Starting phenix.real_space_refine on Fri Jul 3 17:13:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qnb_53242/07_2026/9qnb_53242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qnb_53242/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qnb_53242/07_2026/9qnb_53242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qnb_53242/07_2026/9qnb_53242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qnb_53242/07_2026/9qnb_53242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qnb_53242/07_2026/9qnb_53242.map" } 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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 3.02, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 581.0 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: 0.34 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: 1.97 Time building geometry restraints manager: 1.18 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.250 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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/Z covalent geometry : bond 0.00438 / 0.22 (15012) covalent geometry : angle 0.74861 / 0.33 (20294) hydrogen bonds : bond 0.15035 / 10.10 ( 697) hydrogen bonds : angle 5.92642 / 4.09 ( 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 : 0.338 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: 0.0987 time to fit residues: 25.5804 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 : 0.436 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3843 r_free = 0.3843 target = 0.137388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108386 restraints weight = 24732.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108823 restraints weight = 19054.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109443 restraints weight = 18802.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112323 restraints weight = 14272.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113102 restraints weight = 11134.356| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15012 Z= 0.111 Angle : 0.516 7.576 20294 Z= 0.250 Chirality : 0.041 0.170 2303 Planarity : 0.003 0.044 2632 Dihedral : 7.530 120.110 2186 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.80 % Rotamer: Outliers : 4.07 % Allowed : 28.35 % Favored : 67.58 % 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: 0.06 (0.20), residues: 1907 helix: 1.28 (0.18), residues: 898 sheet: 0.45 (0.34), residues: 238 loop : -1.65 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.009 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/Z covalent geometry : bond 0.00240 / 0.11 (15012) covalent geometry : angle 0.51625 / 0.25 (20294) hydrogen bonds : bond 0.03247 / 2.17 ( 697) hydrogen bonds : angle 4.28100 / 3.01 ( 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: 61 poor density : 164 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 TYR cc_start: 0.8498 (t80) cc_final: 0.8118 (t80) REVERT: E 158 MET cc_start: 0.8076 (mtp) cc_final: 0.7860 (mtp) REVERT: I 31 CYS cc_start: 0.7659 (p) cc_final: 0.7212 (p) REVERT: I 228 TYR cc_start: 0.8869 (m-80) cc_final: 0.8472 (m-80) REVERT: I 258 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6753 (mt-10) REVERT: K 84 MET cc_start: 0.6618 (mmm) cc_final: 0.5946 (ttt) outliers start: 61 outliers final: 36 residues processed: 217 average time/residue: 0.0939 time to fit residues: 31.4423 Evaluate side-chains 186 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER 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 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 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 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 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 253 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 168 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3844 r_free = 0.3844 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108351 restraints weight = 24801.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109145 restraints weight = 18940.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110246 restraints weight = 19510.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111448 restraints weight = 13633.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113018 restraints weight = 12275.845| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15012 Z= 0.110 Angle : 0.507 6.153 20294 Z= 0.246 Chirality : 0.040 0.138 2303 Planarity : 0.003 0.041 2632 Dihedral : 6.544 119.875 2177 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 4.67 % Allowed : 27.89 % Favored : 67.44 % 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: 0.10 (0.20), residues: 1907 helix: 1.30 (0.18), residues: 903 sheet: 0.49 (0.34), residues: 238 loop : -1.61 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 241 TYR 0.013 0.001 TYR K 216 PHE 0.014 0.001 PHE I 129 HIS 0.002 0.001 HIS G 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15012) covalent geometry : angle 0.50665 / 0.25 (20294) hydrogen bonds : bond 0.03066 / 2.06 ( 697) hydrogen bonds : angle 4.09761 / 2.89 ( 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 230 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 160 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7688 (mmt90) REVERT: C 103 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8723 (p) REVERT: C 315 TYR cc_start: 0.8492 (t80) cc_final: 0.8124 (t80) REVERT: E 158 MET cc_start: 0.7937 (mtp) cc_final: 0.7711 (mtp) REVERT: I 228 TYR cc_start: 0.8894 (m-80) cc_final: 0.8516 (m-80) REVERT: I 258 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6700 (mt-10) REVERT: K 84 MET cc_start: 0.6585 (mmm) cc_final: 0.5744 (ttt) outliers start: 70 outliers final: 43 residues processed: 225 average time/residue: 0.0957 time to fit residues: 33.2462 Evaluate side-chains 195 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 165 THR 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 223 SER 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 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 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 184 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: 4.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.136609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107287 restraints weight = 24796.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107977 restraints weight = 19120.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108818 restraints weight = 20703.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110327 restraints weight = 14127.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111679 restraints weight = 12482.102| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1081 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= 0.124 Angle : 0.514 6.075 20294 Z= 0.250 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.040 2632 Dihedral : 6.323 118.536 2177 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.65 % Rotamer: Outliers : 4.54 % Allowed : 28.22 % Favored : 67.24 % 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: 0.08 (0.20), residues: 1907 helix: 1.30 (0.18), residues: 903 sheet: 0.47 (0.34), residues: 238 loop : -1.64 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.011 0.001 TYR E 216 PHE 0.014 0.001 PHE K 129 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15012) covalent geometry : angle 0.51368 / 0.25 (20294) hydrogen bonds : bond 0.03090 / 2.08 ( 697) hydrogen bonds : angle 4.01281 / 2.83 ( 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: 68 poor density : 161 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7703 (mmt90) REVERT: C 103 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 315 TYR cc_start: 0.8495 (t80) cc_final: 0.8113 (t80) REVERT: E 158 MET cc_start: 0.8064 (mtp) cc_final: 0.7840 (mtp) REVERT: I 228 TYR cc_start: 0.8879 (m-80) cc_final: 0.8368 (m-80) REVERT: I 310 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6398 (mmt-90) REVERT: K 84 MET cc_start: 0.6551 (mmm) cc_final: 0.5867 (ttt) REVERT: K 99 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7737 (tt) REVERT: K 162 THR cc_start: 0.9415 (p) cc_final: 0.9137 (t) outliers start: 68 outliers final: 50 residues processed: 222 average time/residue: 0.0901 time to fit residues: 31.1408 Evaluate side-chains 207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 165 THR 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 223 SER Chi-restraints excluded: chain C residue 279 PHE 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 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 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 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 100 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 253 LEU 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 125 MET 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 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: 0.0030 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108668 restraints weight = 24662.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109625 restraints weight = 18659.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110309 restraints weight = 20609.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112134 restraints weight = 13690.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112975 restraints weight = 11822.082| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15012 Z= 0.100 Angle : 0.500 6.013 20294 Z= 0.242 Chirality : 0.040 0.135 2303 Planarity : 0.003 0.039 2632 Dihedral : 6.005 115.509 2173 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 4.20 % Allowed : 29.02 % Favored : 66.78 % 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: 0.21 (0.20), residues: 1907 helix: 1.34 (0.18), residues: 903 sheet: 0.25 (0.31), residues: 293 loop : -1.50 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 241 TYR 0.010 0.001 TYR E 216 PHE 0.017 0.001 PHE I 129 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (15012) covalent geometry : angle 0.50050 / 0.24 (20294) hydrogen bonds : bond 0.02759 / 1.85 ( 697) hydrogen bonds : angle 3.88425 / 2.73 ( 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 228 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7900 (mmt90) cc_final: 0.7691 (mmt90) REVERT: C 103 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8725 (p) REVERT: C 315 TYR cc_start: 0.8499 (t80) cc_final: 0.8110 (t80) REVERT: E 158 MET cc_start: 0.7998 (mtp) cc_final: 0.7793 (mtp) REVERT: I 228 TYR cc_start: 0.8837 (m-80) cc_final: 0.8527 (m-80) REVERT: I 310 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6246 (mmt-90) REVERT: K 84 MET cc_start: 0.6526 (mmm) cc_final: 0.5830 (ttt) outliers start: 63 outliers final: 52 residues processed: 220 average time/residue: 0.0935 time to fit residues: 31.5971 Evaluate side-chains 209 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 82 VAL 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 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 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 238 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 334 VAL 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 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 165 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: 0.9980 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3816 r_free = 0.3816 target = 0.135259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105728 restraints weight = 24845.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106336 restraints weight = 19745.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106947 restraints weight = 19359.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109770 restraints weight = 14815.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110278 restraints weight = 11587.637| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1257 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= 0.172 Angle : 0.548 6.298 20294 Z= 0.269 Chirality : 0.042 0.136 2303 Planarity : 0.003 0.040 2632 Dihedral : 6.086 112.870 2173 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 5.40 % Allowed : 28.42 % Favored : 66.18 % 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: 0.05 (0.20), residues: 1907 helix: 1.25 (0.18), residues: 903 sheet: 0.01 (0.31), residues: 293 loop : -1.56 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 299 TYR 0.014 0.001 TYR I 216 PHE 0.023 0.001 PHE K 129 HIS 0.004 0.001 HIS K 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (15012) covalent geometry : angle 0.54811 / 0.27 (20294) hydrogen bonds : bond 0.03472 / 2.33 ( 697) hydrogen bonds : angle 4.11003 / 2.90 ( 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 230 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 149 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7647 (mmt90) REVERT: C 103 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 133 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7972 (mttm) REVERT: C 315 TYR cc_start: 0.8556 (t80) cc_final: 0.8161 (t80) REVERT: E 158 MET cc_start: 0.8066 (mtp) cc_final: 0.7840 (mtp) REVERT: G 187 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: I 310 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6290 (mmt-90) REVERT: K 84 MET cc_start: 0.6396 (mmm) cc_final: 0.5756 (ttt) REVERT: K 99 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7713 (tt) REVERT: K 162 THR cc_start: 0.9458 (p) cc_final: 0.9171 (t) REVERT: K 216 TYR cc_start: 0.7347 (m-80) cc_final: 0.7123 (m-80) outliers start: 81 outliers final: 61 residues processed: 222 average time/residue: 0.0916 time to fit residues: 31.8244 Evaluate side-chains 211 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 145 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 180 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 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 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 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 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 125 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3793 r_free = 0.3793 target = 0.133466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103978 restraints weight = 24701.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104497 restraints weight = 19452.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105012 restraints weight = 20127.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107505 restraints weight = 15058.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108315 restraints weight = 11958.061| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15012 Z= 0.205 Angle : 0.579 6.446 20294 Z= 0.288 Chirality : 0.043 0.143 2303 Planarity : 0.004 0.040 2632 Dihedral : 6.239 109.599 2173 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % Rotamer: Outliers : 5.40 % Allowed : 28.62 % 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: -0.25 (0.19), residues: 1907 helix: 1.10 (0.18), residues: 896 sheet: 0.19 (0.34), residues: 229 loop : -1.83 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 299 TYR 0.015 0.001 TYR E 216 PHE 0.023 0.002 PHE I 129 HIS 0.005 0.001 HIS K 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (15012) covalent geometry : angle 0.57890 / 0.29 (20294) hydrogen bonds : bond 0.03922 / 2.64 ( 697) hydrogen bonds : angle 4.28883 / 3.03 ( 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 231 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 150 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 HIS cc_start: 0.8062 (m90) cc_final: 0.7803 (m90) REVERT: A 235 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7680 (mmt90) REVERT: C 103 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8798 (p) REVERT: C 133 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7990 (mttm) REVERT: C 315 TYR cc_start: 0.8588 (t80) cc_final: 0.8227 (t80) REVERT: E 158 MET cc_start: 0.8062 (mtp) cc_final: 0.7826 (mtp) REVERT: G 187 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: I 315 TYR cc_start: 0.8713 (t80) cc_final: 0.8484 (t80) REVERT: K 84 MET cc_start: 0.6423 (mmm) cc_final: 0.5864 (ttt) REVERT: K 99 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7782 (tt) REVERT: K 162 THR cc_start: 0.9494 (p) cc_final: 0.9197 (t) REVERT: K 216 TYR cc_start: 0.7310 (m-80) cc_final: 0.7065 (m-80) outliers start: 81 outliers final: 60 residues processed: 223 average time/residue: 0.0914 time to fit residues: 31.8020 Evaluate side-chains 213 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 253 LEU 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 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 125 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 48 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3801 r_free = 0.3801 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104493 restraints weight = 24800.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104914 restraints weight = 19952.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105486 restraints weight = 19917.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108201 restraints weight = 15200.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108673 restraints weight = 11943.630| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15012 Z= 0.182 Angle : 0.562 6.389 20294 Z= 0.278 Chirality : 0.042 0.139 2303 Planarity : 0.003 0.040 2632 Dihedral : 6.147 105.890 2173 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.97 % Rotamer: Outliers : 5.14 % Allowed : 28.75 % 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: -0.27 (0.19), residues: 1907 helix: 1.11 (0.18), residues: 898 sheet: -0.09 (0.34), residues: 240 loop : -1.81 (0.20), 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 0.014 0.001 PHE G 126 HIS 0.005 0.001 HIS K 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (15012) covalent geometry : angle 0.56176 / 0.28 (20294) hydrogen bonds : bond 0.03663 / 2.46 ( 697) hydrogen bonds : angle 4.22539 / 2.98 ( 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 232 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 155 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7914 (mmt90) cc_final: 0.7702 (mmt90) REVERT: C 103 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8760 (p) REVERT: C 133 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7994 (mttm) REVERT: C 315 TYR cc_start: 0.8567 (t80) cc_final: 0.8177 (t80) REVERT: E 158 MET cc_start: 0.8073 (mtp) cc_final: 0.7850 (mtp) REVERT: G 187 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: G 309 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7363 (p) REVERT: I 228 TYR cc_start: 0.8979 (m-80) cc_final: 0.8688 (m-80) REVERT: I 310 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6245 (mmt-90) REVERT: I 315 TYR cc_start: 0.8698 (t80) cc_final: 0.8468 (t80) REVERT: K 84 MET cc_start: 0.6419 (mmm) cc_final: 0.5864 (ttt) REVERT: K 99 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7787 (tt) REVERT: K 162 THR cc_start: 0.9476 (p) cc_final: 0.9201 (t) REVERT: K 216 TYR cc_start: 0.7214 (m-80) cc_final: 0.6901 (m-80) outliers start: 77 outliers final: 61 residues processed: 225 average time/residue: 0.0927 time to fit residues: 32.0934 Evaluate side-chains 215 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 142 VAL Chi-restraints excluded: chain E residue 163 GLU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 121 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** 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 = 0.3784 r_free = 0.3784 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103355 restraints weight = 25096.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104099 restraints weight = 20283.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104509 restraints weight = 21012.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106877 restraints weight = 15389.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107745 restraints weight = 12185.729| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15012 Z= 0.228 Angle : 0.609 6.564 20294 Z= 0.304 Chirality : 0.043 0.142 2303 Planarity : 0.004 0.039 2632 Dihedral : 6.288 104.690 2173 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 4.67 % Allowed : 29.02 % 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: -0.44 (0.19), residues: 1907 helix: 1.00 (0.18), residues: 895 sheet: -0.13 (0.34), residues: 229 loop : -1.90 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 299 TYR 0.017 0.001 TYR I 216 PHE 0.035 0.002 PHE A 129 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (15012) covalent geometry : angle 0.60861 / 0.30 (20294) hydrogen bonds : bond 0.04113 / 2.77 ( 697) hydrogen bonds : angle 4.40682 / 3.11 ( 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 220 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7645 (mmt90) REVERT: C 103 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8784 (p) REVERT: C 133 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7981 (mttm) REVERT: C 315 TYR cc_start: 0.8568 (t80) cc_final: 0.8185 (t80) REVERT: E 158 MET cc_start: 0.8112 (mtp) cc_final: 0.7885 (mtp) REVERT: G 187 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: G 309 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (p) REVERT: I 315 TYR cc_start: 0.8745 (t80) cc_final: 0.8494 (t80) REVERT: K 84 MET cc_start: 0.6438 (mmm) cc_final: 0.5817 (ttt) REVERT: K 162 THR cc_start: 0.9454 (p) cc_final: 0.9194 (t) REVERT: K 216 TYR cc_start: 0.7278 (m-80) cc_final: 0.7020 (m-80) outliers start: 70 outliers final: 63 residues processed: 213 average time/residue: 0.0964 time to fit residues: 31.7193 Evaluate side-chains 215 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 148 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 142 VAL Chi-restraints excluded: chain E residue 163 GLU 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 63 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 142 VAL 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 189 VAL 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 148 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107464 restraints weight = 24588.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107870 restraints weight = 19955.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108517 restraints weight = 19631.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111309 restraints weight = 14972.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112010 restraints weight = 11669.447| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15012 Z= 0.108 Angle : 0.542 8.392 20294 Z= 0.264 Chirality : 0.041 0.136 2303 Planarity : 0.003 0.040 2632 Dihedral : 5.926 98.177 2173 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.65 % Rotamer: Outliers : 3.40 % Allowed : 30.82 % Favored : 65.78 % 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: -0.14 (0.20), residues: 1907 helix: 1.21 (0.18), residues: 903 sheet: 0.03 (0.35), residues: 238 loop : -1.76 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 167 TYR 0.014 0.001 TYR E 216 PHE 0.010 0.001 PHE G 126 HIS 0.010 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15012) covalent geometry : angle 0.54174 / 0.26 (20294) hydrogen bonds : bond 0.02959 / 1.99 ( 697) hydrogen bonds : angle 4.04871 / 2.86 ( 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 209 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8767 (p) REVERT: C 133 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7905 (mttm) REVERT: C 315 TYR cc_start: 0.8562 (t80) cc_final: 0.8213 (t80) REVERT: G 309 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7344 (p) REVERT: I 228 TYR cc_start: 0.8875 (m-80) cc_final: 0.8524 (m-80) REVERT: I 258 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7301 (mt-10) REVERT: I 310 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6226 (mmt-90) REVERT: I 315 TYR cc_start: 0.8674 (t80) cc_final: 0.8421 (t80) REVERT: K 84 MET cc_start: 0.6322 (mmm) cc_final: 0.5911 (ttt) REVERT: K 162 THR cc_start: 0.9375 (p) cc_final: 0.9117 (t) REVERT: K 216 TYR cc_start: 0.7226 (m-80) cc_final: 0.6946 (m-80) outliers start: 51 outliers final: 44 residues processed: 205 average time/residue: 0.1018 time to fit residues: 31.7517 Evaluate side-chains 198 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.152412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123016 restraints weight = 24771.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125715 restraints weight = 15650.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127041 restraints weight = 12316.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127817 restraints weight = 11474.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127836 restraints weight = 10471.762| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15012 Z= 0.126 Angle : 0.549 8.452 20294 Z= 0.267 Chirality : 0.041 0.135 2303 Planarity : 0.003 0.043 2632 Dihedral : 5.826 93.650 2173 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 3.34 % Allowed : 30.69 % 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: -0.06 (0.20), residues: 1907 helix: 1.24 (0.18), residues: 903 sheet: -0.32 (0.31), residues: 300 loop : -1.60 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.013 0.001 TYR E 216 PHE 0.040 0.001 PHE A 129 HIS 0.009 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15012) covalent geometry : angle 0.54914 / 0.27 (20294) hydrogen bonds : bond 0.03093 / 2.08 ( 697) hydrogen bonds : angle 4.02557 / 2.84 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.49 seconds wall clock time: 32 minutes 38.94 seconds (1958.94 seconds total)