Starting phenix.real_space_refine on Sun Jun 29 08:09:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4o_25683/06_2025/7t4o_25683_trim.cif" } resolution = 3.65 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= 0.000 sd= 0.003 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 17751 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: 6 Type Number sf(0) Gaussians Cu 5 5.60 5 P 12 5.49 5 S 87 5.16 5 C 12684 2.51 5 N 3054 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19142 Number of models: 1 Model: "" Number of chains: 9 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: "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: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, I, F, J, G, K Time building chain proxies: 10.72, per 1000 atoms: 0.56 Number of scatterers: 19142 At special positions: 0 Unit cell: (106.288, 106.288, 121.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 5 28.99 S 87 16.00 P 12 15.00 O 3300 8.00 N 3054 7.00 C 12684 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: 4.32 Conformation dependent library (CDL) restraints added in 2.3 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: 87 helices and 21 sheets defined 50.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 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 208 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: 4.040A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.355A pdb=" N LEU C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.549A pdb=" N LEU C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 150 removed outlier: 3.686A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.068A pdb=" N GLU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.549A 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 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 'B' and resid 10 through 45 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.630A pdb=" N ASP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.681A 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: 4.194A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.971A 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 169 removed outlier: 3.942A pdb=" N VAL B 169 " --> pdb=" O PRO B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.822A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.355A pdb=" N LEU G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.549A pdb=" N LEU G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 150 removed outlier: 3.687A pdb=" N THR G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 159 removed outlier: 4.069A pdb=" N GLU G 154 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 3.548A 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 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: 4.355A pdb=" N LEU K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 removed outlier: 3.550A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 150 removed outlier: 3.687A pdb=" N THR K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 159 removed outlier: 4.068A pdb=" N GLU K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.549A 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 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: 3.630A pdb=" N ASP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.680A 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: 4.194A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.971A 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 169 removed outlier: 3.942A pdb=" N VAL F 169 " --> pdb=" O PRO F 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 179 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.821A 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: 3.629A pdb=" N ASP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.681A 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: 4.195A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.971A 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 169 removed outlier: 3.943A pdb=" N VAL J 169 " --> pdb=" O PRO J 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 238 removed outlier: 3.821A pdb=" N PHE J 233 " --> pdb=" O PHE J 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 208 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: 4.039A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 4.121A 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 208 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: 4.039A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP A 123 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 105 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG A 125 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 103 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 127 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.968A 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 58 through 60 removed outlier: 3.600A pdb=" N GLY A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) 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 341 through 342 removed outlier: 6.588A pdb=" N ARG A 323 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N SER A 283 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP A 406 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS A 285 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU A 287 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 360 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AA8, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AA9, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB2, first strand: chain 'J' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP E 123 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 105 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 125 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER E 103 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E 127 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB5, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.599A pdb=" N GLY E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.588A pdb=" N ARG E 323 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER E 283 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP E 406 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS E 285 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU E 287 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 360 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP I 123 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE I 105 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG I 125 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER I 103 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL I 127 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AC1, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.599A pdb=" N GLY I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC3, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.587A pdb=" N ARG I 323 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER I 283 " --> pdb=" O GLN I 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP I 406 " --> pdb=" O SER I 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS I 285 " --> pdb=" O ASP I 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU I 287 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 360 " --> pdb=" O ILE I 304 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3086 1.32 - 1.45: 5668 1.45 - 1.57: 10746 1.57 - 1.69: 39 1.69 - 1.81: 168 Bond restraints: 19707 Sorted by residual: bond pdb=" C19 P1O G 302 " pdb=" O7 P1O G 302 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 P1O K 302 " pdb=" O7 P1O K 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 P1O C 302 " pdb=" O7 P1O C 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C9 P1O K 301 " pdb=" O5 P1O K 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C9 P1O C 301 " pdb=" O5 P1O C 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 19702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25724 2.16 - 4.32: 862 4.32 - 6.48: 123 6.48 - 8.63: 27 8.63 - 10.79: 21 Bond angle restraints: 26757 Sorted by residual: angle pdb=" CA PRO K 200 " pdb=" C PRO K 200 " pdb=" O PRO K 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO C 200 " pdb=" C PRO C 200 " pdb=" O PRO C 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO G 200 " pdb=" C PRO G 200 " pdb=" O PRO G 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" C GLU I 287 " pdb=" N ASP I 288 " pdb=" CA ASP I 288 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLU A 287 " pdb=" N ASP A 288 " pdb=" CA ASP A 288 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 26752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 10810 30.46 - 60.91: 536 60.91 - 91.37: 24 91.37 - 121.83: 6 121.83 - 152.28: 12 Dihedral angle restraints: 11388 sinusoidal: 4740 harmonic: 6648 Sorted by residual: dihedral pdb=" C1 P1O G 302 " pdb=" O3 P1O G 302 " pdb=" P1 P1O G 302 " pdb=" O4 P1O G 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.47 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O C 302 " pdb=" O3 P1O C 302 " pdb=" P1 P1O C 302 " pdb=" O4 P1O C 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.51 152.24 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O K 302 " pdb=" O3 P1O K 302 " pdb=" P1 P1O K 302 " pdb=" O4 P1O K 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.53 152.22 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 11385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1976 0.042 - 0.084: 558 0.084 - 0.126: 280 0.126 - 0.167: 21 0.167 - 0.209: 18 Chirality restraints: 2853 Sorted by residual: chirality pdb=" CA ILE G 193 " pdb=" N ILE G 193 " pdb=" C ILE G 193 " pdb=" CB ILE G 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE K 193 " pdb=" N ILE K 193 " pdb=" C ILE K 193 " pdb=" CB ILE K 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 193 " pdb=" N ILE C 193 " pdb=" C ILE C 193 " pdb=" CB ILE C 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2850 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 95 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO I 96 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 95 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 96 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.038 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 62 2.40 - 3.03: 11348 3.03 - 3.65: 29766 3.65 - 4.28: 45145 4.28 - 4.90: 75650 Nonbonded interactions: 161971 Sorted by model distance: nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.777 2.320 nonbonded pdb=" NE2 HIS I 139 " pdb="CU CU I 501 " model vdw 1.783 2.320 nonbonded pdb=" NE2 HIS E 139 " pdb="CU CU E 501 " model vdw 1.783 2.320 ... (remaining 161966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 414 or resid 501)) selection = (chain 'E' and (resid 33 through 414 or resid 501)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'F' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'J' and (resid 7 through 247 or resid 303 through 304)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 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: 0.960 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 41.190 Find NCS groups from input model: 0.840 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.007 0.125 19707 Z= 0.366 Angle : 0.877 10.792 26757 Z= 0.474 Chirality : 0.049 0.209 2853 Planarity : 0.005 0.071 3261 Dihedral : 16.839 152.282 7134 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 1.85 % Allowed : 0.97 % Favored : 97.18 % 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: 0.05 (0.18), residues: 2274 helix: 0.63 (0.16), residues: 951 sheet: 0.51 (0.29), residues: 348 loop : -0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 54 HIS 0.023 0.002 HIS E 33 PHE 0.026 0.001 PHE G 251 TYR 0.029 0.002 TYR F 37 ARG 0.007 0.001 ARG I 45 Details of bonding type rmsd hydrogen bonds : bond 0.16992 ( 954) hydrogen bonds : angle 7.02098 ( 2835) covalent geometry : bond 0.00663 (19707) covalent geometry : angle 0.87674 (26757) *********************** 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 463 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6685 (pm20) REVERT: A 68 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6315 (mtmt) REVERT: A 75 GLU cc_start: 0.7129 (mp0) cc_final: 0.6922 (pm20) REVERT: A 86 VAL cc_start: 0.8136 (t) cc_final: 0.7669 (t) REVERT: A 112 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7662 (ptp-170) REVERT: A 118 ILE cc_start: 0.8235 (mm) cc_final: 0.7830 (mm) REVERT: A 120 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7598 (mmtm) REVERT: A 158 THR cc_start: 0.7071 (m) cc_final: 0.6808 (m) REVERT: A 181 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 218 MET cc_start: 0.4968 (mmp) cc_final: 0.4494 (mmp) REVERT: A 237 MET cc_start: 0.6290 (mtt) cc_final: 0.5520 (mtt) REVERT: C 49 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.3943 (ptmm) REVERT: C 219 MET cc_start: 0.4543 (tmm) cc_final: 0.4311 (ppp) REVERT: C 266 PHE cc_start: 0.7410 (m-10) cc_final: 0.7069 (m-10) REVERT: B 202 LYS cc_start: 0.6585 (mttm) cc_final: 0.6208 (mtmt) REVERT: B 236 ARG cc_start: 0.5682 (tpp80) cc_final: 0.5134 (mmm160) REVERT: G 49 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.3869 (ptmt) REVERT: K 49 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.3854 (ptmt) REVERT: F 202 LYS cc_start: 0.6465 (mttm) cc_final: 0.6149 (mtmt) REVERT: F 236 ARG cc_start: 0.5715 (tpp80) cc_final: 0.5138 (mmm160) REVERT: J 202 LYS cc_start: 0.6592 (mttm) cc_final: 0.6241 (mtmt) REVERT: J 236 ARG cc_start: 0.5662 (tpp80) cc_final: 0.5111 (mmm160) REVERT: E 36 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6562 (ptpp) REVERT: E 68 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6414 (mttp) REVERT: E 86 VAL cc_start: 0.8217 (t) cc_final: 0.7953 (t) REVERT: E 120 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7537 (mmtm) REVERT: E 151 ILE cc_start: 0.8280 (mm) cc_final: 0.8041 (mm) REVERT: E 181 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7234 (mm-30) REVERT: E 237 MET cc_start: 0.6237 (mtt) cc_final: 0.5781 (mtt) REVERT: E 310 SER cc_start: 0.7863 (t) cc_final: 0.7535 (t) REVERT: I 57 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6577 (pm20) REVERT: I 58 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7202 (mtpp) REVERT: I 68 LYS cc_start: 0.7293 (mtmm) cc_final: 0.6366 (mtmt) REVERT: I 82 ASP cc_start: 0.6187 (m-30) cc_final: 0.5659 (m-30) REVERT: I 86 VAL cc_start: 0.8200 (t) cc_final: 0.7899 (t) REVERT: I 102 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6899 (mt-10) REVERT: I 120 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7605 (mmtm) REVERT: I 151 ILE cc_start: 0.8244 (mm) cc_final: 0.7973 (mm) REVERT: I 158 THR cc_start: 0.7167 (m) cc_final: 0.6892 (m) REVERT: I 181 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7189 (mm-30) REVERT: I 218 MET cc_start: 0.4867 (mmp) cc_final: 0.4635 (mmp) REVERT: I 237 MET cc_start: 0.6273 (mtt) cc_final: 0.5728 (mtt) REVERT: I 285 LYS cc_start: 0.6941 (tmmt) cc_final: 0.6664 (ttpt) REVERT: I 372 GLU cc_start: 0.6656 (pt0) cc_final: 0.5863 (tm-30) outliers start: 36 outliers final: 6 residues processed: 451 average time/residue: 0.3668 time to fit residues: 236.9333 Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 272 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 251 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN F 38 HIS F 184 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.164061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.145130 restraints weight = 21378.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.145567 restraints weight = 18106.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.145565 restraints weight = 17112.998| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19707 Z= 0.161 Angle : 0.627 8.303 26757 Z= 0.326 Chirality : 0.046 0.169 2853 Planarity : 0.006 0.058 3261 Dihedral : 15.320 146.595 3013 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.07 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.38 % 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: 0.26 (0.18), residues: 2274 helix: 0.81 (0.16), residues: 1005 sheet: 0.52 (0.31), residues: 330 loop : -0.56 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 54 HIS 0.007 0.001 HIS J 11 PHE 0.025 0.002 PHE K 251 TYR 0.030 0.002 TYR C 184 ARG 0.009 0.001 ARG E 100 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 954) hydrogen bonds : angle 5.46033 ( 2835) covalent geometry : bond 0.00376 (19707) covalent geometry : angle 0.62743 (26757) *********************** 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 321 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.859 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.5525 (mmp) cc_final: 0.4985 (mmp) REVERT: A 269 MET cc_start: 0.7684 (mtp) cc_final: 0.7452 (mtp) REVERT: C 49 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.5051 (ptmt) REVERT: B 22 ASP cc_start: 0.8186 (m-30) cc_final: 0.7968 (m-30) REVERT: B 236 ARG cc_start: 0.6399 (tpp80) cc_final: 0.5945 (mtp85) REVERT: G 49 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.4865 (ptmt) REVERT: K 49 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.4850 (ptmt) REVERT: K 210 TYR cc_start: 0.7735 (t80) cc_final: 0.7514 (t80) REVERT: F 24 MET cc_start: 0.7106 (mtm) cc_final: 0.6876 (ttp) REVERT: F 236 ARG cc_start: 0.6375 (tpp80) cc_final: 0.5925 (mtp85) REVERT: J 22 ASP cc_start: 0.8169 (m-30) cc_final: 0.7798 (m-30) REVERT: J 236 ARG cc_start: 0.6406 (tpp80) cc_final: 0.5924 (mtp85) REVERT: E 380 ILE cc_start: 0.7147 (tt) cc_final: 0.6823 (pt) REVERT: I 68 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7617 (mttp) REVERT: I 151 ILE cc_start: 0.8118 (mm) cc_final: 0.7909 (mm) outliers start: 31 outliers final: 14 residues processed: 307 average time/residue: 0.3355 time to fit residues: 154.0493 Evaluate side-chains 279 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 142 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN ** I 38 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.155457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132608 restraints weight = 21357.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132371 restraints weight = 28250.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.133908 restraints weight = 19820.309| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 19707 Z= 0.207 Angle : 0.662 7.056 26757 Z= 0.344 Chirality : 0.049 0.279 2853 Planarity : 0.006 0.045 3261 Dihedral : 14.810 143.472 3003 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.62 % Favored : 95.12 % Rotamer: Outliers : 2.97 % Allowed : 11.13 % Favored : 85.90 % 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: 0.12 (0.17), residues: 2274 helix: 0.76 (0.16), residues: 972 sheet: 0.06 (0.29), residues: 345 loop : -0.52 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 54 HIS 0.009 0.002 HIS J 11 PHE 0.025 0.002 PHE G 251 TYR 0.032 0.002 TYR C 184 ARG 0.009 0.001 ARG I 215 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 954) hydrogen bonds : angle 5.27006 ( 2835) covalent geometry : bond 0.00499 (19707) covalent geometry : angle 0.66250 (26757) *********************** 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 352 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.5716 (mmp) cc_final: 0.5483 (mmp) REVERT: C 49 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.4773 (ptmt) REVERT: B 22 ASP cc_start: 0.8515 (m-30) cc_final: 0.8206 (m-30) REVERT: B 236 ARG cc_start: 0.6958 (tpp80) cc_final: 0.6254 (mtp85) REVERT: G 49 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.4517 (ptmt) REVERT: K 49 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.4417 (ptmt) REVERT: K 210 TYR cc_start: 0.7956 (t80) cc_final: 0.7630 (t80) REVERT: F 22 ASP cc_start: 0.8415 (m-30) cc_final: 0.8056 (m-30) REVERT: J 236 ARG cc_start: 0.6926 (tpp80) cc_final: 0.6172 (mtp85) REVERT: E 33 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.6302 (m-70) REVERT: E 82 ASP cc_start: 0.5918 (m-30) cc_final: 0.5680 (m-30) REVERT: E 218 MET cc_start: 0.5552 (mmp) cc_final: 0.5321 (mmp) REVERT: E 381 TYR cc_start: 0.5924 (t80) cc_final: 0.5724 (t80) REVERT: I 56 LYS cc_start: 0.7140 (mttt) cc_final: 0.6643 (mmmm) REVERT: I 68 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7630 (mttp) REVERT: I 151 ILE cc_start: 0.8471 (mm) cc_final: 0.8258 (mm) outliers start: 58 outliers final: 33 residues processed: 331 average time/residue: 0.3648 time to fit residues: 182.5414 Evaluate side-chains 303 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN F 245 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN I 38 GLN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.156258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.135882 restraints weight = 21350.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.136345 restraints weight = 21897.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.137642 restraints weight = 18565.110| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19707 Z= 0.142 Angle : 0.581 7.343 26757 Z= 0.302 Chirality : 0.045 0.196 2853 Planarity : 0.005 0.039 3261 Dihedral : 14.277 145.047 3003 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.35 % Favored : 95.38 % Rotamer: Outliers : 3.08 % Allowed : 13.03 % Favored : 83.90 % 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: 0.22 (0.17), residues: 2274 helix: 0.86 (0.16), residues: 993 sheet: 0.28 (0.29), residues: 327 loop : -0.57 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 253 HIS 0.005 0.001 HIS B 11 PHE 0.022 0.001 PHE C 251 TYR 0.026 0.002 TYR K 184 ARG 0.005 0.000 ARG I 400 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 954) hydrogen bonds : angle 5.04118 ( 2835) covalent geometry : bond 0.00330 (19707) covalent geometry : angle 0.58058 (26757) *********************** 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 349 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: C 49 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.4285 (mttt) REVERT: B 22 ASP cc_start: 0.8534 (m-30) cc_final: 0.8290 (m-30) REVERT: B 223 MET cc_start: 0.7699 (tpp) cc_final: 0.7124 (tpp) REVERT: B 236 ARG cc_start: 0.7030 (tpp80) cc_final: 0.6329 (mtp85) REVERT: B 244 LEU cc_start: 0.5940 (tp) cc_final: 0.5671 (mp) REVERT: G 49 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.4406 (ptmt) REVERT: K 49 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4372 (ptmt) REVERT: J 244 LEU cc_start: 0.5998 (tp) cc_final: 0.5620 (mp) REVERT: E 372 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7050 (tm-30) REVERT: I 151 ILE cc_start: 0.8405 (mm) cc_final: 0.8194 (mm) REVERT: I 310 SER cc_start: 0.7954 (t) cc_final: 0.7695 (m) outliers start: 60 outliers final: 34 residues processed: 323 average time/residue: 0.3347 time to fit residues: 162.3786 Evaluate side-chains 297 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 219 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN B 245 GLN F 245 GLN J 245 GLN E 33 HIS I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.149911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.131827 restraints weight = 21574.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130451 restraints weight = 29285.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.131083 restraints weight = 28655.029| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19707 Z= 0.223 Angle : 0.680 7.164 26757 Z= 0.353 Chirality : 0.049 0.167 2853 Planarity : 0.006 0.042 3261 Dihedral : 14.460 148.714 3003 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 3.49 % Allowed : 14.92 % Favored : 81.59 % 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: -0.06 (0.17), residues: 2274 helix: 0.61 (0.16), residues: 981 sheet: -0.12 (0.27), residues: 363 loop : -0.58 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 253 HIS 0.010 0.002 HIS B 11 PHE 0.021 0.002 PHE K 251 TYR 0.030 0.002 TYR C 184 ARG 0.006 0.001 ARG I 215 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 954) hydrogen bonds : angle 5.22700 ( 2835) covalent geometry : bond 0.00538 (19707) covalent geometry : angle 0.67951 (26757) *********************** 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 342 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 1.969 Fit side-chains REVERT: A 142 MET cc_start: 0.8265 (tpt) cc_final: 0.8001 (tpt) REVERT: A 310 SER cc_start: 0.7981 (t) cc_final: 0.7752 (m) REVERT: C 49 LYS cc_start: 0.5978 (OUTLIER) cc_final: 0.4135 (mttt) REVERT: C 114 THR cc_start: 0.6573 (OUTLIER) cc_final: 0.6118 (t) REVERT: B 22 ASP cc_start: 0.8566 (m-30) cc_final: 0.8195 (m-30) REVERT: B 49 ASP cc_start: 0.7664 (t0) cc_final: 0.7325 (t70) REVERT: B 136 MET cc_start: 0.7580 (tmm) cc_final: 0.7365 (ttt) REVERT: B 223 MET cc_start: 0.7824 (tpp) cc_final: 0.7181 (tpp) REVERT: B 236 ARG cc_start: 0.7351 (tpp80) cc_final: 0.6440 (mtp85) REVERT: G 49 LYS cc_start: 0.5867 (OUTLIER) cc_final: 0.4350 (ptmt) REVERT: K 49 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4445 (ptmt) REVERT: K 199 LEU cc_start: 0.8177 (mm) cc_final: 0.7955 (mm) REVERT: F 22 ASP cc_start: 0.8610 (m-30) cc_final: 0.8280 (m-30) REVERT: F 229 PHE cc_start: 0.7522 (t80) cc_final: 0.7046 (t80) REVERT: F 236 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7347 (mtt180) REVERT: I 56 LYS cc_start: 0.7189 (mttt) cc_final: 0.6625 (mmmm) REVERT: I 151 ILE cc_start: 0.8644 (mm) cc_final: 0.8335 (mm) REVERT: I 310 SER cc_start: 0.7907 (t) cc_final: 0.7643 (m) outliers start: 68 outliers final: 53 residues processed: 320 average time/residue: 0.3283 time to fit residues: 157.8281 Evaluate side-chains 312 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 245 GLN F 245 GLN J 245 GLN E 62 ASN I 33 HIS I 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.132398 restraints weight = 21491.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.131085 restraints weight = 26541.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.132730 restraints weight = 26452.352| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19707 Z= 0.210 Angle : 0.642 7.654 26757 Z= 0.336 Chirality : 0.047 0.166 2853 Planarity : 0.005 0.042 3261 Dihedral : 14.574 158.064 3000 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 3.69 % Allowed : 15.54 % Favored : 80.77 % 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: -0.18 (0.17), residues: 2274 helix: 0.51 (0.15), residues: 999 sheet: -0.15 (0.26), residues: 357 loop : -0.69 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 253 HIS 0.009 0.002 HIS B 11 PHE 0.020 0.002 PHE C 202 TYR 0.029 0.002 TYR C 184 ARG 0.006 0.001 ARG J 198 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 954) hydrogen bonds : angle 5.15312 ( 2835) covalent geometry : bond 0.00502 (19707) covalent geometry : angle 0.64205 (26757) *********************** 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 344 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 2.125 Fit side-chains REVERT: A 142 MET cc_start: 0.8230 (tpt) cc_final: 0.7996 (tpt) REVERT: A 310 SER cc_start: 0.7922 (t) cc_final: 0.7706 (m) REVERT: A 387 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8546 (p90) REVERT: C 49 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.3976 (mttt) REVERT: C 114 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6247 (t) REVERT: B 22 ASP cc_start: 0.8519 (m-30) cc_final: 0.8203 (m-30) REVERT: B 49 ASP cc_start: 0.7661 (t0) cc_final: 0.7348 (t70) REVERT: B 223 MET cc_start: 0.7792 (tpp) cc_final: 0.7198 (tpp) REVERT: B 226 LEU cc_start: 0.8671 (mt) cc_final: 0.8419 (mt) REVERT: B 229 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: B 236 ARG cc_start: 0.7480 (tpp80) cc_final: 0.6482 (mtp85) REVERT: G 49 LYS cc_start: 0.5534 (OUTLIER) cc_final: 0.4143 (ptmt) REVERT: K 49 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.4335 (ptmt) REVERT: F 22 ASP cc_start: 0.8637 (m-30) cc_final: 0.8354 (m-30) REVERT: F 229 PHE cc_start: 0.7536 (t80) cc_final: 0.6999 (t80) REVERT: F 236 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7408 (mtt180) REVERT: J 242 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7274 (mtp180) REVERT: E 310 SER cc_start: 0.7964 (t) cc_final: 0.7650 (m) REVERT: I 56 LYS cc_start: 0.7198 (mttt) cc_final: 0.6670 (mmmm) REVERT: I 60 LYS cc_start: 0.7551 (pttp) cc_final: 0.7122 (ptmt) REVERT: I 151 ILE cc_start: 0.8692 (mm) cc_final: 0.8258 (mm) REVERT: I 310 SER cc_start: 0.7892 (t) cc_final: 0.7662 (m) outliers start: 72 outliers final: 50 residues processed: 319 average time/residue: 0.3380 time to fit residues: 162.2285 Evaluate side-chains 308 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.150297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.141674 restraints weight = 21650.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.126855 restraints weight = 34276.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.127592 restraints weight = 28157.161| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19707 Z= 0.161 Angle : 0.602 8.992 26757 Z= 0.315 Chirality : 0.045 0.165 2853 Planarity : 0.005 0.044 3261 Dihedral : 14.340 164.566 2997 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 3.38 % Allowed : 16.15 % Favored : 80.46 % 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: -0.04 (0.17), residues: 2274 helix: 0.69 (0.16), residues: 999 sheet: -0.26 (0.26), residues: 354 loop : -0.61 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 253 HIS 0.006 0.001 HIS B 11 PHE 0.014 0.001 PHE C 202 TYR 0.025 0.002 TYR K 184 ARG 0.005 0.000 ARG E 400 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 954) hydrogen bonds : angle 5.06998 ( 2835) covalent geometry : bond 0.00376 (19707) covalent geometry : angle 0.60194 (26757) *********************** 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 340 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8226 (tpt) cc_final: 0.7993 (tpt) REVERT: A 310 SER cc_start: 0.8122 (t) cc_final: 0.7867 (m) REVERT: A 387 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8482 (p90) REVERT: C 49 LYS cc_start: 0.4798 (OUTLIER) cc_final: 0.3106 (mttt) REVERT: C 114 THR cc_start: 0.6605 (OUTLIER) cc_final: 0.6120 (t) REVERT: B 22 ASP cc_start: 0.8423 (m-30) cc_final: 0.8127 (m-30) REVERT: B 49 ASP cc_start: 0.7668 (t0) cc_final: 0.7352 (t70) REVERT: B 229 PHE cc_start: 0.7905 (t80) cc_final: 0.7508 (m-80) REVERT: B 236 ARG cc_start: 0.7498 (tpp80) cc_final: 0.6538 (mtp85) REVERT: G 49 LYS cc_start: 0.4613 (OUTLIER) cc_final: 0.3247 (ptmt) REVERT: K 49 LYS cc_start: 0.4748 (OUTLIER) cc_final: 0.3455 (ptmt) REVERT: F 22 ASP cc_start: 0.8552 (m-30) cc_final: 0.8285 (m-30) REVERT: F 178 MET cc_start: 0.8371 (mtt) cc_final: 0.7732 (mtt) REVERT: F 223 MET cc_start: 0.7676 (tpp) cc_final: 0.7115 (tpp) REVERT: F 229 PHE cc_start: 0.7579 (t80) cc_final: 0.7034 (t80) REVERT: J 24 MET cc_start: 0.7196 (mtp) cc_final: 0.6994 (mtm) REVERT: J 242 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7222 (mtp180) REVERT: I 56 LYS cc_start: 0.7290 (mttt) cc_final: 0.6681 (mmmm) REVERT: I 60 LYS cc_start: 0.7544 (pttp) cc_final: 0.7116 (ptmt) REVERT: I 151 ILE cc_start: 0.8677 (mm) cc_final: 0.8258 (mm) REVERT: I 310 SER cc_start: 0.8007 (t) cc_final: 0.7783 (m) outliers start: 66 outliers final: 49 residues processed: 318 average time/residue: 0.3301 time to fit residues: 156.7651 Evaluate side-chains 307 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN E 62 ASN I 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.149214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.140130 restraints weight = 21803.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.125898 restraints weight = 35937.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.126726 restraints weight = 28772.655| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19707 Z= 0.183 Angle : 0.623 7.729 26757 Z= 0.325 Chirality : 0.046 0.163 2853 Planarity : 0.005 0.045 3261 Dihedral : 14.359 173.290 2994 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.74 % Allowed : 16.46 % Favored : 79.79 % 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: -0.10 (0.17), residues: 2274 helix: 0.64 (0.15), residues: 1002 sheet: -0.33 (0.27), residues: 354 loop : -0.61 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 253 HIS 0.008 0.001 HIS B 11 PHE 0.017 0.002 PHE C 202 TYR 0.025 0.002 TYR K 184 ARG 0.005 0.001 ARG I 215 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 954) hydrogen bonds : angle 5.08086 ( 2835) covalent geometry : bond 0.00438 (19707) covalent geometry : angle 0.62328 (26757) *********************** 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 343 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 2.225 Fit side-chains REVERT: A 142 MET cc_start: 0.8253 (tpt) cc_final: 0.8031 (tpt) REVERT: A 310 SER cc_start: 0.8052 (t) cc_final: 0.7846 (m) REVERT: A 387 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8509 (p90) REVERT: C 49 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.3011 (mttt) REVERT: C 114 THR cc_start: 0.6705 (OUTLIER) cc_final: 0.6252 (t) REVERT: B 22 ASP cc_start: 0.8412 (m-30) cc_final: 0.8133 (m-30) REVERT: B 49 ASP cc_start: 0.7693 (t0) cc_final: 0.7368 (t70) REVERT: B 229 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: G 49 LYS cc_start: 0.4561 (OUTLIER) cc_final: 0.3227 (ptmt) REVERT: K 49 LYS cc_start: 0.4724 (OUTLIER) cc_final: 0.3442 (ptmt) REVERT: F 22 ASP cc_start: 0.8530 (m-30) cc_final: 0.8284 (m-30) REVERT: F 223 MET cc_start: 0.7710 (tpp) cc_final: 0.7141 (tpp) REVERT: F 229 PHE cc_start: 0.7582 (t80) cc_final: 0.7013 (t80) REVERT: E 209 ARG cc_start: 0.7236 (ptp-170) cc_final: 0.7001 (ptp-170) REVERT: I 56 LYS cc_start: 0.7315 (mttt) cc_final: 0.6671 (mmmm) REVERT: I 60 LYS cc_start: 0.7597 (pttp) cc_final: 0.7132 (ptmt) REVERT: I 151 ILE cc_start: 0.8740 (mm) cc_final: 0.8325 (mm) REVERT: I 310 SER cc_start: 0.7953 (t) cc_final: 0.7742 (m) outliers start: 73 outliers final: 58 residues processed: 321 average time/residue: 0.3517 time to fit residues: 168.3881 Evaluate side-chains 322 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 4 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 245 GLN J 174 ASN J 245 GLN E 401 GLN I 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.150606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.141971 restraints weight = 21566.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.129456 restraints weight = 31954.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.127921 restraints weight = 32789.225| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19707 Z= 0.151 Angle : 0.591 7.970 26757 Z= 0.309 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.045 3261 Dihedral : 14.196 179.845 2994 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.59 % Allowed : 16.82 % Favored : 79.59 % 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: 0.06 (0.17), residues: 2274 helix: 0.79 (0.16), residues: 1002 sheet: -0.29 (0.27), residues: 354 loop : -0.55 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 253 HIS 0.005 0.001 HIS B 11 PHE 0.014 0.001 PHE K 269 TYR 0.023 0.002 TYR K 184 ARG 0.004 0.000 ARG I 215 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 954) hydrogen bonds : angle 4.99880 ( 2835) covalent geometry : bond 0.00355 (19707) covalent geometry : angle 0.59148 (26757) *********************** 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 342 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 2.056 Fit side-chains REVERT: A 142 MET cc_start: 0.8211 (tpt) cc_final: 0.8010 (tpt) REVERT: A 310 SER cc_start: 0.8003 (t) cc_final: 0.7801 (m) REVERT: A 387 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8487 (p90) REVERT: C 49 LYS cc_start: 0.4808 (OUTLIER) cc_final: 0.3152 (mttt) REVERT: C 114 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6315 (t) REVERT: B 22 ASP cc_start: 0.8417 (m-30) cc_final: 0.8137 (m-30) REVERT: B 49 ASP cc_start: 0.7696 (t0) cc_final: 0.7388 (t70) REVERT: B 229 PHE cc_start: 0.7888 (t80) cc_final: 0.7449 (m-80) REVERT: G 49 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.3435 (ptmt) REVERT: K 49 LYS cc_start: 0.4931 (OUTLIER) cc_final: 0.3627 (ptmt) REVERT: F 22 ASP cc_start: 0.8517 (m-30) cc_final: 0.8267 (m-30) REVERT: F 178 MET cc_start: 0.8379 (mtt) cc_final: 0.7718 (mtt) REVERT: F 223 MET cc_start: 0.7618 (tpp) cc_final: 0.7085 (tpp) REVERT: F 229 PHE cc_start: 0.7574 (t80) cc_final: 0.7004 (t80) REVERT: E 209 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6948 (ptp-170) REVERT: I 56 LYS cc_start: 0.7279 (mttt) cc_final: 0.6675 (mmmm) REVERT: I 60 LYS cc_start: 0.7568 (pttp) cc_final: 0.7130 (ptmt) REVERT: I 151 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8275 (mm) REVERT: I 310 SER cc_start: 0.7886 (t) cc_final: 0.7681 (m) outliers start: 70 outliers final: 59 residues processed: 317 average time/residue: 0.3436 time to fit residues: 161.2754 Evaluate side-chains 319 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 245 GLN J 245 GLN E 62 ASN E 401 GLN I 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.150265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.141238 restraints weight = 21675.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.126682 restraints weight = 35650.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.128026 restraints weight = 27494.867| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19707 Z= 0.162 Angle : 0.600 7.883 26757 Z= 0.313 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.044 3261 Dihedral : 14.082 174.366 2994 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.54 % Allowed : 17.18 % Favored : 79.28 % 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: 0.06 (0.17), residues: 2274 helix: 0.80 (0.16), residues: 1002 sheet: -0.31 (0.27), residues: 354 loop : -0.54 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 253 HIS 0.006 0.001 HIS B 11 PHE 0.012 0.001 PHE C 251 TYR 0.023 0.002 TYR C 184 ARG 0.008 0.000 ARG F 236 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 954) hydrogen bonds : angle 4.98931 ( 2835) covalent geometry : bond 0.00383 (19707) covalent geometry : angle 0.60047 (26757) ********************** 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 336 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 1.863 Fit side-chains REVERT: A 142 MET cc_start: 0.8224 (tpt) cc_final: 0.8006 (tpt) REVERT: A 310 SER cc_start: 0.8017 (t) cc_final: 0.7812 (m) REVERT: A 330 TYR cc_start: 0.8076 (t80) cc_final: 0.7669 (t80) REVERT: A 387 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8469 (p90) REVERT: C 49 LYS cc_start: 0.4492 (OUTLIER) cc_final: 0.2909 (mttt) REVERT: C 114 THR cc_start: 0.6759 (OUTLIER) cc_final: 0.6302 (t) REVERT: B 22 ASP cc_start: 0.8370 (m-30) cc_final: 0.8099 (m-30) REVERT: B 49 ASP cc_start: 0.7712 (t0) cc_final: 0.7404 (t70) REVERT: B 229 PHE cc_start: 0.7906 (t80) cc_final: 0.7521 (m-80) REVERT: G 49 LYS cc_start: 0.4414 (OUTLIER) cc_final: 0.3145 (ptmt) REVERT: K 49 LYS cc_start: 0.4535 (OUTLIER) cc_final: 0.3312 (ptmt) REVERT: F 22 ASP cc_start: 0.8457 (m-30) cc_final: 0.8219 (m-30) REVERT: F 178 MET cc_start: 0.8429 (mtt) cc_final: 0.7783 (mtt) REVERT: F 223 MET cc_start: 0.7639 (tpp) cc_final: 0.7083 (tpp) REVERT: F 236 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7356 (mtt180) REVERT: J 24 MET cc_start: 0.7189 (mtp) cc_final: 0.6922 (mtm) REVERT: E 209 ARG cc_start: 0.7142 (ptp-170) cc_final: 0.6924 (ptp-170) REVERT: I 56 LYS cc_start: 0.7367 (mttt) cc_final: 0.6736 (mmmm) REVERT: I 60 LYS cc_start: 0.7605 (pttp) cc_final: 0.7128 (ptmt) REVERT: I 151 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8323 (mm) outliers start: 69 outliers final: 61 residues processed: 314 average time/residue: 0.3318 time to fit residues: 155.9745 Evaluate side-chains 330 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 263 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 71 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.148204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.139689 restraints weight = 21775.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.124814 restraints weight = 33318.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.126814 restraints weight = 29500.214| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19707 Z= 0.208 Angle : 0.649 8.409 26757 Z= 0.338 Chirality : 0.047 0.162 2853 Planarity : 0.005 0.043 3261 Dihedral : 14.173 175.763 2994 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 3.69 % Allowed : 17.28 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2274 helix: 0.62 (0.15), residues: 1002 sheet: -0.39 (0.27), residues: 354 loop : -0.59 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 253 HIS 0.008 0.002 HIS B 11 PHE 0.021 0.002 PHE E 394 TYR 0.026 0.002 TYR C 184 ARG 0.008 0.001 ARG F 236 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 954) hydrogen bonds : angle 5.09700 ( 2835) covalent geometry : bond 0.00502 (19707) covalent geometry : angle 0.64855 (26757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5861.10 seconds wall clock time: 102 minutes 58.78 seconds (6178.78 seconds total)