Starting phenix.real_space_refine on Sun Apr 5 23:45:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5z_63655/04_2026/9m5z_63655.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 8949 2.51 5 N 2398 2.21 5 O 2726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14168 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2308 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2291 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2333 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2325 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 13, 'TRANS': 280} Chain breaks: 1 Chain: "C" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.23 Number of scatterers: 14168 At special positions: 0 Unit cell: (100.04, 128.74, 138.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 18 15.00 Mg 5 11.99 O 2726 8.00 N 2398 7.00 C 8949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 652.3 milliseconds 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3378 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 6 sheets defined 61.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.577A pdb=" N SER B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.789A pdb=" N MET B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.063A pdb=" N TYR B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.551A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.819A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.916A pdb=" N ARG B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.005A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.902A pdb=" N MET A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 4.034A pdb=" N TYR A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.917A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N ILE A 241 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.586A pdb=" N ARG A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.933A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.927A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.749A pdb=" N MET F 163 " --> pdb=" O MET F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.421A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 242 through 248 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 340 through 347 removed outlier: 3.536A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 62 through 66 Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.654A pdb=" N SER E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.196A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 222 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.896A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.852A pdb=" N SER D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.560A pdb=" N LEU D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.611A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.683A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.414A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.738A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 340 through 348 removed outlier: 3.780A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.735A pdb=" N SER C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 120 through 124 removed outlier: 4.322A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.532A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.203A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.173A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.571A pdb=" N LYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.997A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 187 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE B 232 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE B 189 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA B 234 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 191 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.987A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS A 187 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE A 232 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A 189 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA A 234 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A 191 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.405A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS F 187 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE F 232 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE F 189 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA F 234 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 191 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL F 129 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR F 235 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU F 131 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR F 132 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 81 removed outlier: 3.993A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS E 187 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE E 232 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE E 189 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 234 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 191 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.245A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE D 157 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 157 removed outlier: 6.259A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE C 157 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4134 1.34 - 1.46: 2285 1.46 - 1.58: 7820 1.58 - 1.70: 31 1.70 - 1.82: 126 Bond restraints: 14396 Sorted by residual: bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP D 401 " pdb=" C5 ATP D 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 ... (remaining 14391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 19218 3.75 - 7.49: 175 7.49 - 11.23: 37 11.23 - 14.98: 4 14.98 - 18.72: 10 Bond angle restraints: 19444 Sorted by residual: angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 122.57 17.30 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.88 16.99 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 ... (remaining 19439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7561 17.99 - 35.98: 1131 35.98 - 53.97: 297 53.97 - 71.96: 40 71.96 - 89.96: 23 Dihedral angle restraints: 9052 sinusoidal: 3872 harmonic: 5180 Sorted by residual: dihedral pdb=" CA LEU C 184 " pdb=" C LEU C 184 " pdb=" N GLN C 185 " pdb=" CA GLN C 185 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL F 229 " pdb=" C VAL F 229 " pdb=" N MET F 230 " pdb=" CA MET F 230 " ideal model delta harmonic sigma weight residual 180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU B 184 " pdb=" C LEU B 184 " pdb=" N GLN B 185 " pdb=" CA GLN B 185 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 9049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1909 0.067 - 0.134: 288 0.134 - 0.201: 26 0.201 - 0.268: 4 0.268 - 0.335: 1 Chirality restraints: 2228 Sorted by residual: chirality pdb=" CA ASP B 308 " pdb=" N ASP B 308 " pdb=" C ASP B 308 " pdb=" CB ASP B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA CYS F 187 " pdb=" N CYS F 187 " pdb=" C CYS F 187 " pdb=" CB CYS F 187 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2225 not shown) Planarity restraints: 2437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 337 " 0.060 5.00e-02 4.00e+02 8.96e-02 1.29e+01 pdb=" N PRO C 338 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 338 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 338 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 120 " -0.054 5.00e-02 4.00e+02 7.76e-02 9.62e+00 pdb=" N PRO D 121 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 271 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C LEU D 271 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU D 271 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS D 272 " 0.016 2.00e-02 2.50e+03 ... (remaining 2434 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 34 2.40 - 3.02: 7667 3.02 - 3.65: 22740 3.65 - 4.27: 34104 4.27 - 4.90: 56053 Nonbonded interactions: 120598 Sorted by model distance: nonbonded pdb=" O2B ATP D 401 " pdb="MG MG D 402 " model vdw 1.775 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 402 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR B 140 " pdb="MG MG B 402 " model vdw 2.016 2.170 nonbonded pdb=" O2G ATP F 401 " pdb="MG MG F 402 " model vdw 2.026 2.170 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 402 " model vdw 2.029 2.170 ... (remaining 120593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 319 or resid 337 through 401)) selection = (chain 'B' and (resid 45 through 319 or resid 337 through 401)) selection = (chain 'C' and (resid 45 through 319 or resid 337 through 401)) selection = (chain 'D' and (resid 45 through 319 or resid 337 through 401)) selection = (chain 'E' and (resid 45 through 319 or resid 337 through 401)) selection = (chain 'F' and (resid 45 through 319 or resid 337 through 401)) } 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=0.00 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: 13.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.005 0.110 14396 Z= 0.364 Angle : 0.991 18.725 19444 Z= 0.662 Chirality : 0.049 0.335 2228 Planarity : 0.005 0.090 2437 Dihedral : 18.035 89.955 5674 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.32 % Allowed : 25.02 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1735 helix: 0.14 (0.16), residues: 945 sheet: 0.19 (0.51), residues: 102 loop : -0.07 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 74 TYR 0.023 0.001 TYR B 264 PHE 0.032 0.002 PHE F 197 TRP 0.023 0.001 TRP F 220 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00531 (14396) covalent geometry : angle 0.99109 (19444) hydrogen bonds : bond 0.15990 ( 677) hydrogen bonds : angle 5.93525 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 265 time to evaluate : 0.546 Fit side-chains REVERT: B 219 LEU cc_start: 0.8711 (mt) cc_final: 0.8285 (mp) REVERT: B 235 THR cc_start: 0.8975 (p) cc_final: 0.8769 (t) REVERT: F 113 MET cc_start: 0.7120 (mmp) cc_final: 0.6785 (pmm) REVERT: F 308 ASP cc_start: 0.7848 (t0) cc_final: 0.7437 (t0) REVERT: E 338 PRO cc_start: 0.7346 (Cg_exo) cc_final: 0.7110 (Cg_endo) outliers start: 5 outliers final: 2 residues processed: 268 average time/residue: 0.1088 time to fit residues: 43.3270 Evaluate side-chains 253 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain C residue 81 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN C 193 GLN C 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.190006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136865 restraints weight = 17769.556| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.66 r_work: 0.3509 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14396 Z= 0.128 Angle : 0.553 8.518 19444 Z= 0.276 Chirality : 0.040 0.159 2228 Planarity : 0.004 0.051 2437 Dihedral : 10.878 88.455 2103 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 23.92 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1735 helix: 0.76 (0.17), residues: 971 sheet: -0.02 (0.50), residues: 114 loop : 0.32 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.018 0.001 TYR F 313 PHE 0.011 0.001 PHE F 253 TRP 0.016 0.001 TRP F 220 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00302 (14396) covalent geometry : angle 0.55279 (19444) hydrogen bonds : bond 0.03678 ( 677) hydrogen bonds : angle 4.69334 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.554 Fit side-chains REVERT: B 219 LEU cc_start: 0.8606 (mt) cc_final: 0.8139 (mp) REVERT: A 74 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6576 (mtm-85) REVERT: A 350 MET cc_start: 0.3654 (tpt) cc_final: 0.1366 (tmm) REVERT: F 113 MET cc_start: 0.6854 (mmp) cc_final: 0.6514 (ptp) REVERT: F 257 LEU cc_start: 0.8381 (mt) cc_final: 0.7973 (mp) REVERT: F 308 ASP cc_start: 0.7833 (t0) cc_final: 0.7588 (t0) REVERT: E 338 PRO cc_start: 0.7151 (Cg_exo) cc_final: 0.6908 (Cg_endo) REVERT: C 350 MET cc_start: 0.7468 (mmm) cc_final: 0.7175 (tpp) outliers start: 40 outliers final: 23 residues processed: 281 average time/residue: 0.1110 time to fit residues: 46.5843 Evaluate side-chains 268 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 132 optimal weight: 0.0020 chunk 129 optimal weight: 0.8980 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.187247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133648 restraints weight = 17874.347| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.67 r_work: 0.3466 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14396 Z= 0.151 Angle : 0.549 7.857 19444 Z= 0.270 Chirality : 0.040 0.150 2228 Planarity : 0.003 0.046 2437 Dihedral : 10.877 89.606 2102 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.15 % Allowed : 25.14 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1735 helix: 1.04 (0.17), residues: 968 sheet: -0.18 (0.47), residues: 127 loop : 0.48 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 228 TYR 0.021 0.001 TYR F 313 PHE 0.010 0.001 PHE F 197 TRP 0.015 0.001 TRP F 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00360 (14396) covalent geometry : angle 0.54852 (19444) hydrogen bonds : bond 0.03451 ( 677) hydrogen bonds : angle 4.55615 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.468 Fit side-chains REVERT: B 56 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8069 (mtpp) REVERT: B 74 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7045 (mtm-85) REVERT: B 219 LEU cc_start: 0.8667 (mt) cc_final: 0.8234 (mp) REVERT: B 235 THR cc_start: 0.9057 (p) cc_final: 0.8853 (t) REVERT: B 284 GLN cc_start: 0.7205 (tp-100) cc_final: 0.6933 (tp-100) REVERT: A 74 ARG cc_start: 0.6851 (mtm-85) cc_final: 0.6585 (mtm-85) REVERT: A 350 MET cc_start: 0.3575 (tpt) cc_final: 0.1292 (tmm) REVERT: F 184 LEU cc_start: 0.8543 (mt) cc_final: 0.8235 (mt) REVERT: F 228 ARG cc_start: 0.5889 (mmp80) cc_final: 0.5635 (mmp80) REVERT: F 257 LEU cc_start: 0.8426 (mt) cc_final: 0.8076 (mp) REVERT: F 308 ASP cc_start: 0.7865 (t0) cc_final: 0.7528 (t0) REVERT: E 338 PRO cc_start: 0.7099 (Cg_exo) cc_final: 0.6854 (Cg_endo) REVERT: D 350 MET cc_start: 0.7194 (tpt) cc_final: 0.6106 (ttp) REVERT: C 289 ASN cc_start: 0.8871 (m-40) cc_final: 0.8547 (m-40) outliers start: 49 outliers final: 34 residues processed: 274 average time/residue: 0.1068 time to fit residues: 43.7102 Evaluate side-chains 279 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 151 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134595 restraints weight = 17719.999| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.64 r_work: 0.3486 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14396 Z= 0.127 Angle : 0.530 12.199 19444 Z= 0.259 Chirality : 0.040 0.138 2228 Planarity : 0.003 0.043 2437 Dihedral : 10.672 89.648 2102 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.34 % Allowed : 25.02 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1735 helix: 1.30 (0.17), residues: 954 sheet: -0.13 (0.46), residues: 123 loop : 0.46 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 318 TYR 0.021 0.001 TYR F 313 PHE 0.012 0.001 PHE F 197 TRP 0.015 0.001 TRP F 220 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00299 (14396) covalent geometry : angle 0.53033 (19444) hydrogen bonds : bond 0.03120 ( 677) hydrogen bonds : angle 4.42647 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.608 Fit side-chains REVERT: B 56 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8081 (mtpp) REVERT: B 74 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7008 (mtm-85) REVERT: B 219 LEU cc_start: 0.8649 (mt) cc_final: 0.8208 (mp) REVERT: B 231 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 284 GLN cc_start: 0.7235 (tp-100) cc_final: 0.6939 (tp-100) REVERT: A 141 MET cc_start: 0.7520 (mtm) cc_final: 0.7231 (mtm) REVERT: A 350 MET cc_start: 0.3658 (tpt) cc_final: 0.1282 (tmm) REVERT: F 74 ARG cc_start: 0.6770 (mtp85) cc_final: 0.6383 (mtp85) REVERT: F 184 LEU cc_start: 0.8570 (mt) cc_final: 0.8279 (mt) REVERT: F 228 ARG cc_start: 0.5868 (mmp80) cc_final: 0.5633 (mmp80) REVERT: F 257 LEU cc_start: 0.8349 (mt) cc_final: 0.7988 (mp) REVERT: F 308 ASP cc_start: 0.7859 (t0) cc_final: 0.7459 (t0) REVERT: D 350 MET cc_start: 0.7180 (tpt) cc_final: 0.6192 (ttp) REVERT: C 289 ASN cc_start: 0.8772 (m-40) cc_final: 0.8446 (m-40) REVERT: C 341 THR cc_start: 0.8298 (p) cc_final: 0.7949 (m) outliers start: 52 outliers final: 34 residues processed: 287 average time/residue: 0.1095 time to fit residues: 47.2259 Evaluate side-chains 280 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 50 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 182 ASN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.184115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130169 restraints weight = 17833.506| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.63 r_work: 0.3430 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14396 Z= 0.182 Angle : 0.572 10.290 19444 Z= 0.279 Chirality : 0.041 0.152 2228 Planarity : 0.004 0.043 2437 Dihedral : 10.659 88.192 2102 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.60 % Allowed : 25.59 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1735 helix: 1.30 (0.17), residues: 952 sheet: -0.28 (0.47), residues: 123 loop : 0.46 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.024 0.001 TYR F 313 PHE 0.013 0.002 PHE E 197 TRP 0.014 0.001 TRP F 220 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00438 (14396) covalent geometry : angle 0.57229 (19444) hydrogen bonds : bond 0.03227 ( 677) hydrogen bonds : angle 4.45927 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.629 Fit side-chains REVERT: B 56 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8103 (mtpp) REVERT: B 243 ASP cc_start: 0.7869 (t0) cc_final: 0.7452 (m-30) REVERT: B 284 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6952 (tp-100) REVERT: B 293 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 141 MET cc_start: 0.7559 (mtm) cc_final: 0.7334 (mtm) REVERT: A 350 MET cc_start: 0.3724 (tpt) cc_final: 0.1264 (tmm) REVERT: F 74 ARG cc_start: 0.6793 (mtp85) cc_final: 0.6381 (mtp85) REVERT: F 184 LEU cc_start: 0.8615 (mt) cc_final: 0.8329 (mt) REVERT: F 289 ASN cc_start: 0.8185 (m-40) cc_final: 0.7697 (m-40) REVERT: D 350 MET cc_start: 0.7221 (tpt) cc_final: 0.6237 (ttp) REVERT: C 289 ASN cc_start: 0.8862 (m-40) cc_final: 0.8365 (m-40) REVERT: C 341 THR cc_start: 0.8322 (p) cc_final: 0.7766 (m) outliers start: 56 outliers final: 39 residues processed: 285 average time/residue: 0.1062 time to fit residues: 45.5754 Evaluate side-chains 285 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 238 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123607 restraints weight = 17941.599| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.59 r_work: 0.3351 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 14396 Z= 0.326 Angle : 0.723 9.543 19444 Z= 0.352 Chirality : 0.045 0.156 2228 Planarity : 0.005 0.059 2437 Dihedral : 10.995 89.711 2102 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.05 % Allowed : 26.11 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1735 helix: 0.88 (0.17), residues: 966 sheet: -0.78 (0.42), residues: 153 loop : 0.45 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.026 0.002 TYR F 313 PHE 0.021 0.002 PHE E 154 TRP 0.017 0.002 TRP F 220 HIS 0.002 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00785 (14396) covalent geometry : angle 0.72289 (19444) hydrogen bonds : bond 0.03850 ( 677) hydrogen bonds : angle 4.79233 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8083 (mttp) REVERT: B 175 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7652 (t0) REVERT: B 243 ASP cc_start: 0.8032 (t0) cc_final: 0.7597 (m-30) REVERT: B 284 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6927 (tp-100) REVERT: B 293 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7547 (t80) REVERT: A 350 MET cc_start: 0.3644 (tpt) cc_final: 0.1201 (tmm) REVERT: F 74 ARG cc_start: 0.6826 (mtp85) cc_final: 0.6545 (mtp85) REVERT: F 184 LEU cc_start: 0.8691 (mt) cc_final: 0.8459 (mt) REVERT: F 289 ASN cc_start: 0.8365 (m-40) cc_final: 0.7807 (m-40) REVERT: F 308 ASP cc_start: 0.7773 (t0) cc_final: 0.7004 (t0) REVERT: E 163 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7373 (mtt) REVERT: D 347 LYS cc_start: 0.7717 (tmtt) cc_final: 0.7426 (mmtt) REVERT: D 350 MET cc_start: 0.7345 (tpt) cc_final: 0.6358 (ttp) REVERT: C 289 ASN cc_start: 0.8908 (m-40) cc_final: 0.8450 (m-40) outliers start: 63 outliers final: 46 residues processed: 279 average time/residue: 0.1068 time to fit residues: 44.4146 Evaluate side-chains 277 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN D 171 ASN C 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.182942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129215 restraints weight = 17742.228| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.60 r_work: 0.3412 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14396 Z= 0.152 Angle : 0.580 8.653 19444 Z= 0.284 Chirality : 0.041 0.143 2228 Planarity : 0.003 0.046 2437 Dihedral : 10.830 89.640 2102 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.34 % Allowed : 26.24 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1735 helix: 1.26 (0.17), residues: 946 sheet: -0.74 (0.47), residues: 118 loop : 0.30 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.023 0.001 TYR F 313 PHE 0.011 0.001 PHE E 154 TRP 0.014 0.001 TRP F 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00366 (14396) covalent geometry : angle 0.58045 (19444) hydrogen bonds : bond 0.03222 ( 677) hydrogen bonds : angle 4.58465 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.463 Fit side-chains REVERT: B 56 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8076 (mttp) REVERT: B 284 GLN cc_start: 0.7221 (tp-100) cc_final: 0.6941 (tp-100) REVERT: B 293 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 158 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.5207 (ttt-90) REVERT: A 350 MET cc_start: 0.3643 (tpt) cc_final: 0.1180 (tmm) REVERT: F 74 ARG cc_start: 0.6789 (mtp85) cc_final: 0.6402 (mtp85) REVERT: F 184 LEU cc_start: 0.8623 (mt) cc_final: 0.8350 (mt) REVERT: F 289 ASN cc_start: 0.8386 (m-40) cc_final: 0.7796 (m-40) REVERT: F 308 ASP cc_start: 0.7762 (t0) cc_final: 0.7011 (t0) REVERT: E 163 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7289 (mtt) REVERT: D 284 GLN cc_start: 0.8172 (tp40) cc_final: 0.7938 (tp-100) REVERT: D 347 LYS cc_start: 0.7685 (tmtt) cc_final: 0.7403 (mmtt) REVERT: D 350 MET cc_start: 0.7349 (tpt) cc_final: 0.6362 (ttp) REVERT: C 237 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8048 (mtp85) REVERT: C 289 ASN cc_start: 0.8850 (m-40) cc_final: 0.8369 (m-40) REVERT: C 341 THR cc_start: 0.8239 (p) cc_final: 0.7789 (m) outliers start: 52 outliers final: 40 residues processed: 276 average time/residue: 0.1080 time to fit residues: 44.8009 Evaluate side-chains 276 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 178 PHE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 147 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.185521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136334 restraints weight = 17743.343| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.94 r_work: 0.3442 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14396 Z= 0.121 Angle : 0.555 8.719 19444 Z= 0.271 Chirality : 0.040 0.148 2228 Planarity : 0.004 0.045 2437 Dihedral : 10.638 89.240 2102 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.02 % Allowed : 26.88 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1735 helix: 1.50 (0.18), residues: 935 sheet: -1.06 (0.44), residues: 133 loop : 0.39 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.020 0.001 TYR F 313 PHE 0.017 0.001 PHE F 197 TRP 0.012 0.001 TRP F 220 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00288 (14396) covalent geometry : angle 0.55526 (19444) hydrogen bonds : bond 0.02999 ( 677) hydrogen bonds : angle 4.43857 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.529 Fit side-chains REVERT: B 56 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8056 (mttp) REVERT: B 219 LEU cc_start: 0.8655 (mt) cc_final: 0.8233 (mp) REVERT: B 284 GLN cc_start: 0.7196 (tp-100) cc_final: 0.6901 (tp-100) REVERT: B 293 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7463 (t80) REVERT: A 141 MET cc_start: 0.7870 (mtt) cc_final: 0.7538 (mtp) REVERT: A 158 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5134 (ttt-90) REVERT: A 350 MET cc_start: 0.3568 (tpt) cc_final: 0.1119 (tmm) REVERT: F 74 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6332 (mtp85) REVERT: F 184 LEU cc_start: 0.8562 (mt) cc_final: 0.8323 (mt) REVERT: F 289 ASN cc_start: 0.8392 (m-40) cc_final: 0.7799 (m110) REVERT: F 308 ASP cc_start: 0.7744 (t0) cc_final: 0.7028 (t0) REVERT: E 50 GLN cc_start: 0.8366 (mt0) cc_final: 0.8088 (mt0) REVERT: E 163 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: D 113 MET cc_start: 0.8490 (ptp) cc_final: 0.8269 (ptp) REVERT: D 284 GLN cc_start: 0.8103 (tp40) cc_final: 0.7890 (tp-100) REVERT: D 347 LYS cc_start: 0.7656 (tmtt) cc_final: 0.7362 (mmtt) REVERT: D 350 MET cc_start: 0.7367 (tpt) cc_final: 0.6346 (ttp) REVERT: C 89 THR cc_start: 0.8632 (m) cc_final: 0.8184 (p) REVERT: C 237 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8068 (mtp85) REVERT: C 289 ASN cc_start: 0.8781 (m-40) cc_final: 0.8307 (m-40) REVERT: C 341 THR cc_start: 0.8235 (p) cc_final: 0.7844 (m) outliers start: 47 outliers final: 39 residues processed: 277 average time/residue: 0.1083 time to fit residues: 44.8801 Evaluate side-chains 280 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130783 restraints weight = 17872.235| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.63 r_work: 0.3437 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14396 Z= 0.156 Angle : 0.585 11.556 19444 Z= 0.283 Chirality : 0.041 0.156 2228 Planarity : 0.004 0.049 2437 Dihedral : 10.589 89.871 2102 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.41 % Allowed : 27.07 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1735 helix: 1.40 (0.17), residues: 953 sheet: -0.96 (0.43), residues: 141 loop : 0.54 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 248 TYR 0.025 0.001 TYR F 313 PHE 0.016 0.001 PHE F 197 TRP 0.007 0.001 TRP E 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00377 (14396) covalent geometry : angle 0.58477 (19444) hydrogen bonds : bond 0.03033 ( 677) hydrogen bonds : angle 4.41592 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.516 Fit side-chains REVERT: B 56 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8071 (mttp) REVERT: B 284 GLN cc_start: 0.7239 (tp-100) cc_final: 0.6945 (tp-100) REVERT: B 293 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 158 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.5208 (ttt-90) REVERT: A 350 MET cc_start: 0.3648 (tpt) cc_final: 0.1185 (tmm) REVERT: F 74 ARG cc_start: 0.6724 (mtp85) cc_final: 0.6330 (mtp85) REVERT: F 184 LEU cc_start: 0.8492 (mt) cc_final: 0.8225 (mt) REVERT: F 223 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6619 (tp) REVERT: F 289 ASN cc_start: 0.8440 (m-40) cc_final: 0.7848 (m110) REVERT: E 50 GLN cc_start: 0.8400 (mt0) cc_final: 0.8090 (mt0) REVERT: E 163 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7310 (mtt) REVERT: D 284 GLN cc_start: 0.8139 (tp40) cc_final: 0.7926 (tp-100) REVERT: D 347 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7408 (mmtt) REVERT: D 350 MET cc_start: 0.7327 (tpt) cc_final: 0.6324 (ttp) REVERT: C 89 THR cc_start: 0.8646 (m) cc_final: 0.8171 (p) REVERT: C 237 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8113 (mtp85) REVERT: C 289 ASN cc_start: 0.8813 (m-40) cc_final: 0.8298 (m-40) REVERT: C 313 TYR cc_start: 0.8130 (t80) cc_final: 0.7629 (t80) REVERT: C 341 THR cc_start: 0.8287 (p) cc_final: 0.7840 (m) outliers start: 53 outliers final: 45 residues processed: 276 average time/residue: 0.1047 time to fit residues: 43.5826 Evaluate side-chains 289 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 162 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 125 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.186093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137074 restraints weight = 17715.082| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.74 r_work: 0.3460 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14396 Z= 0.123 Angle : 0.563 10.705 19444 Z= 0.274 Chirality : 0.040 0.149 2228 Planarity : 0.004 0.055 2437 Dihedral : 10.488 89.708 2102 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.09 % Allowed : 27.33 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1735 helix: 1.50 (0.18), residues: 950 sheet: -1.12 (0.43), residues: 133 loop : 0.50 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 248 TYR 0.024 0.001 TYR F 313 PHE 0.019 0.001 PHE F 197 TRP 0.006 0.001 TRP F 220 HIS 0.002 0.000 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00298 (14396) covalent geometry : angle 0.56322 (19444) hydrogen bonds : bond 0.02903 ( 677) hydrogen bonds : angle 4.35252 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3470 Ramachandran restraints generated. 1735 Oldfield, 0 Emsley, 1735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8112 (mtpp) REVERT: B 219 LEU cc_start: 0.8648 (mt) cc_final: 0.8232 (mp) REVERT: B 284 GLN cc_start: 0.7198 (tp-100) cc_final: 0.6911 (tp-100) REVERT: B 293 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7477 (t80) REVERT: A 158 ARG cc_start: 0.5621 (ptp-110) cc_final: 0.5140 (ttt-90) REVERT: A 350 MET cc_start: 0.3590 (tpt) cc_final: 0.1177 (tmm) REVERT: F 74 ARG cc_start: 0.6666 (mtp85) cc_final: 0.6279 (mtp85) REVERT: F 184 LEU cc_start: 0.8430 (mt) cc_final: 0.8188 (mt) REVERT: F 289 ASN cc_start: 0.8471 (m-40) cc_final: 0.7890 (m110) REVERT: E 50 GLN cc_start: 0.8417 (mt0) cc_final: 0.8050 (mt0) REVERT: E 112 MET cc_start: 0.8075 (mmm) cc_final: 0.7856 (mmm) REVERT: E 163 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7261 (mtt) REVERT: E 313 TYR cc_start: 0.7652 (t80) cc_final: 0.7138 (t80) REVERT: D 284 GLN cc_start: 0.8117 (tp40) cc_final: 0.7912 (tp-100) REVERT: D 347 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7376 (mmtt) REVERT: D 350 MET cc_start: 0.7347 (tpt) cc_final: 0.6338 (ttp) REVERT: C 237 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8133 (mtp85) REVERT: C 289 ASN cc_start: 0.8814 (m-40) cc_final: 0.8283 (m-40) REVERT: C 313 TYR cc_start: 0.8131 (t80) cc_final: 0.7598 (t80) REVERT: C 341 THR cc_start: 0.8269 (p) cc_final: 0.7816 (m) outliers start: 48 outliers final: 41 residues processed: 276 average time/residue: 0.1020 time to fit residues: 42.5536 Evaluate side-chains 279 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 217 MET Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129756 restraints weight = 17844.598| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.62 r_work: 0.3421 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14396 Z= 0.190 Angle : 0.611 10.674 19444 Z= 0.298 Chirality : 0.042 0.153 2228 Planarity : 0.004 0.050 2437 Dihedral : 10.514 88.384 2102 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.28 % Allowed : 27.07 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1735 helix: 1.45 (0.18), residues: 947 sheet: -0.90 (0.44), residues: 136 loop : 0.49 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 248 TYR 0.026 0.001 TYR F 313 PHE 0.017 0.002 PHE F 197 TRP 0.009 0.001 TRP E 220 HIS 0.002 0.001 HIS E 206 Details of bonding type rmsd covalent geometry : bond 0.00462 (14396) covalent geometry : angle 0.61140 (19444) hydrogen bonds : bond 0.03076 ( 677) hydrogen bonds : angle 4.42739 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5392.38 seconds wall clock time: 92 minutes 34.43 seconds (5554.43 seconds total)