0.8411 (t80) cc_final: 0.8036 (t80) REVERT: E 158 MET cc_start: 0.8012 (mtp) cc_final: 0.7771 (mtp) REVERT: G 187 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: I 258 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6829 (mt-10) REVERT: K 84 MET cc_start: 0.6545 (mmm) cc_final: 0.5934 (ttt) REVERT: K 162 THR cc_start: 0.9367 (p) cc_final: 0.9112 (t) outliers start: 12 outliers final: 10 residues processed: 169 average time/residue: 0.1093 time to fit residues: 27.9918 Evaluate side-chains 162 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107132 restraints weight = 24787.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107788 restraints weight = 19113.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108565 restraints weight = 21112.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110077 restraints weight = 14260.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111011 restraints weight = 12576.718| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15012 Z= 0.140 Angle : 0.533 7.144 20294 Z= 0.262 Chirality : 0.041 0.172 2303 Planarity : 0.003 0.045 2632 Dihedral : 7.759 121.387 2186 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.65 % Rotamer: Outliers : 4.40 % Allowed : 28.09 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.02 (0.20), residues: 1907 helix: 1.24 (0.18), residues: 898 sheet: 0.35 (0.34), residues: 238 loop : -1.62 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.010 0.001 TYR E 216 PHE 0.022 0.001 PHE K 129 HIS 0.004 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00311 (15012) covalent geometry : angle 0.53321 (20294) hydrogen bonds : bond 0.03665 ( 697) hydrogen bonds : angle 4.43932 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 TYR cc_start: 0.8512 (t80) cc_final: 0.8143 (t80) REVERT: E 158 MET cc_start: 0.8020 (mtp) cc_final: 0.7759 (mtp) REVERT: I 31 CYS cc_start: 0.7661 (p) cc_final: 0.7215 (p) REVERT: I 228 TYR cc_start: 0.8954 (m-80) cc_final: 0.8552 (m-80) REVERT: I 258 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6691 (mt-10) REVERT: K 84 MET cc_start: 0.6556 (mmm) cc_final: 0.5954 (ttt) REVERT: K 99 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7780 (tt) REVERT: K 162 THR cc_start: 0.9461 (p) cc_final: 0.9167 (t) outliers start: 66 outliers final: 44 residues processed: 218 average time/residue: 0.1116 time to fit residues: 37.2936 Evaluate side-chains 194 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107739 restraints weight = 24749.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108430 restraints weight = 19325.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109473 restraints weight = 20380.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110681 restraints weight = 14104.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112150 restraints weight = 12690.508| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15012 Z= 0.127 Angle : 0.517 6.047 20294 Z= 0.253 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.042 2632 Dihedral : 6.813 120.304 2180 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 4.94 % Allowed : 28.22 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.01 (0.20), residues: 1907 helix: 1.23 (0.18), residues: 898 sheet: 0.32 (0.34), residues: 238 loop : -1.64 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.011 0.001 TYR E 216 PHE 0.013 0.001 PHE I 129 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00286 (15012) covalent geometry : angle 0.51746 (20294) hydrogen bonds : bond 0.03307 ( 697) hydrogen bonds : angle 4.20427 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7954 (mmt90) cc_final: 0.7715 (mmt90) REVERT: C 103 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 315 TYR cc_start: 0.8511 (t80) cc_final: 0.8151 (t80) REVERT: E 158 MET cc_start: 0.7972 (mtp) cc_final: 0.7725 (mtp) REVERT: I 228 TYR cc_start: 0.8925 (m-80) cc_final: 0.8699 (m-80) REVERT: I 258 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6734 (mt-10) REVERT: K 84 MET cc_start: 0.6558 (mmm) cc_final: 0.5770 (ttt) REVERT: K 162 THR cc_start: 0.9404 (p) cc_final: 0.9107 (t) outliers start: 74 outliers final: 46 residues processed: 231 average time/residue: 0.1137 time to fit residues: 40.4872 Evaluate side-chains 197 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 279 PHE Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.136959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107550 restraints weight = 24718.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107990 restraints weight = 19009.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108782 restraints weight = 17909.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112632 restraints weight = 13961.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112937 restraints weight = 10152.495| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15012 Z= 0.118 Angle : 0.513 6.102 20294 Z= 0.250 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.041 2632 Dihedral : 6.532 118.873 2180 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 4.74 % Allowed : 28.55 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.00 (0.20), residues: 1907 helix: 1.23 (0.18), residues: 903 sheet: 0.37 (0.34), residues: 238 loop : -1.66 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 241 TYR 0.012 0.001 TYR E 216 PHE 0.017 0.001 PHE K 129 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00264 (15012) covalent geometry : angle 0.51345 (20294) hydrogen bonds : bond 0.03082 ( 697) hydrogen bonds : angle 4.06700 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 158 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.8050 (m90) cc_final: 0.7830 (m90) REVERT: A 235 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7722 (mmt90) REVERT: C 103 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (p) REVERT: C 315 TYR cc_start: 0.8506 (t80) cc_final: 0.8096 (t80) REVERT: E 158 MET cc_start: 0.8098 (mtp) cc_final: 0.7884 (mtp) REVERT: G 187 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: I 228 TYR cc_start: 0.8846 (m-80) cc_final: 0.8644 (m-80) REVERT: I 310 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6270 (mmt-90) REVERT: K 84 MET cc_start: 0.6554 (mmm) cc_final: 0.5840 (ttt) REVERT: K 99 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7684 (tt) REVERT: K 162 THR cc_start: 0.9426 (p) cc_final: 0.9118 (t) outliers start: 71 outliers final: 53 residues processed: 223 average time/residue: 0.1079 time to fit residues: 37.1081 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 10.0000 chunk 41 optimal weight: 0.1980 chunk 85 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 120 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107291 restraints weight = 24752.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108063 restraints weight = 19222.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108902 restraints weight = 20908.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110504 restraints weight = 14040.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111417 restraints weight = 12354.480| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15012 Z= 0.120 Angle : 0.512 6.087 20294 Z= 0.250 Chirality : 0.041 0.136 2303 Planarity : 0.003 0.041 2632 Dihedral : 6.249 116.260 2177 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.60 % Rotamer: Outliers : 5.60 % Allowed : 27.95 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: 0.01 (0.20), residues: 1907 helix: 1.24 (0.18), residues: 903 sheet: 0.39 (0.34), residues: 238 loop : -1.67 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.012 0.001 TYR E 216 PHE 0.013 0.001 PHE I 129 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00269 (15012) covalent geometry : angle 0.51218 (20294) hydrogen bonds : bond 0.03035 ( 697) hydrogen bonds : angle 3.99889 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 160 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7633 (mmt90) REVERT: C 103 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (p) REVERT: C 133 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7887 (mttm) REVERT: C 315 TYR cc_start: 0.8508 (t80) cc_final: 0.8115 (t80) REVERT: E 158 MET cc_start: 0.7960 (mtp) cc_final: 0.7739 (mtp) REVERT: G 187 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: I 228 TYR cc_start: 0.8862 (m-80) cc_final: 0.8509 (m-80) REVERT: I 310 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6276 (mmt-90) REVERT: K 84 MET cc_start: 0.6529 (mmm) cc_final: 0.5785 (ttt) REVERT: K 99 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7734 (tt) REVERT: K 162 THR cc_start: 0.9377 (p) cc_final: 0.9088 (t) outliers start: 84 outliers final: 66 residues processed: 235 average time/residue: 0.1113 time to fit residues: 40.1926 Evaluate side-chains 223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 188 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107031 restraints weight = 24724.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107850 restraints weight = 19501.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108596 restraints weight = 21319.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110136 restraints weight = 14415.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111044 restraints weight = 12663.446| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15012 Z= 0.131 Angle : 0.520 6.115 20294 Z= 0.254 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.040 2632 Dihedral : 6.131 112.412 2175 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 5.40 % Allowed : 28.09 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.01 (0.20), residues: 1907 helix: 1.23 (0.18), residues: 903 sheet: 0.36 (0.34), residues: 238 loop : -1.68 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 167 TYR 0.012 0.001 TYR E 216 PHE 0.018 0.001 PHE K 129 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00297 (15012) covalent geometry : angle 0.52029 (20294) hydrogen bonds : bond 0.03133 ( 697) hydrogen bonds : angle 4.01495 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 157 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.7934 (m-70) cc_final: 0.7685 (m90) REVERT: A 235 ARG cc_start: 0.7864 (mmt90) cc_final: 0.7637 (mmt90) REVERT: C 103 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8742 (p) REVERT: C 315 TYR cc_start: 0.8555 (t80) cc_final: 0.8182 (t80) REVERT: E 158 MET cc_start: 0.8001 (mtp) cc_final: 0.7781 (mtp) REVERT: G 187 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: I 310 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6274 (mmt-90) REVERT: K 84 MET cc_start: 0.6375 (mmm) cc_final: 0.5671 (ttt) REVERT: K 99 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7728 (tt) REVERT: K 162 THR cc_start: 0.9412 (p) cc_final: 0.9099 (t) outliers start: 81 outliers final: 64 residues processed: 232 average time/residue: 0.1008 time to fit residues: 36.3664 Evaluate side-chains 219 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104658 restraints weight = 24638.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105396 restraints weight = 19466.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106130 restraints weight = 20510.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108044 restraints weight = 14493.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.108454 restraints weight = 12398.792| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15012 Z= 0.187 Angle : 0.563 6.347 20294 Z= 0.279 Chirality : 0.042 0.140 2303 Planarity : 0.004 0.041 2632 Dihedral : 6.143 109.545 2173 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.91 % Rotamer: Outliers : 5.34 % Allowed : 28.35 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.17 (0.19), residues: 1907 helix: 1.13 (0.18), residues: 898 sheet: 0.10 (0.34), residues: 240 loop : -1.72 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 299 TYR 0.015 0.001 TYR E 216 PHE 0.020 0.002 PHE K 129 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00429 (15012) covalent geometry : angle 0.56275 (20294) hydrogen bonds : bond 0.03717 ( 697) hydrogen bonds : angle 4.21294 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.7838 (m-70) cc_final: 0.7512 (m90) REVERT: A 235 ARG cc_start: 0.7874 (mmt90) cc_final: 0.7664 (mmt90) REVERT: C 103 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 315 TYR cc_start: 0.8567 (t80) cc_final: 0.8212 (t80) REVERT: E 158 MET cc_start: 0.8059 (mtp) cc_final: 0.7832 (mtp) REVERT: G 187 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: K 84 MET cc_start: 0.6367 (mmm) cc_final: 0.5886 (ttt) REVERT: K 99 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7773 (tt) REVERT: K 216 TYR cc_start: 0.7386 (m-80) cc_final: 0.7104 (m-80) outliers start: 80 outliers final: 61 residues processed: 226 average time/residue: 0.0997 time to fit residues: 35.1338 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104679 restraints weight = 24717.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105327 restraints weight = 19405.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106057 restraints weight = 20465.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108026 restraints weight = 14499.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108361 restraints weight = 12375.638| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15012 Z= 0.180 Angle : 0.559 6.404 20294 Z= 0.277 Chirality : 0.042 0.140 2303 Planarity : 0.003 0.041 2632 Dihedral : 6.115 105.976 2173 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 5.20 % Allowed : 28.69 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.24 (0.19), residues: 1907 helix: 1.10 (0.18), residues: 898 sheet: -0.03 (0.34), residues: 240 loop : -1.75 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 299 TYR 0.015 0.001 TYR E 216 PHE 0.027 0.002 PHE I 129 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00414 (15012) covalent geometry : angle 0.55925 (20294) hydrogen bonds : bond 0.03626 ( 697) hydrogen bonds : angle 4.21231 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 155 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 138 HIS cc_start: 0.7822 (m-70) cc_final: 0.7509 (m90) REVERT: A 235 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7694 (mmt90) REVERT: C 103 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 133 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8001 (mttm) REVERT: C 315 TYR cc_start: 0.8557 (t80) cc_final: 0.8172 (t80) REVERT: E 158 MET cc_start: 0.8058 (mtp) cc_final: 0.7836 (mtp) REVERT: G 187 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: I 228 TYR cc_start: 0.8976 (m-80) cc_final: 0.8689 (m-80) REVERT: I 258 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7248 (mt-10) REVERT: I 310 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6218 (mmt-90) REVERT: I 315 TYR cc_start: 0.8702 (t80) cc_final: 0.8486 (t80) REVERT: K 84 MET cc_start: 0.6373 (mmm) cc_final: 0.5930 (ttt) REVERT: K 99 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7782 (tt) REVERT: K 162 THR cc_start: 0.9436 (p) cc_final: 0.9130 (t) REVERT: K 216 TYR cc_start: 0.7336 (m-80) cc_final: 0.7086 (m-80) outliers start: 78 outliers final: 62 residues processed: 227 average time/residue: 0.0989 time to fit residues: 34.7983 Evaluate side-chains 219 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 152 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107239 restraints weight = 24829.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107982 restraints weight = 19213.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108519 restraints weight = 19038.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111123 restraints weight = 14364.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112217 restraints weight = 11375.472| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15012 Z= 0.111 Angle : 0.524 6.836 20294 Z= 0.255 Chirality : 0.040 0.134 2303 Planarity : 0.003 0.041 2632 Dihedral : 5.843 99.398 2173 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 3.94 % Allowed : 29.95 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.03 (0.20), residues: 1907 helix: 1.26 (0.18), residues: 900 sheet: 0.40 (0.35), residues: 227 loop : -1.73 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 241 TYR 0.012 0.001 TYR E 216 PHE 0.028 0.001 PHE K 129 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00250 (15012) covalent geometry : angle 0.52447 (20294) hydrogen bonds : bond 0.02891 ( 697) hydrogen bonds : angle 3.97630 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.7772 (m-70) cc_final: 0.7409 (m90) REVERT: C 103 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (p) REVERT: C 133 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7790 (mttm) REVERT: C 315 TYR cc_start: 0.8575 (t80) cc_final: 0.8189 (t80) REVERT: E 158 MET cc_start: 0.8011 (mtp) cc_final: 0.7781 (mtp) REVERT: G 187 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: I 228 TYR cc_start: 0.8867 (m-80) cc_final: 0.8479 (m-80) REVERT: I 258 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7318 (mt-10) REVERT: I 310 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6254 (mmt-90) REVERT: K 84 MET cc_start: 0.6382 (mmm) cc_final: 0.5863 (ttt) REVERT: K 162 THR cc_start: 0.9414 (p) cc_final: 0.9127 (t) outliers start: 59 outliers final: 53 residues processed: 215 average time/residue: 0.1025 time to fit residues: 33.9401 Evaluate side-chains 212 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 92 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107522 restraints weight = 24736.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108296 restraints weight = 19210.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109207 restraints weight = 20409.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110527 restraints weight = 14146.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111545 restraints weight = 12605.702| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 15012 Z= 0.131 Angle : 0.741 59.199 20294 Z= 0.413 Chirality : 0.041 0.381 2303 Planarity : 0.003 0.042 2632 Dihedral : 5.855 99.364 2173 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 4.07 % Allowed : 29.95 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.02 (0.20), residues: 1907 helix: 1.26 (0.18), residues: 900 sheet: 0.43 (0.35), residues: 227 loop : -1.74 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 27 TYR 0.011 0.001 TYR E 216 PHE 0.021 0.001 PHE E 259 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00302 (15012) covalent geometry : angle 0.74094 (20294) hydrogen bonds : bond 0.02882 ( 697) hydrogen bonds : angle 3.97222 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.7682 (m-70) cc_final: 0.7350 (m90) REVERT: C 103 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8708 (p) REVERT: C 133 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7900 (mttm) REVERT: C 315 TYR cc_start: 0.8567 (t80) cc_final: 0.8202 (t80) REVERT: E 158 MET cc_start: 0.7940 (mtp) cc_final: 0.7719 (mtp) REVERT: G 187 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: I 228 TYR cc_start: 0.8891 (m-80) cc_final: 0.8532 (m-80) REVERT: I 258 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7270 (mt-10) REVERT: I 310 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6273 (mmt-90) REVERT: K 84 MET cc_start: 0.6352 (mmm) cc_final: 0.5850 (ttt) REVERT: K 162 THR cc_start: 0.9393 (p) cc_final: 0.9109 (t) outliers start: 61 outliers final: 55 residues processed: 212 average time/residue: 0.1030 time to fit residues: 33.5013 Evaluate side-chains 213 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain K residue 31 CYS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 160 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.136812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107593 restraints weight = 24670.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108250 restraints weight = 19595.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108836 restraints weight = 19158.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111540 restraints weight = 14638.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112434 restraints weight = 11492.518| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 15012 Z= 0.136 Angle : 0.679 47.023 20294 Z= 0.371 Chirality : 0.041 0.453 2303 Planarity : 0.003 0.042 2632 Dihedral : 5.855 99.364 2173 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 3.94 % Allowed : 30.02 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % 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: -0.02 (0.20), residues: 1907 helix: 1.26 (0.18), residues: 900 sheet: 0.43 (0.35), residues: 227 loop : -1.74 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 27 TYR 0.011 0.001 TYR E 216 PHE 0.021 0.001 PHE E 259 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00310 (15012) covalent geometry : angle 0.67940 (20294) hydrogen bonds : bond 0.02882 ( 697) hydrogen bonds : angle 3.97222 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.97 seconds wall clock time: 34 minutes 40.10 seconds (2080.10 seconds total)