Starting phenix.real_space_refine on Thu May 29 23:45:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr5_40720/05_2025/8sr5_40720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr5_40720/05_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_40720/05_2025/8sr5_40720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr5_40720/05_2025/8sr5_40720.map" model { file = "/net/cci-nas-00/data/ceres_data/8sr5_40720/05_2025/8sr5_40720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr5_40720/05_2025/8sr5_40720.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17727 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 87 5.16 5 C 12246 2.51 5 N 3042 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: G, K, F, J, E, I Time building chain proxies: 9.59, per 1000 atoms: 0.52 Number of scatterers: 18588 At special positions: 0 Unit cell: (106.349, 104.762, 119.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 87 16.00 O 3207 8.00 N 3042 7.00 C 12246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 49.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 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: 6.44 Time building geometry restraints manager: 5.36 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: 0.13 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 43.100 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 19173 Z= 0.338 Angle : 0.784 36.751 26139 Z= 0.471 Chirality : 0.045 0.208 2841 Planarity : 0.004 0.038 3240 Dihedral : 13.263 86.169 6672 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.85 % Favored : 93.76 % Rotamer: Outliers : 0.77 % Allowed : 0.67 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2274 helix: 0.94 (0.16), residues: 981 sheet: 0.73 (0.35), residues: 246 loop : -0.67 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 206 HIS 0.004 0.001 HIS I 139 PHE 0.013 0.001 PHE J 50 TYR 0.070 0.002 TYR B 37 ARG 0.006 0.001 ARG K 198 Details of bonding type rmsd hydrogen bonds : bond 0.16023 ( 927) hydrogen bonds : angle 6.79385 ( 2691) covalent geometry : bond 0.00583 (19173) covalent geometry : angle 0.78386 (26139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 389 time to evaluate : 2.076 Fit side-chains REVERT: A 137 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5974 (m170) REVERT: A 237 MET cc_start: 0.7828 (mtm) cc_final: 0.7541 (mtp) REVERT: A 368 ASP cc_start: 0.8396 (t70) cc_final: 0.8131 (t0) REVERT: A 375 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7211 (mtp-110) REVERT: B 113 TYR cc_start: 0.7869 (m-80) cc_final: 0.7518 (m-80) REVERT: B 199 MET cc_start: 0.6549 (mtm) cc_final: 0.6254 (mtm) REVERT: E 237 MET cc_start: 0.7804 (mtm) cc_final: 0.7498 (mtp) REVERT: E 251 MET cc_start: 0.7541 (ttp) cc_final: 0.7299 (ttt) REVERT: E 368 ASP cc_start: 0.8412 (t70) cc_final: 0.8119 (t0) REVERT: E 375 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7178 (mtp-110) REVERT: I 117 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7530 (mm-30) REVERT: I 137 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6029 (m170) REVERT: I 237 MET cc_start: 0.7836 (mtm) cc_final: 0.7506 (mtp) REVERT: I 251 MET cc_start: 0.7538 (ttp) cc_final: 0.7302 (ttt) REVERT: I 285 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7878 (tttp) REVERT: I 316 GLU cc_start: 0.8370 (tt0) cc_final: 0.8155 (tt0) REVERT: I 368 ASP cc_start: 0.8431 (t70) cc_final: 0.8208 (t0) REVERT: I 375 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7166 (mtp-110) REVERT: F 113 TYR cc_start: 0.7902 (m-80) cc_final: 0.7535 (m-80) REVERT: F 199 MET cc_start: 0.6562 (mtm) cc_final: 0.6254 (mtm) REVERT: J 199 MET cc_start: 0.6645 (mtm) cc_final: 0.6338 (mtm) REVERT: J 242 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7791 (mtp85) outliers start: 15 outliers final: 1 residues processed: 401 average time/residue: 0.3599 time to fit residues: 208.4490 Evaluate side-chains 276 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 273 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain I residue 137 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 245 GLN E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 245 GLN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN J 245 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115660 restraints weight = 23103.667| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.99 r_work: 0.3116 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19173 Z= 0.180 Angle : 0.604 9.161 26139 Z= 0.315 Chirality : 0.045 0.162 2841 Planarity : 0.005 0.036 3240 Dihedral : 4.943 53.264 2526 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.77 % Rotamer: Outliers : 1.08 % Allowed : 8.15 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2274 helix: 0.96 (0.16), residues: 1002 sheet: -0.32 (0.29), residues: 348 loop : -0.37 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.007 0.002 HIS E 139 PHE 0.013 0.001 PHE J 31 TYR 0.035 0.002 TYR J 37 ARG 0.004 0.001 ARG K 125 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 927) hydrogen bonds : angle 5.39279 ( 2691) covalent geometry : bond 0.00427 (19173) covalent geometry : angle 0.60413 (26139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 2.246 Fit side-chains REVERT: A 137 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7196 (m170) REVERT: A 237 MET cc_start: 0.8646 (mtm) cc_final: 0.8401 (mtt) REVERT: A 358 GLU cc_start: 0.8313 (tt0) cc_final: 0.7849 (tt0) REVERT: A 375 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7653 (mtp-110) REVERT: B 113 TYR cc_start: 0.8479 (m-80) cc_final: 0.8223 (m-80) REVERT: E 137 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7162 (m170) REVERT: E 239 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7279 (t80) REVERT: E 375 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7684 (mtp-110) REVERT: I 137 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.7032 (m170) REVERT: I 237 MET cc_start: 0.8660 (mtm) cc_final: 0.8370 (mtp) REVERT: I 239 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7308 (t80) REVERT: I 251 MET cc_start: 0.8493 (ttp) cc_final: 0.8236 (ttt) REVERT: I 285 LYS cc_start: 0.8834 (tmmt) cc_final: 0.8410 (tttp) REVERT: I 375 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7710 (mtp-110) REVERT: K 198 ARG cc_start: 0.8536 (mmt90) cc_final: 0.8321 (mmt90) REVERT: K 263 THR cc_start: 0.9038 (t) cc_final: 0.8606 (m) REVERT: F 113 TYR cc_start: 0.8569 (m-80) cc_final: 0.8279 (m-80) REVERT: F 199 MET cc_start: 0.6952 (mtm) cc_final: 0.6668 (mtm) outliers start: 21 outliers final: 9 residues processed: 328 average time/residue: 0.3330 time to fit residues: 162.4151 Evaluate side-chains 292 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 278 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN I 143 ASN F 117 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111277 restraints weight = 22541.272| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.78 r_work: 0.3014 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19173 Z= 0.175 Angle : 0.576 9.660 26139 Z= 0.300 Chirality : 0.044 0.153 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.894 52.877 2526 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 1.33 % Allowed : 11.08 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2274 helix: 1.03 (0.16), residues: 1002 sheet: -0.24 (0.29), residues: 345 loop : -0.36 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.007 0.001 HIS F 11 PHE 0.013 0.001 PHE J 31 TYR 0.025 0.002 TYR J 37 ARG 0.005 0.000 ARG F 242 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 927) hydrogen bonds : angle 5.21522 ( 2691) covalent geometry : bond 0.00416 (19173) covalent geometry : angle 0.57623 (26139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 2.017 Fit side-chains REVERT: A 137 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7269 (m170) REVERT: A 237 MET cc_start: 0.8677 (mtm) cc_final: 0.8440 (mtt) REVERT: A 375 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7704 (mtp-110) REVERT: B 113 TYR cc_start: 0.8477 (m-80) cc_final: 0.8212 (m-80) REVERT: E 137 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7289 (m170) REVERT: E 237 MET cc_start: 0.8629 (mtm) cc_final: 0.8291 (mtt) REVERT: E 239 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7303 (t80) REVERT: E 375 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7699 (mtp-110) REVERT: I 137 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.7046 (m170) REVERT: I 237 MET cc_start: 0.8647 (mtm) cc_final: 0.8418 (mtp) REVERT: I 239 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7288 (t80) REVERT: I 251 MET cc_start: 0.8560 (ttp) cc_final: 0.8280 (ttt) REVERT: I 285 LYS cc_start: 0.8925 (tmmt) cc_final: 0.8475 (tttp) REVERT: I 288 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (p0) REVERT: I 375 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7681 (mtp-110) REVERT: G 114 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (p) REVERT: F 113 TYR cc_start: 0.8570 (m-80) cc_final: 0.8276 (m-80) REVERT: F 199 MET cc_start: 0.6910 (mtm) cc_final: 0.6607 (mtm) outliers start: 26 outliers final: 14 residues processed: 297 average time/residue: 0.3173 time to fit residues: 142.2728 Evaluate side-chains 287 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 266 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 239 PHE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 207 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN F 232 HIS ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107948 restraints weight = 22760.650| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.75 r_work: 0.3028 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19173 Z= 0.171 Angle : 0.567 10.121 26139 Z= 0.294 Chirality : 0.044 0.161 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.860 52.042 2526 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 1.79 % Allowed : 12.10 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2274 helix: 1.06 (0.16), residues: 1002 sheet: -0.15 (0.29), residues: 327 loop : -0.46 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 206 HIS 0.005 0.001 HIS J 11 PHE 0.015 0.001 PHE J 31 TYR 0.028 0.002 TYR K 210 ARG 0.006 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 927) hydrogen bonds : angle 5.08334 ( 2691) covalent geometry : bond 0.00408 (19173) covalent geometry : angle 0.56660 (26139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 2.206 Fit side-chains REVERT: A 137 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7487 (m170) REVERT: A 237 MET cc_start: 0.8682 (mtm) cc_final: 0.8434 (mtt) REVERT: A 375 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7731 (mtp-110) REVERT: E 137 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7423 (m170) REVERT: E 237 MET cc_start: 0.8668 (mtm) cc_final: 0.8319 (mtt) REVERT: E 375 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7738 (mtp-110) REVERT: I 137 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7275 (m170) REVERT: I 237 MET cc_start: 0.8676 (mtm) cc_final: 0.8411 (mtp) REVERT: I 251 MET cc_start: 0.8636 (ttp) cc_final: 0.8337 (ttt) REVERT: I 285 LYS cc_start: 0.8970 (tmmt) cc_final: 0.8511 (tttp) REVERT: I 375 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7693 (mtp-110) REVERT: G 114 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (p) REVERT: F 113 TYR cc_start: 0.8546 (m-80) cc_final: 0.8264 (m-80) outliers start: 35 outliers final: 26 residues processed: 300 average time/residue: 0.3404 time to fit residues: 153.5980 Evaluate side-chains 289 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain 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 46 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 344 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 137 HIS Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 0.0370 chunk 188 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 HIS E 108 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115897 restraints weight = 23471.504| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.07 r_work: 0.3069 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19173 Z= 0.130 Angle : 0.544 10.367 26139 Z= 0.281 Chirality : 0.043 0.158 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.746 50.785 2526 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 1.85 % Allowed : 13.08 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2274 helix: 1.19 (0.16), residues: 1002 sheet: -0.13 (0.29), residues: 327 loop : -0.41 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 237 HIS 0.006 0.001 HIS J 11 PHE 0.012 0.001 PHE J 31 TYR 0.023 0.002 TYR K 184 ARG 0.006 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 927) hydrogen bonds : angle 4.97211 ( 2691) covalent geometry : bond 0.00297 (19173) covalent geometry : angle 0.54396 (26139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 2.546 Fit side-chains REVERT: A 237 MET cc_start: 0.8673 (mtm) cc_final: 0.8408 (mtt) REVERT: A 375 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7582 (mtp-110) REVERT: E 137 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7555 (m170) REVERT: E 237 MET cc_start: 0.8695 (mtm) cc_final: 0.8310 (mtt) REVERT: E 239 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7286 (t80) REVERT: E 375 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7616 (mtp-110) REVERT: I 137 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7501 (m170) REVERT: I 237 MET cc_start: 0.8659 (mtm) cc_final: 0.8379 (mtp) REVERT: I 239 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7185 (t80) REVERT: I 251 MET cc_start: 0.8581 (ttp) cc_final: 0.8246 (ttt) REVERT: I 285 LYS cc_start: 0.8921 (tmmt) cc_final: 0.8401 (tttp) REVERT: I 375 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7671 (mtp-110) REVERT: C 129 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7978 (ttp80) REVERT: G 114 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8077 (p) REVERT: F 113 TYR cc_start: 0.8508 (m-80) cc_final: 0.8207 (m-80) outliers start: 36 outliers final: 21 residues processed: 275 average time/residue: 0.3344 time to fit residues: 138.7224 Evaluate side-chains 268 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 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 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 82 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 114 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 131 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 191 optimal weight: 0.0000 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 200 optimal weight: 0.0060 chunk 29 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN I 108 GLN F 103 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109308 restraints weight = 23270.645| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.96 r_work: 0.3072 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2694 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= 0.117 Angle : 0.530 11.051 26139 Z= 0.273 Chirality : 0.042 0.160 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.542 50.154 2524 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 2.00 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2274 helix: 1.30 (0.16), residues: 990 sheet: -0.03 (0.29), residues: 321 loop : -0.40 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 237 HIS 0.003 0.001 HIS J 232 PHE 0.012 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.006 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 927) hydrogen bonds : angle 4.88883 ( 2691) covalent geometry : bond 0.00263 (19173) covalent geometry : angle 0.53043 (26139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 2.294 Fit side-chains REVERT: A 237 MET cc_start: 0.8635 (mtm) cc_final: 0.8386 (mtt) REVERT: A 375 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7614 (mmm160) REVERT: B 93 VAL cc_start: 0.8895 (t) cc_final: 0.8629 (m) REVERT: E 137 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7562 (m170) REVERT: E 237 MET cc_start: 0.8684 (mtm) cc_final: 0.8308 (mtt) REVERT: E 239 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7331 (t80) REVERT: E 375 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7623 (mtp-110) REVERT: I 237 MET cc_start: 0.8670 (mtm) cc_final: 0.8280 (mtt) REVERT: I 239 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7231 (t80) REVERT: I 251 MET cc_start: 0.8500 (ttp) cc_final: 0.8186 (ttt) REVERT: I 285 LYS cc_start: 0.8892 (tmmt) cc_final: 0.8399 (tttp) REVERT: I 375 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7634 (mtp85) REVERT: G 114 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8016 (p) REVERT: F 93 VAL cc_start: 0.8898 (t) cc_final: 0.8639 (m) REVERT: F 113 TYR cc_start: 0.8440 (m-80) cc_final: 0.8126 (m-80) REVERT: J 47 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7787 (t0) outliers start: 39 outliers final: 26 residues processed: 283 average time/residue: 0.3138 time to fit residues: 133.6691 Evaluate side-chains 278 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 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 60 LYS Chi-restraints excluded: chain I residue 82 ASP 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 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 103 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 191 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 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 = 0.3598 r_free = 0.3598 target = 0.141306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110695 restraints weight = 23286.202| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.98 r_work: 0.2863 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19173 Z= 0.187 Angle : 0.571 11.570 26139 Z= 0.295 Chirality : 0.044 0.158 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.528 51.860 2522 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 2.05 % Allowed : 13.44 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2274 helix: 1.23 (0.16), residues: 990 sheet: -0.21 (0.28), residues: 327 loop : -0.45 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 237 HIS 0.004 0.001 HIS J 232 PHE 0.015 0.001 PHE J 31 TYR 0.023 0.002 TYR G 210 ARG 0.005 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 927) hydrogen bonds : angle 4.96700 ( 2691) covalent geometry : bond 0.00449 (19173) covalent geometry : angle 0.57146 (26139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.061 Fit side-chains REVERT: A 237 MET cc_start: 0.8584 (mtm) cc_final: 0.8305 (mtt) REVERT: A 375 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7450 (mmm160) REVERT: E 237 MET cc_start: 0.8550 (mtm) cc_final: 0.8134 (mtt) REVERT: E 304 ILE cc_start: 0.8804 (mt) cc_final: 0.8562 (mm) REVERT: E 375 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7465 (mtp-110) REVERT: I 237 MET cc_start: 0.8534 (mtm) cc_final: 0.8242 (mtp) REVERT: I 251 MET cc_start: 0.8576 (ttp) cc_final: 0.8182 (ttt) REVERT: I 285 LYS cc_start: 0.8796 (tmmt) cc_final: 0.8206 (tttp) REVERT: I 375 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7500 (mmm160) REVERT: G 114 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7988 (p) REVERT: F 113 TYR cc_start: 0.8508 (m-80) cc_final: 0.8159 (m-80) REVERT: F 197 ILE cc_start: 0.4753 (OUTLIER) cc_final: 0.4502 (mt) REVERT: J 47 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7828 (t0) outliers start: 40 outliers final: 31 residues processed: 273 average time/residue: 0.3028 time to fit residues: 126.3258 Evaluate side-chains 274 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 53 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 184 GLN J 103 ASN ** J 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110237 restraints weight = 23167.996| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.98 r_work: 0.3047 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19173 Z= 0.128 Angle : 0.545 12.412 26139 Z= 0.278 Chirality : 0.043 0.160 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.478 50.941 2522 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 2.10 % Allowed : 13.49 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2274 helix: 1.32 (0.16), residues: 990 sheet: -0.17 (0.28), residues: 321 loop : -0.41 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 237 HIS 0.002 0.001 HIS J 40 PHE 0.012 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.005 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 927) hydrogen bonds : angle 4.88787 ( 2691) covalent geometry : bond 0.00294 (19173) covalent geometry : angle 0.54469 (26139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 1.903 Fit side-chains REVERT: A 237 MET cc_start: 0.8637 (mtm) cc_final: 0.8393 (mtt) REVERT: A 375 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7567 (mmm160) REVERT: E 237 MET cc_start: 0.8665 (mtm) cc_final: 0.8294 (mtt) REVERT: E 304 ILE cc_start: 0.8937 (mt) cc_final: 0.8736 (mm) REVERT: E 375 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7639 (mtp-110) REVERT: I 237 MET cc_start: 0.8678 (mtm) cc_final: 0.8305 (mtt) REVERT: I 251 MET cc_start: 0.8544 (ttp) cc_final: 0.8197 (ttt) REVERT: I 285 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8393 (tttp) REVERT: I 375 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7597 (mmt90) REVERT: G 114 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8010 (p) REVERT: K 129 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8156 (ttp-110) REVERT: F 113 TYR cc_start: 0.8486 (m-80) cc_final: 0.8185 (m-80) REVERT: F 197 ILE cc_start: 0.4771 (OUTLIER) cc_final: 0.4517 (mt) outliers start: 41 outliers final: 30 residues processed: 275 average time/residue: 0.3054 time to fit residues: 128.9106 Evaluate side-chains 265 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 319 THR 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 B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 103 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 198 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 217 optimal weight: 0.0030 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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** F 103 ASN J 103 ASN J 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110124 restraints weight = 23179.529| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.97 r_work: 0.3048 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2930 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= 0.123 Angle : 0.545 13.257 26139 Z= 0.277 Chirality : 0.043 0.159 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.430 50.732 2522 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.85 % Allowed : 13.85 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2274 helix: 1.39 (0.16), residues: 990 sheet: -0.19 (0.28), residues: 321 loop : -0.37 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 237 HIS 0.002 0.001 HIS B 232 PHE 0.012 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.005 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 927) hydrogen bonds : angle 4.86011 ( 2691) covalent geometry : bond 0.00281 (19173) covalent geometry : angle 0.54454 (26139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8631 (mtm) cc_final: 0.8365 (mtt) REVERT: A 375 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7554 (mmm160) REVERT: E 163 MET cc_start: 0.8715 (ttt) cc_final: 0.8469 (ttt) REVERT: E 237 MET cc_start: 0.8663 (mtm) cc_final: 0.8260 (mtt) REVERT: E 304 ILE cc_start: 0.8934 (mt) cc_final: 0.8731 (mm) REVERT: E 375 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7649 (mtt180) REVERT: I 237 MET cc_start: 0.8664 (mtm) cc_final: 0.8409 (mtp) REVERT: I 251 MET cc_start: 0.8538 (ttp) cc_final: 0.8201 (ttt) REVERT: I 285 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8394 (tttp) REVERT: I 375 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7604 (mmt90) REVERT: C 129 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8128 (ttp-110) REVERT: G 198 ARG cc_start: 0.8596 (mmt90) cc_final: 0.8202 (mmt90) REVERT: K 126 GLU cc_start: 0.8717 (tp30) cc_final: 0.8216 (tp30) REVERT: K 129 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8148 (ttp-110) REVERT: F 113 TYR cc_start: 0.8465 (m-80) cc_final: 0.8169 (m-80) REVERT: F 197 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4508 (mt) outliers start: 36 outliers final: 30 residues processed: 269 average time/residue: 0.3099 time to fit residues: 127.9702 Evaluate side-chains 265 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 319 THR 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 B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP 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 F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 103 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 0.0980 chunk 127 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 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** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110639 restraints weight = 23392.417| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.97 r_work: 0.2837 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19173 Z= 0.178 Angle : 0.573 14.092 26139 Z= 0.292 Chirality : 0.044 0.160 2841 Planarity : 0.004 0.035 3240 Dihedral : 4.504 52.358 2522 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 13.85 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2274 helix: 1.29 (0.16), residues: 1002 sheet: -0.23 (0.28), residues: 321 loop : -0.38 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 237 HIS 0.003 0.001 HIS I 137 PHE 0.015 0.001 PHE J 31 TYR 0.022 0.002 TYR C 184 ARG 0.005 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 927) hydrogen bonds : angle 4.90838 ( 2691) covalent geometry : bond 0.00426 (19173) covalent geometry : angle 0.57270 (26139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.045 Fit side-chains REVERT: A 237 MET cc_start: 0.8612 (mtm) cc_final: 0.8305 (mtt) REVERT: A 375 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7436 (mmm160) REVERT: E 237 MET cc_start: 0.8573 (mtm) cc_final: 0.8113 (mtt) REVERT: E 304 ILE cc_start: 0.8868 (mt) cc_final: 0.8628 (mm) REVERT: E 375 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7522 (mmm160) REVERT: I 237 MET cc_start: 0.8574 (mtm) cc_final: 0.8264 (mtp) REVERT: I 251 MET cc_start: 0.8615 (ttp) cc_final: 0.8228 (ttt) REVERT: I 285 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8211 (tttp) REVERT: I 375 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7451 (mmt90) REVERT: C 126 GLU cc_start: 0.8521 (tp30) cc_final: 0.7616 (tp30) REVERT: C 129 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.7829 (ttp-110) REVERT: G 126 GLU cc_start: 0.8490 (tp30) cc_final: 0.8214 (tp30) REVERT: K 126 GLU cc_start: 0.8672 (tp30) cc_final: 0.8053 (tp30) REVERT: K 129 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.7946 (ttp-110) REVERT: F 113 TYR cc_start: 0.8523 (m-80) cc_final: 0.8176 (m-80) REVERT: F 197 ILE cc_start: 0.4755 (OUTLIER) cc_final: 0.4488 (mt) outliers start: 35 outliers final: 30 residues processed: 261 average time/residue: 0.3220 time to fit residues: 128.3127 Evaluate side-chains 264 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 2.254 ------------------------------------------------------------------------------- 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 319 THR 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 B residue 93 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 82 ASP 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 F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 191 optimal weight: 0.2980 chunk 209 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** F 103 ASN J 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109480 restraints weight = 23152.168| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.95 r_work: 0.3041 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19173 Z= 0.129 Angle : 0.552 14.580 26139 Z= 0.279 Chirality : 0.043 0.160 2841 Planarity : 0.004 0.036 3240 Dihedral : 4.481 51.524 2522 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 1.79 % Allowed : 13.90 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2274 helix: 1.39 (0.16), residues: 1002 sheet: -0.24 (0.28), residues: 321 loop : -0.36 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 237 HIS 0.003 0.001 HIS F 11 PHE 0.012 0.001 PHE J 31 TYR 0.022 0.001 TYR C 184 ARG 0.005 0.000 ARG B 9 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 927) hydrogen bonds : angle 4.83533 ( 2691) covalent geometry : bond 0.00298 (19173) covalent geometry : angle 0.55210 (26139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9554.62 seconds wall clock time: 166 minutes 26.79 seconds (9986.79 seconds total)