Starting phenix.real_space_refine on Sat Jun 28 07:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.map" model { file = "/net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr5_40720/06_2025/8sr5_40720.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17727 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 87 5.16 5 C 12246 2.51 5 N 3042 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: G, K, F, J, E, I Time building chain proxies: 9.01, per 1000 atoms: 0.48 Number of scatterers: 18588 At special positions: 0 Unit cell: (106.349, 104.762, 119.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 87 16.00 O 3207 8.00 N 3042 7.00 C 12246 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: 4.21 Conformation dependent library (CDL) restraints added in 2.1 seconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 49.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 206 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.969A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 45 Processing helix chain 'B' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 140 through 165 removed outlier: 4.251A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.736A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 206 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.969A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 206 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.970A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.991A pdb=" N LEU C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 123 through 150 removed outlier: 3.805A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.579A pdb=" N ASP C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 199 Processing helix chain 'C' and resid 208 through 220 Proline residue: C 217 - end of helix Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.527A pdb=" N TRP C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'G' and resid 48 through 52 removed outlier: 3.991A pdb=" N LEU G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 123 through 150 removed outlier: 3.806A pdb=" N THR G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.579A pdb=" N ASP G 156 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 199 Processing helix chain 'G' and resid 208 through 220 Proline residue: G 217 - end of helix Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.528A pdb=" N TRP G 253 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 48 through 52 removed outlier: 3.990A pdb=" N LEU K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 Processing helix chain 'K' and resid 123 through 150 removed outlier: 3.806A pdb=" N THR K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS K 134 " --> pdb=" O ARG K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 159 removed outlier: 3.580A pdb=" N ASP K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 199 Processing helix chain 'K' and resid 208 through 220 Proline residue: K 217 - end of helix Processing helix chain 'K' and resid 248 through 253 removed outlier: 3.527A pdb=" N TRP K 253 " --> pdb=" O VAL K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'F' and resid 10 through 45 Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 140 through 165 removed outlier: 4.252A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.737A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 Processing helix chain 'J' and resid 45 through 51 removed outlier: 4.024A pdb=" N ASP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.913A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 Processing helix chain 'J' and resid 140 through 165 removed outlier: 4.251A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.736A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.552A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 301 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.551A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB4, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.551A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 301 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.552A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.188A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AB8, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.552A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS I 301 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.552A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AC4, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AC5, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'J' and resid 170 through 173 927 hydrogen bonds defined for protein. 2691 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: 5.59 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 3 1.20 - 1.35: 5673 1.35 - 1.50: 6240 1.50 - 1.66: 7089 1.66 - 1.81: 168 Bond restraints: 19173 Sorted by residual: bond pdb=" C LEU F 244 " pdb=" N GLN F 245 " ideal model delta sigma weight residual 1.334 1.045 0.290 1.52e-02 4.33e+03 3.63e+02 bond pdb=" C LEU J 244 " pdb=" N GLN J 245 " ideal model delta sigma weight residual 1.334 1.045 0.289 1.52e-02 4.33e+03 3.62e+02 bond pdb=" C LEU B 244 " pdb=" N GLN B 245 " ideal model delta sigma weight residual 1.334 1.045 0.289 1.52e-02 4.33e+03 3.62e+02 bond pdb=" C GLN F 245 " pdb=" N SER F 246 " ideal model delta sigma weight residual 1.335 1.261 0.074 1.35e-02 5.49e+03 3.01e+01 bond pdb=" C GLN B 245 " pdb=" N SER B 246 " ideal model delta sigma weight residual 1.335 1.261 0.074 1.35e-02 5.49e+03 2.99e+01 ... (remaining 19168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 26124 7.35 - 14.70: 6 14.70 - 22.05: 6 22.05 - 29.40: 0 29.40 - 36.75: 3 Bond angle restraints: 26139 Sorted by residual: angle pdb=" C LEU F 244 " pdb=" N GLN F 245 " pdb=" CA GLN F 245 " ideal model delta sigma weight residual 122.24 158.99 -36.75 1.57e+00 4.06e-01 5.48e+02 angle pdb=" C LEU B 244 " pdb=" N GLN B 245 " pdb=" CA GLN B 245 " ideal model delta sigma weight residual 122.24 158.96 -36.72 1.57e+00 4.06e-01 5.47e+02 angle pdb=" C LEU J 244 " pdb=" N GLN J 245 " pdb=" CA GLN J 245 " ideal model delta sigma weight residual 122.24 158.93 -36.69 1.57e+00 4.06e-01 5.46e+02 angle pdb=" O LEU F 244 " pdb=" C LEU F 244 " pdb=" N GLN F 245 " ideal model delta sigma weight residual 122.86 107.44 15.42 1.18e+00 7.18e-01 1.71e+02 angle pdb=" O LEU B 244 " pdb=" C LEU B 244 " pdb=" N GLN B 245 " ideal model delta sigma weight residual 122.86 107.47 15.39 1.18e+00 7.18e-01 1.70e+02 ... (remaining 26134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9852 17.23 - 34.47: 879 34.47 - 51.70: 168 51.70 - 68.94: 18 68.94 - 86.17: 9 Dihedral angle restraints: 10926 sinusoidal: 4278 harmonic: 6648 Sorted by residual: dihedral pdb=" CA MET J 45 " pdb=" C MET J 45 " pdb=" N GLY J 46 " pdb=" CA GLY J 46 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET F 45 " pdb=" C MET F 45 " pdb=" N GLY F 46 " pdb=" CA GLY F 46 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET B 45 " pdb=" C MET B 45 " pdb=" N GLY B 46 " pdb=" CA GLY B 46 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2013 0.042 - 0.083: 568 0.083 - 0.125: 230 0.125 - 0.167: 24 0.167 - 0.208: 6 Chirality restraints: 2841 Sorted by residual: chirality pdb=" CA HIS E 137 " pdb=" N HIS E 137 " pdb=" C HIS E 137 " pdb=" CB HIS E 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA HIS A 137 " pdb=" N HIS A 137 " pdb=" C HIS A 137 " pdb=" CB HIS A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA HIS I 137 " pdb=" N HIS I 137 " pdb=" C HIS I 137 " pdb=" CB HIS I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2838 not shown) Planarity restraints: 3240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " 0.038 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR F 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.038 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " 0.039 2.00e-02 2.50e+03 2.90e-02 1.69e+01 pdb=" CG TYR J 37 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.004 2.00e-02 2.50e+03 ... (remaining 3237 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 203 2.54 - 3.13: 14735 3.13 - 3.72: 30349 3.72 - 4.31: 42922 4.31 - 4.90: 71654 Nonbonded interactions: 159863 Sorted by model distance: nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.949 2.320 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.950 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.951 2.320 nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.982 2.320 nonbonded pdb=" ND1 HIS I 48 " pdb="CU CU I 502 " model vdw 1.982 2.320 ... (remaining 159858 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: 0.11 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.030 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.006 0.290 19173 Z= 0.338 Angle : 0.784 36.751 26139 Z= 0.471 Chirality : 0.045 0.208 2841 Planarity : 0.004 0.038 3240 Dihedral : 13.263 86.169 6672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.85 % Favored : 93.76 % Rotamer: Outliers : 0.77 % Allowed : 0.67 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2274 helix: 0.94 (0.16), residues: 981 sheet: 0.73 (0.35), residues: 246 loop : -0.67 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 206 HIS 0.004 0.001 HIS I 139 PHE 0.013 0.001 PHE J 50 TYR 0.070 0.002 TYR B 37 ARG 0.006 0.001 ARG K 198 Details of bonding type rmsd hydrogen bonds : bond 0.16023 ( 927) hydrogen bonds : angle 6.79385 ( 2691) covalent geometry : bond 0.00583 (19173) covalent geometry : angle 0.78386 (26139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 389 time to evaluate : 1.929 Fit side-chains REVERT: A 137 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5974 (m170) REVERT: A 237 MET cc_start: 0.7828 (mtm) cc_final: 0.7541 (mtp) REVERT: A 368 ASP cc_start: 0.8396 (t70) cc_final: 0.8131 (t0) REVERT: A 375 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7211 (mtp-110) REVERT: B 113 TYR cc_start: 0.7869 (m-80) cc_final: 0.7518 (m-80) REVERT: B 199 MET cc_start: 0.6549 (mtm) cc_final: 0.6254 (mtm) REVERT: E 237 MET cc_start: 0.7804 (mtm) cc_final: 0.7498 (mtp) REVERT: E 251 MET cc_start: 0.7541 (ttp) cc_final: 0.7299 (ttt) REVERT: E 368 ASP cc_start: 0.8412 (t70) cc_final: 0.8119 (t0) REVERT: E 375 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7178 (mtp-110) REVERT: I 117 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7530 (mm-30) REVERT: I 137 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6029 (m170) REVERT: I 237 MET cc_start: 0.7836 (mtm) cc_final: 0.7506 (mtp) REVERT: I 251 MET cc_start: 0.7538 (ttp) cc_final: 0.7302 (ttt) REVERT: I 285 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7878 (tttp) REVERT: I 316 GLU cc_start: 0.8370 (tt0) cc_final: 0.8155 (tt0) REVERT: I 368 ASP cc_start: 0.8431 (t70) cc_final: 0.8208 (t0) REVERT: I 375 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7166 (mtp-110) REVERT: F 113 TYR cc_start: 0.7902 (m-80) cc_final: 0.7535 (m-80) REVERT: F 199 MET cc_start: 0.6562 (mtm) cc_final: 0.6254 (mtm) REVERT: J 199 MET cc_start: 0.6645 (mtm) cc_final: 0.6338 (mtm) REVERT: J 242 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7791 (mtp85) outliers start: 15 outliers final: 1 residues processed: 401 average time/residue: 0.3542 time to fit residues: 206.0128 Evaluate side-chains 276 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 273 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain I residue 137 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 245 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 245 GLN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN J 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115698 restraints weight = 23100.541| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.99 r_work: 0.3118 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19173 Z= 0.180 Angle : 0.604 9.165 26139 Z= 0.315 Chirality : 0.045 0.162 2841 Planarity : 0.005 0.036 3240 Dihedral : 4.941 53.230 2526 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.77 % Rotamer: Outliers : 1.13 % Allowed : 8.00 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2274 helix: 0.96 (0.16), residues: 1002 sheet: -0.32 (0.29), residues: 348 loop : -0.37 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.007 0.002 HIS E 139 PHE 0.013 0.001 PHE J 31 TYR 0.035 0.002 TYR J 37 ARG 0.004 0.001 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 927) hydrogen bonds : angle 5.39042 ( 2691) covalent geometry : bond 0.00427 (19173) covalent geometry : angle 0.60414 (26139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 2.195 Fit side-chains REVERT: A 137 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.7193 (m170) REVERT: A 237 MET cc_start: 0.8652 (mtm) cc_final: 0.8407 (mtt) REVERT: A 358 GLU cc_start: 0.8325 (tt0) cc_final: 0.7850 (tt0) REVERT: A 375 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7639 (mtp-110) REVERT: B 113 TYR cc_start: 0.8487 (m-80) cc_final: 0.8228 (m-80) REVERT: E 137 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7168 (m170) REVERT: E 239 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7275 (t80) REVERT: E 375 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7664 (mtp-110) REVERT: I 137 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7022 (m170) REVERT: I 237 MET cc_start: 0.8667 (mtm) cc_final: 0.8377 (mtp) REVERT: I 239 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7301 (t80) REVERT: I 251 MET cc_start: 0.8497 (ttp) cc_final: 0.8241 (ttt) REVERT: I 285 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8402 (tttp) REVERT: I 375 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7696 (mtp-110) REVERT: K 198 ARG cc_start: 0.8534 (mmt90) cc_final: 0.8316 (mmt90) REVERT: K 263 THR cc_start: 0.9034 (t) cc_final: 0.8604 (m) REVERT: F 113 TYR cc_start: 0.8575 (m-80) cc_final: 0.8284 (m-80) REVERT: F 199 MET cc_start: 0.6952 (mtm) cc_final: 0.6670 (mtm) outliers start: 22 outliers final: 9 residues processed: 328 average time/residue: 0.3377 time to fit residues: 164.0418 Evaluate side-chains 292 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 278 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 HIS E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN I 143 ASN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN F 232 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN J 245 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107388 restraints weight = 22614.241| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.75 r_work: 0.2885 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19173 Z= 0.209 Angle : 0.600 9.880 26139 Z= 0.313 Chirality : 0.046 0.170 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.978 53.609 2526 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 1.74 % Allowed : 10.72 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2274 helix: 0.94 (0.16), residues: 1002 sheet: -0.29 (0.28), residues: 345 loop : -0.39 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 206 HIS 0.008 0.002 HIS F 11 PHE 0.014 0.001 PHE J 31 TYR 0.029 0.002 TYR J 37 ARG 0.005 0.000 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 927) hydrogen bonds : angle 5.22347 ( 2691) covalent geometry : bond 0.00502 (19173) covalent geometry : angle 0.60007 (26139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 2.148 Fit side-chains REVERT: A 137 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7223 (m170) REVERT: A 237 MET cc_start: 0.8626 (mtm) cc_final: 0.8367 (mtt) REVERT: A 368 ASP cc_start: 0.8711 (t0) cc_final: 0.8497 (t0) REVERT: A 375 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7556 (mtp-110) REVERT: E 137 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7245 (m170) REVERT: E 237 MET cc_start: 0.8622 (mtm) cc_final: 0.8270 (mtt) REVERT: E 304 ILE cc_start: 0.8797 (mt) cc_final: 0.8562 (mm) REVERT: E 375 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7549 (mtp-110) REVERT: I 137 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7010 (m170) REVERT: I 237 MET cc_start: 0.8621 (mtm) cc_final: 0.8366 (mtp) REVERT: I 251 MET cc_start: 0.8598 (ttp) cc_final: 0.8268 (ttt) REVERT: I 285 LYS cc_start: 0.8865 (tmmt) cc_final: 0.8354 (tttp) REVERT: I 368 ASP cc_start: 0.8715 (t0) cc_final: 0.8502 (t0) REVERT: I 375 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7518 (mtp-110) REVERT: G 114 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8139 (p) REVERT: F 113 TYR cc_start: 0.8570 (m-80) cc_final: 0.8210 (m-80) REVERT: F 199 MET cc_start: 0.6925 (mtm) cc_final: 0.6601 (mtm) outliers start: 34 outliers final: 21 residues processed: 302 average time/residue: 0.3563 time to fit residues: 162.3725 Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 344 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 207 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109149 restraints weight = 22717.727| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.75 r_work: 0.3018 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19173 Z= 0.141 Angle : 0.549 9.805 26139 Z= 0.284 Chirality : 0.043 0.163 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.837 51.502 2526 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 1.28 % Allowed : 12.41 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2274 helix: 1.12 (0.16), residues: 1002 sheet: -0.18 (0.29), residues: 327 loop : -0.45 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.004 0.001 HIS J 11 PHE 0.013 0.001 PHE J 31 TYR 0.023 0.002 TYR C 210 ARG 0.006 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 927) hydrogen bonds : angle 5.07563 ( 2691) covalent geometry : bond 0.00326 (19173) covalent geometry : angle 0.54866 (26139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 2.517 Fit side-chains REVERT: A 237 MET cc_start: 0.8646 (mtm) cc_final: 0.8414 (mtt) REVERT: A 375 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7720 (mtp-110) REVERT: E 137 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7508 (m170) REVERT: E 237 MET cc_start: 0.8651 (mtm) cc_final: 0.8332 (mtt) REVERT: E 239 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7333 (t80) REVERT: E 375 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7739 (mtp-110) REVERT: I 137 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7356 (m170) REVERT: I 237 MET cc_start: 0.8658 (mtm) cc_final: 0.8409 (mtp) REVERT: I 239 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7262 (t80) REVERT: I 251 MET cc_start: 0.8606 (ttp) cc_final: 0.8307 (ttt) REVERT: I 285 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8542 (tttp) REVERT: I 368 ASP cc_start: 0.8572 (t0) cc_final: 0.8372 (t0) REVERT: I 375 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: G 114 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8155 (p) REVERT: F 113 TYR cc_start: 0.8535 (m-80) cc_final: 0.8262 (m-80) outliers start: 25 outliers final: 17 residues processed: 283 average time/residue: 0.4077 time to fit residues: 175.3601 Evaluate side-chains 270 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105687 restraints weight = 23118.487| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.80 r_work: 0.2963 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19173 Z= 0.183 Angle : 0.575 10.654 26139 Z= 0.298 Chirality : 0.045 0.160 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.747 52.974 2524 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 2.46 % Allowed : 12.51 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2274 helix: 1.10 (0.16), residues: 1002 sheet: -0.23 (0.28), residues: 327 loop : -0.46 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.004 0.001 HIS J 232 PHE 0.015 0.001 PHE J 31 TYR 0.026 0.002 TYR G 210 ARG 0.006 0.001 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 927) hydrogen bonds : angle 5.02423 ( 2691) covalent geometry : bond 0.00440 (19173) covalent geometry : angle 0.57512 (26139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 2.924 Fit side-chains REVERT: A 237 MET cc_start: 0.8701 (mtm) cc_final: 0.8461 (mtt) REVERT: A 375 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7697 (mtp-110) REVERT: E 237 MET cc_start: 0.8692 (mtm) cc_final: 0.8445 (mtt) REVERT: E 375 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7736 (mtp-110) REVERT: I 137 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7358 (m170) REVERT: I 237 MET cc_start: 0.8678 (mtm) cc_final: 0.8419 (mtp) REVERT: I 251 MET cc_start: 0.8696 (ttp) cc_final: 0.8367 (ttt) REVERT: I 285 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8496 (tttp) REVERT: I 368 ASP cc_start: 0.8546 (t0) cc_final: 0.8317 (t0) REVERT: I 375 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7711 (mtp85) REVERT: G 114 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8169 (p) REVERT: F 113 TYR cc_start: 0.8548 (m-80) cc_final: 0.8277 (m-80) outliers start: 48 outliers final: 36 residues processed: 285 average time/residue: 0.3801 time to fit residues: 167.8857 Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 131 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 200 optimal weight: 0.0870 chunk 29 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.115615 restraints weight = 23378.497| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.06 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19173 Z= 0.120 Angle : 0.539 11.321 26139 Z= 0.277 Chirality : 0.043 0.161 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.630 51.117 2524 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 1.79 % Allowed : 13.85 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2274 helix: 1.26 (0.16), residues: 990 sheet: -0.10 (0.28), residues: 321 loop : -0.43 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 152 HIS 0.002 0.001 HIS A 139 PHE 0.012 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.006 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 927) hydrogen bonds : angle 4.92430 ( 2691) covalent geometry : bond 0.00270 (19173) covalent geometry : angle 0.53886 (26139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 2.257 Fit side-chains REVERT: A 237 MET cc_start: 0.8648 (mtm) cc_final: 0.8399 (mtt) REVERT: A 375 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7588 (mtp-110) REVERT: E 137 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7664 (m170) REVERT: E 163 MET cc_start: 0.8764 (ttt) cc_final: 0.8526 (ttt) REVERT: E 237 MET cc_start: 0.8652 (mtm) cc_final: 0.8279 (mtt) REVERT: E 375 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7619 (mtp-110) REVERT: I 137 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7602 (m170) REVERT: I 237 MET cc_start: 0.8659 (mtm) cc_final: 0.8408 (mtp) REVERT: I 251 MET cc_start: 0.8624 (ttp) cc_final: 0.8270 (ttt) REVERT: I 285 LYS cc_start: 0.8908 (tmmt) cc_final: 0.8399 (tttp) REVERT: I 375 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7657 (mtp85) REVERT: G 114 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8016 (p) REVERT: F 113 TYR cc_start: 0.8492 (m-80) cc_final: 0.8193 (m-80) outliers start: 35 outliers final: 21 residues processed: 276 average time/residue: 0.3604 time to fit residues: 152.2409 Evaluate side-chains 267 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 210 TYR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain J residue 8 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106679 restraints weight = 23353.024| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.96 r_work: 0.2804 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19173 Z= 0.244 Angle : 0.610 11.871 26139 Z= 0.316 Chirality : 0.046 0.162 2841 Planarity : 0.004 0.037 3240 Dihedral : 4.833 54.501 2524 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 2.31 % Allowed : 14.00 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2274 helix: 1.15 (0.16), residues: 990 sheet: -0.06 (0.29), residues: 309 loop : -0.60 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 237 HIS 0.004 0.001 HIS J 40 PHE 0.017 0.002 PHE J 31 TYR 0.029 0.002 TYR G 210 ARG 0.006 0.001 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 927) hydrogen bonds : angle 5.04287 ( 2691) covalent geometry : bond 0.00590 (19173) covalent geometry : angle 0.61007 (26139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.967 Fit side-chains REVERT: A 237 MET cc_start: 0.8617 (mtm) cc_final: 0.8344 (mtt) REVERT: A 375 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7456 (mmm160) REVERT: E 237 MET cc_start: 0.8577 (mtm) cc_final: 0.8110 (mtt) REVERT: E 375 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7433 (mtp-110) REVERT: I 137 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7486 (m170) REVERT: I 237 MET cc_start: 0.8597 (mtm) cc_final: 0.8241 (mtp) REVERT: I 251 MET cc_start: 0.8713 (ttp) cc_final: 0.8456 (ttt) REVERT: I 285 LYS cc_start: 0.8800 (tmmt) cc_final: 0.8206 (tttp) REVERT: I 375 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7530 (mtt180) REVERT: G 114 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8032 (p) REVERT: F 113 TYR cc_start: 0.8541 (m-80) cc_final: 0.8218 (m-80) outliers start: 45 outliers final: 35 residues processed: 269 average time/residue: 0.3127 time to fit residues: 128.2199 Evaluate side-chains 271 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106556 restraints weight = 23333.049| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.95 r_work: 0.2819 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19173 Z= 0.146 Angle : 0.563 13.039 26139 Z= 0.288 Chirality : 0.044 0.165 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.742 53.031 2524 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 1.85 % Allowed : 14.72 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2274 helix: 1.28 (0.16), residues: 990 sheet: -0.22 (0.28), residues: 321 loop : -0.45 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.003 0.001 HIS F 40 PHE 0.013 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.006 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 927) hydrogen bonds : angle 4.96605 ( 2691) covalent geometry : bond 0.00342 (19173) covalent geometry : angle 0.56305 (26139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 2.288 Fit side-chains REVERT: A 167 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7608 (mtm-85) REVERT: A 237 MET cc_start: 0.8589 (mtm) cc_final: 0.8306 (mtt) REVERT: A 316 GLU cc_start: 0.8760 (tt0) cc_final: 0.8547 (tt0) REVERT: A 375 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7378 (mmm160) REVERT: E 167 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7453 (mtm-85) REVERT: E 237 MET cc_start: 0.8540 (mtm) cc_final: 0.8056 (mtt) REVERT: E 375 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7403 (mtp-110) REVERT: I 137 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7601 (m170) REVERT: I 167 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7513 (mtm-85) REVERT: I 237 MET cc_start: 0.8579 (mtm) cc_final: 0.8208 (mtp) REVERT: I 251 MET cc_start: 0.8649 (ttp) cc_final: 0.8222 (ttt) REVERT: I 285 LYS cc_start: 0.8777 (tmmt) cc_final: 0.8203 (tttp) REVERT: I 375 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7549 (mmt90) REVERT: C 129 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8007 (ttp-110) REVERT: G 114 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7983 (p) REVERT: K 129 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8087 (ttp-110) REVERT: F 113 TYR cc_start: 0.8519 (m-80) cc_final: 0.8149 (m-80) outliers start: 36 outliers final: 25 residues processed: 260 average time/residue: 0.3494 time to fit residues: 135.5118 Evaluate side-chains 256 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 217 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN B 103 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN F 103 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110300 restraints weight = 23438.608| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.95 r_work: 0.3087 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19173 Z= 0.141 Angle : 0.569 13.648 26139 Z= 0.291 Chirality : 0.044 0.162 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.689 53.130 2524 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 2.10 % Allowed : 14.67 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2274 helix: 1.31 (0.16), residues: 990 sheet: -0.26 (0.28), residues: 321 loop : -0.43 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 206 HIS 0.002 0.001 HIS A 137 PHE 0.013 0.001 PHE J 31 TYR 0.022 0.001 TYR K 184 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 927) hydrogen bonds : angle 4.94306 ( 2691) covalent geometry : bond 0.00329 (19173) covalent geometry : angle 0.56921 (26139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 2.075 Fit side-chains revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7588 (mtm-85) REVERT: A 237 MET cc_start: 0.8650 (mtm) cc_final: 0.8383 (mtt) REVERT: A 375 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7638 (mmm160) REVERT: E 163 MET cc_start: 0.8766 (ttt) cc_final: 0.8515 (ttt) REVERT: E 167 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7433 (mtm-85) REVERT: E 237 MET cc_start: 0.8673 (mtm) cc_final: 0.8365 (mtt) REVERT: E 375 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7705 (mtp-110) REVERT: I 137 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7721 (m170) REVERT: I 167 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7511 (mtm-85) REVERT: I 237 MET cc_start: 0.8672 (mtm) cc_final: 0.8352 (mtt) REVERT: I 251 MET cc_start: 0.8739 (ttp) cc_final: 0.8355 (ttt) REVERT: I 285 LYS cc_start: 0.8959 (tmmt) cc_final: 0.8488 (tttp) REVERT: I 375 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7837 (mmt90) REVERT: C 126 GLU cc_start: 0.8554 (tp30) cc_final: 0.8283 (tp30) REVERT: G 126 GLU cc_start: 0.8499 (tp30) cc_final: 0.8279 (tp30) REVERT: G 198 ARG cc_start: 0.8709 (mmt90) cc_final: 0.8344 (mmt90) REVERT: K 126 GLU cc_start: 0.8715 (tp30) cc_final: 0.8513 (tp30) REVERT: F 113 TYR cc_start: 0.8507 (m-80) cc_final: 0.8239 (m-80) outliers start: 41 outliers final: 31 residues processed: 270 average time/residue: 0.3243 time to fit residues: 131.6839 Evaluate side-chains 268 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 103 ASN Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 0.4980 chunk 127 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 123 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 overall best weight: 0.2926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN B 103 ASN F 103 ASN F 184 GLN J 103 ASN J 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113002 restraints weight = 23352.712| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19173 Z= 0.115 Angle : 0.557 14.597 26139 Z= 0.283 Chirality : 0.043 0.162 2841 Planarity : 0.004 0.037 3240 Dihedral : 4.626 52.346 2524 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 1.59 % Allowed : 14.92 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2274 helix: 1.37 (0.16), residues: 990 sheet: -0.28 (0.28), residues: 321 loop : -0.40 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.002 0.001 HIS B 232 PHE 0.013 0.001 PHE A 392 TYR 0.022 0.001 TYR C 184 ARG 0.009 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 927) hydrogen bonds : angle 4.88197 ( 2691) covalent geometry : bond 0.00251 (19173) covalent geometry : angle 0.55696 (26139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7558 (mtm-85) REVERT: A 237 MET cc_start: 0.8645 (mtm) cc_final: 0.8367 (mtt) REVERT: A 375 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7610 (mmm160) REVERT: E 163 MET cc_start: 0.8749 (ttt) cc_final: 0.8502 (ttt) REVERT: E 167 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7388 (mtm-85) REVERT: E 237 MET cc_start: 0.8671 (mtm) cc_final: 0.8356 (mtt) REVERT: E 375 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7726 (mmm160) REVERT: I 137 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7758 (m170) REVERT: I 167 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7534 (mtm-85) REVERT: I 237 MET cc_start: 0.8672 (mtm) cc_final: 0.8361 (mtt) REVERT: I 251 MET cc_start: 0.8651 (ttp) cc_final: 0.8291 (ttt) REVERT: I 285 LYS cc_start: 0.8933 (tmmt) cc_final: 0.8509 (tttp) REVERT: I 375 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7807 (mmt90) REVERT: C 126 GLU cc_start: 0.8537 (tp30) cc_final: 0.8273 (tp30) REVERT: G 126 GLU cc_start: 0.8516 (tp30) cc_final: 0.8279 (tp30) REVERT: F 113 TYR cc_start: 0.8461 (m-80) cc_final: 0.8178 (m-80) outliers start: 31 outliers final: 25 residues processed: 271 average time/residue: 0.3257 time to fit residues: 132.5707 Evaluate side-chains 269 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 103 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109868 restraints weight = 23412.186| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.96 r_work: 0.3029 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19173 Z= 0.184 Angle : 0.589 14.564 26139 Z= 0.300 Chirality : 0.044 0.158 2841 Planarity : 0.004 0.037 3240 Dihedral : 4.694 54.143 2524 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 2.05 % Allowed : 14.87 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2274 helix: 1.37 (0.16), residues: 990 sheet: -0.34 (0.28), residues: 321 loop : -0.47 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 237 HIS 0.003 0.001 HIS E 192 PHE 0.015 0.001 PHE J 31 TYR 0.022 0.002 TYR C 184 ARG 0.008 0.000 ARG J 104 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 927) hydrogen bonds : angle 4.86750 ( 2691) covalent geometry : bond 0.00442 (19173) covalent geometry : angle 0.58913 (26139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9752.86 seconds wall clock time: 171 minutes 13.55 seconds (10273.55 seconds total)