Starting phenix.real_space_refine on Tue Aug 26 02:56:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr5_40720/08_2025/8sr5_40720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr5_40720/08_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_40720/08_2025/8sr5_40720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr5_40720/08_2025/8sr5_40720.map" model { file = "/net/cci-nas-00/data/ceres_data/8sr5_40720/08_2025/8sr5_40720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr5_40720/08_2025/8sr5_40720.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: E, I, F, J, G, K Time building chain proxies: 4.06, per 1000 atoms: 0.22 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: 1.65 Conformation dependent library (CDL) restraints added in 798.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.78 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: 3.11 Time building geometry restraints manager: 2.11 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- 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 : 13.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG K 198 TYR 0.070 0.002 TYR B 37 PHE 0.013 0.001 PHE J 50 TRP 0.039 0.002 TRP E 206 HIS 0.004 0.001 HIS I 139 Details of bonding type rmsd covalent geometry : bond 0.00583 (19173) covalent geometry : angle 0.78386 (26139) hydrogen bonds : bond 0.16023 ( 927) hydrogen bonds : angle 6.79385 ( 2691) *********************** 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 : 0.491 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: 0.7540 (mtp) REVERT: A 368 ASP cc_start: 0.8396 (t70) cc_final: 0.8130 (t0) REVERT: A 375 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7210 (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: 0.6253 (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: 0.6030 (m170) REVERT: I 237 MET cc_start: 0.7836 (mtm) cc_final: 0.7505 (mtp) REVERT: I 251 MET cc_start: 0.7538 (ttp) cc_final: 0.7301 (ttt) REVERT: I 285 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7877 (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: 0.6336 (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: 0.1459 time to fit residues: 85.6095 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 : 0.520 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** 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 I 401 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119858 restraints weight = 23329.096| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.04 r_work: 0.3096 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19173 Z= 0.157 Angle : 0.591 9.160 26139 Z= 0.307 Chirality : 0.044 0.161 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.910 52.852 2526 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.94 % Rotamer: Outliers : 0.97 % Allowed : 8.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2274 helix: 1.02 (0.16), residues: 1002 sheet: -0.27 (0.29), residues: 348 loop : -0.34 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 125 TYR 0.034 0.002 TYR J 37 PHE 0.010 0.001 PHE C 269 TRP 0.015 0.001 TRP E 206 HIS 0.008 0.002 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00366 (19173) covalent geometry : angle 0.59059 (26139) hydrogen bonds : bond 0.04171 ( 927) hydrogen bonds : angle 5.39955 ( 2691) *********************** 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 342 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 0.651 Fit side-chains REVERT: A 137 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7198 (m170) REVERT: A 143 ASN cc_start: 0.8609 (m110) cc_final: 0.8281 (m110) REVERT: A 237 MET cc_start: 0.8626 (mtm) cc_final: 0.8373 (mtt) REVERT: A 358 GLU cc_start: 0.8311 (tt0) cc_final: 0.8103 (tm-30) REVERT: A 375 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7599 (mtp-110) REVERT: B 199 MET cc_start: 0.6869 (mtm) cc_final: 0.6622 (mtm) REVERT: E 137 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.7137 (m170) REVERT: E 163 MET cc_start: 0.8819 (ttt) cc_final: 0.8506 (ttt) REVERT: E 239 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7246 (t80) REVERT: E 375 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7619 (mtp-110) REVERT: I 137 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7018 (m170) REVERT: I 143 ASN cc_start: 0.8599 (m110) cc_final: 0.8349 (m-40) REVERT: I 237 MET cc_start: 0.8639 (mtm) cc_final: 0.8339 (mtp) REVERT: I 239 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7265 (t80) REVERT: I 251 MET cc_start: 0.8413 (ttp) cc_final: 0.8186 (ttt) REVERT: I 285 LYS cc_start: 0.8789 (tmmt) cc_final: 0.8378 (tttp) REVERT: I 375 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7660 (mtp-110) REVERT: K 198 ARG cc_start: 0.8506 (mmt90) cc_final: 0.8295 (mmt90) REVERT: K 263 THR cc_start: 0.9010 (t) cc_final: 0.8559 (m) REVERT: F 113 TYR cc_start: 0.8549 (m-80) cc_final: 0.8267 (m-80) REVERT: F 199 MET cc_start: 0.6903 (mtm) cc_final: 0.6615 (mtm) outliers start: 19 outliers final: 9 residues processed: 336 average time/residue: 0.1568 time to fit residues: 78.5575 Evaluate side-chains 303 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 289 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 117 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 108 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN E 108 GLN E 143 ASN I 62 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116404 restraints weight = 23161.116| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.00 r_work: 0.3085 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19173 Z= 0.144 Angle : 0.560 9.996 26139 Z= 0.291 Chirality : 0.044 0.161 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.807 52.002 2526 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 1.13 % Allowed : 10.51 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2274 helix: 1.13 (0.16), residues: 1002 sheet: -0.15 (0.29), residues: 348 loop : -0.32 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 242 TYR 0.025 0.002 TYR F 37 PHE 0.011 0.001 PHE E 71 TRP 0.012 0.001 TRP E 206 HIS 0.005 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00335 (19173) covalent geometry : angle 0.56011 (26139) hydrogen bonds : bond 0.03878 ( 927) hydrogen bonds : angle 5.18201 ( 2691) *********************** 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 306 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 284 time to evaluate : 0.746 Fit side-chains REVERT: A 137 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7196 (m170) REVERT: A 237 MET cc_start: 0.8637 (mtm) cc_final: 0.8389 (mtt) REVERT: A 375 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7627 (mtp-110) REVERT: B 199 MET cc_start: 0.6886 (mtm) cc_final: 0.6428 (mtm) REVERT: E 137 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7258 (m170) REVERT: E 143 ASN cc_start: 0.8658 (m110) cc_final: 0.8257 (m-40) REVERT: E 237 MET cc_start: 0.8620 (mtm) cc_final: 0.8251 (mtt) REVERT: E 239 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7177 (t80) REVERT: E 288 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8495 (p0) REVERT: E 375 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7617 (mtp-110) REVERT: I 137 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7087 (m170) REVERT: I 237 MET cc_start: 0.8625 (mtm) cc_final: 0.8389 (mtp) REVERT: I 239 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7165 (t80) REVERT: I 251 MET cc_start: 0.8439 (ttp) cc_final: 0.8189 (ttt) REVERT: I 285 LYS cc_start: 0.8840 (tmmt) cc_final: 0.8379 (tttp) REVERT: I 288 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8493 (p0) REVERT: I 375 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7637 (mtp-110) REVERT: G 114 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (p) REVERT: K 198 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8212 (mmt90) REVERT: F 199 MET cc_start: 0.6908 (mtm) cc_final: 0.6597 (mtm) outliers start: 22 outliers final: 8 residues processed: 300 average time/residue: 0.1520 time to fit residues: 69.5575 Evaluate side-chains 281 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 288 ASP 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 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 122 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 141 optimal weight: 0.7980 chunk 110 optimal weight: 0.1980 chunk 69 optimal weight: 0.2980 chunk 217 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** E 62 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120080 restraints weight = 23297.571| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3173 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19173 Z= 0.117 Angle : 0.532 9.747 26139 Z= 0.275 Chirality : 0.043 0.155 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.673 50.405 2526 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.49 % Allowed : 11.54 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2274 helix: 1.26 (0.16), residues: 999 sheet: -0.06 (0.29), residues: 327 loop : -0.39 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 242 TYR 0.023 0.002 TYR C 184 PHE 0.011 0.001 PHE A 394 TRP 0.011 0.001 TRP B 237 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00263 (19173) covalent geometry : angle 0.53178 (26139) hydrogen bonds : bond 0.03586 ( 927) hydrogen bonds : angle 4.97785 ( 2691) *********************** 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 305 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.491 Fit side-chains REVERT: A 104 TYR cc_start: 0.8996 (m-80) cc_final: 0.8787 (m-80) REVERT: A 143 ASN cc_start: 0.8481 (m-40) cc_final: 0.8141 (m-40) REVERT: A 237 MET cc_start: 0.8621 (mtm) cc_final: 0.8358 (mtt) REVERT: A 375 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7656 (mtp-110) REVERT: B 199 MET cc_start: 0.6773 (mtm) cc_final: 0.6524 (mtm) REVERT: E 137 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7335 (m170) REVERT: E 237 MET cc_start: 0.8651 (mtm) cc_final: 0.8266 (mtt) REVERT: E 239 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7253 (t80) REVERT: E 288 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8499 (p0) REVERT: E 375 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7662 (mtp-110) REVERT: I 137 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7083 (m170) REVERT: I 237 MET cc_start: 0.8654 (mtm) cc_final: 0.8395 (mtp) REVERT: I 239 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7231 (t80) REVERT: I 251 MET cc_start: 0.8369 (ttp) cc_final: 0.8127 (ttt) REVERT: I 288 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8550 (p0) REVERT: I 375 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7716 (mtp85) REVERT: G 198 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8138 (mmt90) REVERT: F 93 VAL cc_start: 0.8900 (t) cc_final: 0.8667 (m) REVERT: J 93 VAL cc_start: 0.8898 (t) cc_final: 0.8663 (m) outliers start: 29 outliers final: 15 residues processed: 298 average time/residue: 0.1314 time to fit residues: 59.9519 Evaluate side-chains 285 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 344 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 239 PHE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL 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 J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 221 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 175 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 187 ASN E 108 GLN J 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113892 restraints weight = 23324.922| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.97 r_work: 0.3149 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19173 Z= 0.119 Angle : 0.533 10.340 26139 Z= 0.275 Chirality : 0.043 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.505 49.935 2524 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 1.74 % Allowed : 11.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2274 helix: 1.33 (0.16), residues: 999 sheet: 0.01 (0.29), residues: 327 loop : -0.37 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 9 TYR 0.022 0.001 TYR C 184 PHE 0.009 0.001 PHE A 71 TRP 0.013 0.001 TRP J 237 HIS 0.003 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00269 (19173) covalent geometry : angle 0.53328 (26139) hydrogen bonds : bond 0.03529 ( 927) hydrogen bonds : angle 4.89901 ( 2691) *********************** 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 302 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.714 Fit side-chains REVERT: A 237 MET cc_start: 0.8604 (mtm) cc_final: 0.8343 (mtt) REVERT: A 375 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7587 (mtp-110) REVERT: B 199 MET cc_start: 0.6812 (mtm) cc_final: 0.6549 (mtm) REVERT: E 237 MET cc_start: 0.8681 (mtm) cc_final: 0.8280 (mtt) REVERT: E 239 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7187 (t80) REVERT: E 288 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8516 (p0) REVERT: E 375 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7629 (mtp-110) REVERT: I 137 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (m170) REVERT: I 237 MET cc_start: 0.8641 (mtm) cc_final: 0.8379 (mtp) REVERT: I 239 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7240 (t80) REVERT: I 251 MET cc_start: 0.8335 (ttp) cc_final: 0.8083 (ttt) REVERT: I 288 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8514 (p0) REVERT: I 375 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7633 (mtp85) REVERT: K 198 ARG cc_start: 0.8473 (mmt90) cc_final: 0.8099 (mmt90) REVERT: F 93 VAL cc_start: 0.8873 (t) cc_final: 0.8645 (m) REVERT: J 93 VAL cc_start: 0.8873 (t) cc_final: 0.8643 (m) outliers start: 34 outliers final: 17 residues processed: 293 average time/residue: 0.1285 time to fit residues: 57.6724 Evaluate side-chains 284 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 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 E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 344 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 288 ASP 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 K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 166 optimal weight: 0.0020 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 174 optimal weight: 5.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 F 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112562 restraints weight = 23331.765| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.97 r_work: 0.3152 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19173 Z= 0.116 Angle : 0.527 11.107 26139 Z= 0.270 Chirality : 0.042 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.362 50.117 2522 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 12.87 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2274 helix: 1.36 (0.16), residues: 996 sheet: 0.10 (0.29), residues: 321 loop : -0.38 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 9 TYR 0.022 0.001 TYR C 184 PHE 0.010 0.001 PHE A 394 TRP 0.014 0.001 TRP F 237 HIS 0.003 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00262 (19173) covalent geometry : angle 0.52661 (26139) hydrogen bonds : bond 0.03490 ( 927) hydrogen bonds : angle 4.84695 ( 2691) *********************** 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 309 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.488 Fit side-chains REVERT: A 143 ASN cc_start: 0.8484 (m-40) cc_final: 0.8080 (m-40) REVERT: A 237 MET cc_start: 0.8587 (mtm) cc_final: 0.8345 (mtt) REVERT: A 375 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7521 (mtp85) REVERT: B 199 MET cc_start: 0.6834 (mtm) cc_final: 0.6566 (mtm) REVERT: E 237 MET cc_start: 0.8653 (mtm) cc_final: 0.8242 (mtt) REVERT: E 239 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7196 (t80) REVERT: E 288 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8538 (p0) REVERT: E 375 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7700 (mtt180) REVERT: I 137 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7406 (m170) REVERT: I 237 MET cc_start: 0.8628 (mtm) cc_final: 0.8232 (mtt) REVERT: I 239 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7183 (t80) REVERT: I 251 MET cc_start: 0.8346 (ttp) cc_final: 0.8079 (ttt) REVERT: I 375 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7627 (mtp85) REVERT: K 198 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8050 (mmt90) REVERT: F 93 VAL cc_start: 0.8850 (t) cc_final: 0.8619 (m) REVERT: J 93 VAL cc_start: 0.8853 (t) cc_final: 0.8624 (m) outliers start: 35 outliers final: 23 residues processed: 300 average time/residue: 0.1418 time to fit residues: 64.4108 Evaluate side-chains 279 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 60 LYS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 288 ASP 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 60 LYS Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE 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 213 LEU 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 K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 33 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 219 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN F 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111031 restraints weight = 23436.661| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.98 r_work: 0.3131 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2648 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= 0.131 Angle : 0.542 11.040 26139 Z= 0.278 Chirality : 0.043 0.155 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.378 50.427 2522 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 1.79 % Allowed : 13.33 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2274 helix: 1.34 (0.16), residues: 999 sheet: 0.02 (0.29), residues: 321 loop : -0.36 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 9 TYR 0.023 0.002 TYR K 184 PHE 0.011 0.001 PHE A 98 TRP 0.016 0.001 TRP J 237 HIS 0.003 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00305 (19173) covalent geometry : angle 0.54192 (26139) hydrogen bonds : bond 0.03549 ( 927) hydrogen bonds : angle 4.83997 ( 2691) *********************** 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 287 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.706 Fit side-chains REVERT: A 237 MET cc_start: 0.8591 (mtm) cc_final: 0.8338 (mtt) REVERT: A 375 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7608 (mmm160) REVERT: B 199 MET cc_start: 0.6877 (mtm) cc_final: 0.6608 (mtm) REVERT: E 237 MET cc_start: 0.8687 (mtm) cc_final: 0.8289 (mtt) REVERT: E 239 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7300 (t80) REVERT: E 288 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8535 (p0) REVERT: E 375 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7682 (mtt180) REVERT: I 137 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7445 (m170) REVERT: I 237 MET cc_start: 0.8624 (mtm) cc_final: 0.8221 (mtt) REVERT: I 239 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7184 (t80) REVERT: I 251 MET cc_start: 0.8387 (ttp) cc_final: 0.8107 (ttt) REVERT: I 375 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7605 (mtp-110) REVERT: K 198 ARG cc_start: 0.8504 (mmt90) cc_final: 0.8068 (mmt90) REVERT: F 93 VAL cc_start: 0.8877 (t) cc_final: 0.8620 (m) REVERT: J 93 VAL cc_start: 0.8868 (t) cc_final: 0.8613 (m) outliers start: 35 outliers final: 26 residues processed: 277 average time/residue: 0.1539 time to fit residues: 64.2351 Evaluate side-chains 277 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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 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 E residue 260 ILE Chi-restraints excluded: chain E residue 288 ASP 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 E residue 354 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE 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 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 0.0060 chunk 129 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113913 restraints weight = 23166.763| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.98 r_work: 0.3139 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2749 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= 0.122 Angle : 0.536 11.985 26139 Z= 0.273 Chirality : 0.042 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.356 50.258 2522 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 1.79 % Allowed : 13.44 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2274 helix: 1.38 (0.16), residues: 999 sheet: -0.03 (0.29), residues: 321 loop : -0.33 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 9 TYR 0.022 0.001 TYR K 184 PHE 0.010 0.001 PHE A 98 TRP 0.017 0.001 TRP J 237 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00283 (19173) covalent geometry : angle 0.53590 (26139) hydrogen bonds : bond 0.03503 ( 927) hydrogen bonds : angle 4.81296 ( 2691) *********************** 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 290 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.704 Fit side-chains REVERT: A 237 MET cc_start: 0.8583 (mtm) cc_final: 0.8341 (mtt) REVERT: A 375 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7603 (mmm160) REVERT: B 93 VAL cc_start: 0.8866 (t) cc_final: 0.8606 (m) REVERT: B 199 MET cc_start: 0.6871 (mtm) cc_final: 0.6592 (mtm) REVERT: E 143 ASN cc_start: 0.8360 (m-40) cc_final: 0.8070 (m-40) REVERT: E 237 MET cc_start: 0.8679 (mtm) cc_final: 0.8254 (mtt) REVERT: E 239 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7257 (t80) REVERT: E 375 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7689 (mtt180) REVERT: I 137 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7503 (m170) REVERT: I 237 MET cc_start: 0.8621 (mtm) cc_final: 0.8227 (mtt) REVERT: I 239 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7220 (t80) REVERT: I 251 MET cc_start: 0.8399 (ttp) cc_final: 0.8112 (ttt) REVERT: I 375 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7700 (mmm160) REVERT: K 198 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8084 (mmt90) REVERT: F 93 VAL cc_start: 0.8893 (t) cc_final: 0.8636 (m) REVERT: F 197 ILE cc_start: 0.4725 (OUTLIER) cc_final: 0.4472 (mt) REVERT: J 93 VAL cc_start: 0.8870 (t) cc_final: 0.8613 (m) outliers start: 35 outliers final: 25 residues processed: 279 average time/residue: 0.1504 time to fit residues: 63.4978 Evaluate side-chains 279 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain E residue 260 ILE 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 137 HIS Chi-restraints excluded: chain I residue 239 PHE 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 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 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 130 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 144 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109547 restraints weight = 23363.104| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.98 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19173 Z= 0.167 Angle : 0.571 13.063 26139 Z= 0.292 Chirality : 0.044 0.156 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.453 51.886 2522 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 1.64 % Allowed : 13.64 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2274 helix: 1.31 (0.16), residues: 996 sheet: -0.15 (0.29), residues: 321 loop : -0.39 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 9 TYR 0.025 0.002 TYR C 210 PHE 0.013 0.001 PHE A 98 TRP 0.019 0.001 TRP B 237 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00400 (19173) covalent geometry : angle 0.57128 (26139) hydrogen bonds : bond 0.03782 ( 927) hydrogen bonds : angle 4.87967 ( 2691) *********************** 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 288 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.656 Fit side-chains REVERT: A 237 MET cc_start: 0.8643 (mtm) cc_final: 0.8360 (mtt) REVERT: A 273 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8190 (ttpp) REVERT: A 375 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7629 (mmm160) REVERT: B 199 MET cc_start: 0.6952 (mtm) cc_final: 0.6656 (mtm) REVERT: E 375 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7611 (mtp-110) REVERT: I 137 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (m170) REVERT: I 237 MET cc_start: 0.8649 (mtm) cc_final: 0.8352 (mtp) REVERT: I 251 MET cc_start: 0.8578 (ttp) cc_final: 0.8237 (ttt) REVERT: I 375 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7697 (mmm160) REVERT: J 47 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7922 (t0) outliers start: 32 outliers final: 24 residues processed: 277 average time/residue: 0.1472 time to fit residues: 62.1123 Evaluate side-chains 270 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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 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 260 ILE 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 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 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 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 196 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** J 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108360 restraints weight = 23259.094| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.95 r_work: 0.3023 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19173 Z= 0.180 Angle : 0.584 15.131 26139 Z= 0.296 Chirality : 0.044 0.157 2841 Planarity : 0.004 0.034 3240 Dihedral : 4.544 52.817 2522 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 1.49 % Allowed : 13.90 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2274 helix: 1.23 (0.16), residues: 1002 sheet: -0.22 (0.28), residues: 321 loop : -0.41 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 9 TYR 0.026 0.002 TYR C 210 PHE 0.013 0.001 PHE A 98 TRP 0.021 0.001 TRP J 237 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00435 (19173) covalent geometry : angle 0.58382 (26139) hydrogen bonds : bond 0.03829 ( 927) hydrogen bonds : angle 4.91398 ( 2691) ********************** 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 271 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.705 Fit side-chains REVERT: A 237 MET cc_start: 0.8677 (mtm) cc_final: 0.8378 (mtt) REVERT: A 272 MET cc_start: 0.8541 (mtp) cc_final: 0.8200 (mmt) REVERT: A 375 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7627 (mmm160) REVERT: B 199 MET cc_start: 0.6979 (mtm) cc_final: 0.6682 (mtm) REVERT: E 237 MET cc_start: 0.8679 (mtm) cc_final: 0.8358 (mtt) REVERT: E 375 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7566 (mtp-110) REVERT: I 137 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7626 (m170) REVERT: I 237 MET cc_start: 0.8693 (mtm) cc_final: 0.8377 (mtp) REVERT: I 251 MET cc_start: 0.8647 (ttp) cc_final: 0.8274 (ttt) REVERT: I 375 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7664 (mmm160) REVERT: K 198 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8273 (mmt90) outliers start: 29 outliers final: 26 residues processed: 263 average time/residue: 0.1491 time to fit residues: 59.6265 Evaluate side-chains 262 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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 18 SER Chi-restraints excluded: chain B residue 47 ASP 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 260 ILE 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 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 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 43 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 167 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** I 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106683 restraints weight = 23480.858| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.97 r_work: 0.2996 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19173 Z= 0.200 Angle : 0.601 14.513 26139 Z= 0.306 Chirality : 0.045 0.156 2841 Planarity : 0.004 0.034 3240 Dihedral : 4.637 53.874 2522 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 1.54 % Allowed : 14.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 2274 helix: 1.15 (0.16), residues: 1005 sheet: -0.30 (0.28), residues: 324 loop : -0.43 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 129 TYR 0.030 0.002 TYR G 210 PHE 0.013 0.001 PHE A 98 TRP 0.022 0.001 TRP J 237 HIS 0.004 0.001 HIS F 11 Details of bonding type rmsd covalent geometry : bond 0.00485 (19173) covalent geometry : angle 0.60140 (26139) hydrogen bonds : bond 0.03950 ( 927) hydrogen bonds : angle 4.95000 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.32 seconds wall clock time: 83 minutes 1.04 seconds (4981.04 seconds total)