Starting phenix.real_space_refine on Sun Jun 29 19:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.map" model { file = "/net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tu5_26126/06_2025/7tu5_26126.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19206 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 42 5.16 5 C 12624 2.51 5 N 3396 2.21 5 O 3588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.44, per 1000 atoms: 0.38 Number of scatterers: 19656 At special positions: 0 Unit cell: (125.97, 133.722, 98.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 Mg 6 11.99 O 3588 8.00 N 3396 7.00 C 12624 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: 5.12 Conformation dependent library (CDL) restraints added in 2.9 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 64 through 91 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS A 208 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 325 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.769A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 64 through 91 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.631A pdb=" N PHE B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG B 142 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 147 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS B 208 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 298 through 325 Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 64 through 91 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG C 142 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 145 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 147 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS C 208 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 228 Processing helix chain 'C' and resid 243 through 268 removed outlier: 3.761A pdb=" N TYR C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 325 Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 64 through 91 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG D 142 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS D 208 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 325 Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 64 through 91 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG E 142 " --> pdb=" O TYR E 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP E 145 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 147 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS E 208 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 228 Processing helix chain 'E' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR E 247 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 261 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 325 Processing helix chain 'E' and resid 325 through 332 Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 411 through 425 Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 64 through 91 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG F 142 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 147 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS F 208 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 228 Processing helix chain 'F' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR F 247 " --> pdb=" O HIS F 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 4.191A pdb=" N ALA F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU F 283 " --> pdb=" O TYR F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 298 through 325 Processing helix chain 'F' and resid 325 through 332 Processing helix chain 'F' and resid 338 through 342 Processing helix chain 'F' and resid 344 through 359 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 411 through 425 Processing helix chain 'F' and resid 427 through 439 1237 hydrogen bonds defined for protein. 3567 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: 6.09 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3192 1.29 - 1.42: 5292 1.42 - 1.55: 11459 1.55 - 1.68: 19 1.68 - 1.81: 66 Bond restraints: 20028 Sorted by residual: bond pdb=" C ARG B 77 " pdb=" O ARG B 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.29e+01 bond pdb=" C ARG E 77 " pdb=" O ARG E 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.28e+01 bond pdb=" C ARG C 77 " pdb=" O ARG C 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.27e+01 bond pdb=" C ARG F 77 " pdb=" O ARG F 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 ... (remaining 20023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 25814 1.85 - 3.71: 975 3.71 - 5.56: 279 5.56 - 7.42: 34 7.42 - 9.27: 6 Bond angle restraints: 27108 Sorted by residual: angle pdb=" N HIS E 63 " pdb=" CA HIS E 63 " pdb=" C HIS E 63 " ideal model delta sigma weight residual 110.10 119.37 -9.27 1.49e+00 4.50e-01 3.87e+01 angle pdb=" N HIS A 63 " pdb=" CA HIS A 63 " pdb=" C HIS A 63 " ideal model delta sigma weight residual 110.10 119.35 -9.25 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N HIS C 63 " pdb=" CA HIS C 63 " pdb=" C HIS C 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS B 63 " pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS D 63 " pdb=" CA HIS D 63 " pdb=" C HIS D 63 " ideal model delta sigma weight residual 110.10 119.32 -9.22 1.49e+00 4.50e-01 3.83e+01 ... (remaining 27103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 10464 17.18 - 34.36: 1086 34.36 - 51.55: 288 51.55 - 68.73: 78 68.73 - 85.91: 24 Dihedral angle restraints: 11940 sinusoidal: 4446 harmonic: 7494 Sorted by residual: dihedral pdb=" C ILE F 260 " pdb=" N ILE F 260 " pdb=" CA ILE F 260 " pdb=" CB ILE F 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE B 260 " pdb=" N ILE B 260 " pdb=" CA ILE B 260 " pdb=" CB ILE B 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE A 260 " pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta harmonic sigma weight residual -122.00 -134.50 12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 11937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2824 0.091 - 0.183: 181 0.183 - 0.274: 31 0.274 - 0.366: 26 0.366 - 0.457: 16 Chirality restraints: 3078 Sorted by residual: chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE F 260 " pdb=" N ILE F 260 " pdb=" C ILE F 260 " pdb=" CB ILE F 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE A 260 " pdb=" N ILE A 260 " pdb=" C ILE A 260 " pdb=" CB ILE A 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 3075 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 259 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE F 259 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE F 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 259 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ILE D 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE D 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 259 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ILE B 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE B 260 " -0.017 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 54 2.51 - 3.11: 14099 3.11 - 3.70: 30873 3.70 - 4.30: 45208 4.30 - 4.90: 76609 Nonbonded interactions: 166843 Sorted by model distance: nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS B 116 " pdb="MG MG B 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 601 " model vdw 1.911 2.250 ... (remaining 166838 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 40.870 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.072 20028 Z= 0.624 Angle : 0.846 9.271 27108 Z= 0.543 Chirality : 0.064 0.457 3078 Planarity : 0.005 0.049 3456 Dihedral : 15.879 85.912 7140 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.54 % Allowed : 15.43 % Favored : 83.02 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2538 helix: 0.86 (0.13), residues: 1662 sheet: None (None), residues: 0 loop : -0.26 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 240 HIS 0.009 0.001 HIS F 63 PHE 0.022 0.001 PHE D 158 TYR 0.021 0.002 TYR E 305 ARG 0.011 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.15063 ( 1237) hydrogen bonds : angle 4.99010 ( 3567) covalent geometry : bond 0.00927 (20028) covalent geometry : angle 0.84565 (27108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 582 time to evaluate : 2.170 Fit side-chains REVERT: B 220 PHE cc_start: 0.7959 (t80) cc_final: 0.7728 (t80) REVERT: C 261 ASP cc_start: 0.7070 (m-30) cc_final: 0.6648 (m-30) REVERT: D 261 ASP cc_start: 0.6989 (m-30) cc_final: 0.6678 (m-30) REVERT: E 261 ASP cc_start: 0.7121 (m-30) cc_final: 0.6686 (m-30) outliers start: 30 outliers final: 7 residues processed: 589 average time/residue: 1.5146 time to fit residues: 988.2019 Evaluate side-chains 539 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 532 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 161 ASN B 153 GLN C 393 HIS D 3 ASN D 153 GLN D 343 ASN E 3 ASN E 161 ASN F 3 ASN F 343 ASN F 347 GLN F 393 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118881 restraints weight = 22470.443| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.15 r_work: 0.3548 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20028 Z= 0.119 Angle : 0.442 4.756 27108 Z= 0.243 Chirality : 0.035 0.146 3078 Planarity : 0.004 0.038 3456 Dihedral : 4.130 54.166 2831 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.19 % Allowed : 16.87 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2538 helix: 1.73 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.14 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 240 HIS 0.004 0.001 HIS A 393 PHE 0.013 0.001 PHE F 220 TYR 0.017 0.001 TYR B 305 ARG 0.007 0.000 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 1237) hydrogen bonds : angle 3.67573 ( 3567) covalent geometry : bond 0.00263 (20028) covalent geometry : angle 0.44156 (27108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 554 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7632 (m-30) cc_final: 0.7430 (m-30) REVERT: A 323 MET cc_start: 0.8581 (mmt) cc_final: 0.8246 (mmt) REVERT: B 373 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7934 (t80) outliers start: 62 outliers final: 20 residues processed: 587 average time/residue: 1.5439 time to fit residues: 1002.3607 Evaluate side-chains 563 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 542 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 400 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 389 ASN A 395 ASN B 153 GLN B 267 ASN B 395 ASN C 153 GLN C 389 ASN C 393 HIS C 395 ASN D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 153 GLN E 161 ASN E 395 ASN F 170 GLN F 343 ASN F 395 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.115772 restraints weight = 22261.454| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.15 r_work: 0.3499 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20028 Z= 0.173 Angle : 0.485 4.944 27108 Z= 0.262 Chirality : 0.038 0.142 3078 Planarity : 0.004 0.039 3456 Dihedral : 3.826 33.845 2821 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.62 % Allowed : 18.26 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.16), residues: 2538 helix: 1.65 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.03 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 240 HIS 0.005 0.001 HIS E 393 PHE 0.018 0.001 PHE C 220 TYR 0.017 0.002 TYR B 305 ARG 0.007 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 1237) hydrogen bonds : angle 3.72793 ( 3567) covalent geometry : bond 0.00411 (20028) covalent geometry : angle 0.48476 (27108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 558 time to evaluate : 2.148 Fit side-chains REVERT: D 136 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (tttm) outliers start: 51 outliers final: 23 residues processed: 584 average time/residue: 1.5295 time to fit residues: 990.5992 Evaluate side-chains 579 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 555 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 144 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 343 ASN A 389 ASN B 161 ASN C 3 ASN C 161 ASN C 345 GLN C 393 HIS D 3 ASN D 161 ASN D 176 GLN D 343 ASN E 3 ASN E 161 ASN E 214 GLN F 120 ASN F 267 ASN F 343 ASN F 353 ASN F 415 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115442 restraints weight = 22338.206| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.16 r_work: 0.3493 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20028 Z= 0.170 Angle : 0.478 4.847 27108 Z= 0.258 Chirality : 0.038 0.152 3078 Planarity : 0.004 0.038 3456 Dihedral : 3.761 22.838 2817 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.52 % Allowed : 19.08 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2538 helix: 1.61 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.05 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.005 0.001 HIS E 393 PHE 0.019 0.001 PHE C 220 TYR 0.014 0.001 TYR B 305 ARG 0.008 0.000 ARG D 433 Details of bonding type rmsd hydrogen bonds : bond 0.05155 ( 1237) hydrogen bonds : angle 3.72326 ( 3567) covalent geometry : bond 0.00407 (20028) covalent geometry : angle 0.47791 (27108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 572 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8185 (tttm) REVERT: D 136 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (tmtm) REVERT: E 150 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: F 176 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8254 (mp10) outliers start: 49 outliers final: 25 residues processed: 601 average time/residue: 1.4593 time to fit residues: 973.6625 Evaluate side-chains 582 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 553 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 82 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 226 optimal weight: 0.4980 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 176 GLN A 389 ASN B 161 ASN C 120 ASN C 345 GLN C 393 HIS D 3 ASN D 161 ASN D 176 GLN D 343 ASN E 3 ASN E 161 ASN F 6 HIS F 343 ASN F 347 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.116846 restraints weight = 22496.253| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.15 r_work: 0.3515 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20028 Z= 0.127 Angle : 0.446 6.368 27108 Z= 0.241 Chirality : 0.035 0.133 3078 Planarity : 0.004 0.036 3456 Dihedral : 3.572 22.090 2815 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.03 % Allowed : 19.19 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2538 helix: 1.76 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.004 0.001 HIS C 204 PHE 0.016 0.001 PHE C 220 TYR 0.011 0.001 TYR D 279 ARG 0.008 0.000 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1237) hydrogen bonds : angle 3.65482 ( 3567) covalent geometry : bond 0.00293 (20028) covalent geometry : angle 0.44586 (27108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 570 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8344 (mp-120) REVERT: A 340 ASP cc_start: 0.7366 (m-30) cc_final: 0.7123 (m-30) REVERT: C 136 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8153 (tttm) REVERT: D 136 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8241 (tmtm) REVERT: F 176 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8234 (mp10) outliers start: 59 outliers final: 33 residues processed: 603 average time/residue: 1.5455 time to fit residues: 1033.8714 Evaluate side-chains 586 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 549 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 389 ASN B 153 GLN B 161 ASN C 267 ASN C 345 GLN C 393 HIS C 415 ASN D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN F 3 ASN F 343 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116437 restraints weight = 22429.045| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.16 r_work: 0.3509 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20028 Z= 0.139 Angle : 0.458 6.310 27108 Z= 0.248 Chirality : 0.036 0.162 3078 Planarity : 0.004 0.038 3456 Dihedral : 3.558 21.159 2814 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.45 % Allowed : 19.34 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2538 helix: 1.74 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.004 0.001 HIS C 204 PHE 0.018 0.001 PHE C 220 TYR 0.010 0.001 TYR D 210 ARG 0.009 0.000 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 1237) hydrogen bonds : angle 3.67383 ( 3567) covalent geometry : bond 0.00326 (20028) covalent geometry : angle 0.45822 (27108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 557 time to evaluate : 2.200 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8199 (tttm) REVERT: D 136 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8280 (tmtm) REVERT: D 142 ARG cc_start: 0.8088 (ptm-80) cc_final: 0.7843 (ptm-80) REVERT: E 150 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8224 (mtpt) outliers start: 67 outliers final: 40 residues processed: 592 average time/residue: 1.4514 time to fit residues: 954.0655 Evaluate side-chains 578 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 535 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 343 ASN A 389 ASN B 153 GLN B 161 ASN C 120 ASN C 267 ASN C 345 GLN C 393 HIS D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 170 GLN E 176 GLN F 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116620 restraints weight = 22161.140| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.15 r_work: 0.3514 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20028 Z= 0.134 Angle : 0.462 7.112 27108 Z= 0.249 Chirality : 0.036 0.151 3078 Planarity : 0.004 0.039 3456 Dihedral : 3.557 20.709 2814 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.14 % Allowed : 20.01 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2538 helix: 1.75 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 240 HIS 0.004 0.001 HIS C 204 PHE 0.018 0.001 PHE F 220 TYR 0.010 0.001 TYR D 210 ARG 0.009 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 1237) hydrogen bonds : angle 3.67156 ( 3567) covalent geometry : bond 0.00313 (20028) covalent geometry : angle 0.46161 (27108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 553 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8184 (tttm) REVERT: D 136 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8256 (tmtm) REVERT: D 142 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.7815 (ptm-80) REVERT: D 336 GLN cc_start: 0.8455 (mt0) cc_final: 0.8220 (mt0) REVERT: E 150 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8242 (mtpt) outliers start: 61 outliers final: 44 residues processed: 587 average time/residue: 1.4293 time to fit residues: 930.6840 Evaluate side-chains 603 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 556 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 400 GLN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 151 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 343 ASN A 389 ASN B 153 GLN B 161 ASN C 345 GLN C 393 HIS D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 170 GLN E 176 GLN F 3 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114771 restraints weight = 22330.267| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.14 r_work: 0.3484 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20028 Z= 0.209 Angle : 0.526 7.502 27108 Z= 0.282 Chirality : 0.040 0.185 3078 Planarity : 0.004 0.042 3456 Dihedral : 3.780 20.499 2814 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.98 % Allowed : 20.16 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.16), residues: 2538 helix: 1.54 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.07 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.006 0.001 HIS D 243 PHE 0.022 0.002 PHE C 220 TYR 0.013 0.002 TYR B 325 ARG 0.009 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.05532 ( 1237) hydrogen bonds : angle 3.78709 ( 3567) covalent geometry : bond 0.00509 (20028) covalent geometry : angle 0.52580 (27108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 565 time to evaluate : 2.203 Fit side-chains REVERT: A 439 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7789 (mmtt) REVERT: C 136 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8228 (tttm) REVERT: D 136 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8294 (tmtm) REVERT: D 216 GLU cc_start: 0.7313 (mp0) cc_final: 0.7078 (mp0) REVERT: E 150 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8268 (mtpt) REVERT: E 176 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7955 (mp-120) outliers start: 58 outliers final: 36 residues processed: 596 average time/residue: 1.5031 time to fit residues: 994.3735 Evaluate side-chains 597 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 557 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 130 optimal weight: 0.0670 chunk 169 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 389 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN C 170 GLN C 345 GLN C 393 HIS D 3 ASN D 125 HIS D 161 ASN D 343 ASN E 3 ASN E 170 GLN E 176 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115033 restraints weight = 22329.561| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.14 r_work: 0.3489 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20028 Z= 0.192 Angle : 0.518 7.945 27108 Z= 0.279 Chirality : 0.039 0.204 3078 Planarity : 0.004 0.042 3456 Dihedral : 3.787 20.376 2814 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.62 % Allowed : 20.99 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2538 helix: 1.53 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.08 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 240 HIS 0.005 0.001 HIS D 243 PHE 0.021 0.002 PHE F 220 TYR 0.013 0.001 TYR D 279 ARG 0.010 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.05364 ( 1237) hydrogen bonds : angle 3.78647 ( 3567) covalent geometry : bond 0.00465 (20028) covalent geometry : angle 0.51831 (27108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 551 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: A 439 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7772 (mmtt) REVERT: C 136 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8230 (tttm) REVERT: D 136 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8292 (tmtm) REVERT: E 150 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: E 176 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8078 (mp-120) outliers start: 51 outliers final: 40 residues processed: 576 average time/residue: 1.5154 time to fit residues: 968.3711 Evaluate side-chains 605 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 561 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 200 optimal weight: 0.8980 chunk 233 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 181 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 389 ASN B 161 ASN B 389 ASN C 170 GLN C 345 GLN C 393 HIS D 3 ASN D 161 ASN D 176 GLN D 343 ASN E 3 ASN E 161 ASN E 170 GLN F 347 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116369 restraints weight = 22366.729| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.15 r_work: 0.3510 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20028 Z= 0.137 Angle : 0.479 8.053 27108 Z= 0.259 Chirality : 0.036 0.154 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.628 19.948 2814 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.42 % Favored : 98.54 % Rotamer: Outliers : 2.37 % Allowed : 21.35 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2538 helix: 1.81 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : 0.36 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.004 0.001 HIS C 204 PHE 0.019 0.001 PHE F 220 TYR 0.014 0.001 TYR D 279 ARG 0.010 0.000 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 1237) hydrogen bonds : angle 3.71953 ( 3567) covalent geometry : bond 0.00318 (20028) covalent geometry : angle 0.47937 (27108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 548 time to evaluate : 2.185 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8196 (tttm) REVERT: C 334 PHE cc_start: 0.8412 (t80) cc_final: 0.8142 (t80) REVERT: D 336 GLN cc_start: 0.8496 (mt0) cc_final: 0.8274 (mt0) REVERT: E 150 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8242 (mtpt) outliers start: 46 outliers final: 35 residues processed: 569 average time/residue: 1.5843 time to fit residues: 1001.2129 Evaluate side-chains 566 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 529 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 400 GLN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 178 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 173 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 389 ASN B 161 ASN C 63 HIS C 161 ASN C 393 HIS D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.128382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115419 restraints weight = 22451.389| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.15 r_work: 0.3496 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20028 Z= 0.171 Angle : 0.512 8.254 27108 Z= 0.275 Chirality : 0.038 0.169 3078 Planarity : 0.004 0.043 3456 Dihedral : 3.712 20.189 2814 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Rotamer: Outliers : 2.31 % Allowed : 21.40 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2538 helix: 1.72 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : 0.30 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 240 HIS 0.005 0.001 HIS D 243 PHE 0.020 0.001 PHE F 220 TYR 0.013 0.001 TYR F 325 ARG 0.010 0.001 ARG F 433 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 1237) hydrogen bonds : angle 3.76449 ( 3567) covalent geometry : bond 0.00409 (20028) covalent geometry : angle 0.51204 (27108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21870.39 seconds wall clock time: 372 minutes 3.96 seconds (22323.96 seconds total)