Starting phenix.real_space_refine on Mon Oct 26 16:42:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.cif Found real_map, /net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38kn_78881/10_2026/38kn_78881.map" } resolution = 1.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 150 5.16 5 C 13085 2.51 5 N 3515 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21165 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2931 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Conformer: "B" Number of residues, atoms: 370, 2892 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} bond proxies already assigned to first conformer: 2907 Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1193 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "a" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "b" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "c" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "d" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Restraints were copied for chains: B, C, D, E, b, c, d, e Time building chain proxies: 4.35, per 1000 atoms: 0.21 Number of scatterers: 21165 At special positions: 0 Unit cell: (100.74, 115.34, 213.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 10 15.00 Mg 5 11.99 O 4400 8.00 N 3515 7.00 C 13085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4940 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 30 sheets defined 50.2% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.763A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.607A pdb=" N ILE A 77 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 288 through 298 removed outlier: 4.737A pdb=" N LYS A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 350 through 351 No H-bonds generated for 'chain 'A' and resid 350 through 351' Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.883A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.764A pdb=" N LYS B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.606A pdb=" N ILE B 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.736A pdb=" N LYS B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 350 through 351 No H-bonds generated for 'chain 'B' and resid 350 through 351' Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.883A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.764A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.606A pdb=" N ILE C 77 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 288 through 298 removed outlier: 4.738A pdb=" N LYS C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 350 through 351 No H-bonds generated for 'chain 'C' and resid 350 through 351' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.882A pdb=" N ARG C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.763A pdb=" N LYS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.607A pdb=" N ILE D 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 204 through 219 Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 286 Processing helix chain 'D' and resid 288 through 298 removed outlier: 4.736A pdb=" N LYS D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 349 Processing helix chain 'D' and resid 350 through 351 No H-bonds generated for 'chain 'D' and resid 350 through 351' Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.881A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.765A pdb=" N LYS E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.607A pdb=" N ILE E 77 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 204 through 219 Processing helix chain 'E' and resid 224 through 231 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 275 through 286 Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.737A pdb=" N LYS E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 339 through 349 Processing helix chain 'E' and resid 350 through 351 No H-bonds generated for 'chain 'E' and resid 350 through 351' Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 361 through 368 Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.883A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 21 removed outlier: 3.778A pdb=" N LYS a 12 " --> pdb=" O ASP a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 61 removed outlier: 3.602A pdb=" N PHE a 53 " --> pdb=" O PRO a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 122 removed outlier: 4.641A pdb=" N ARG a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA a 116 " --> pdb=" O SER a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 137 Processing helix chain 'a' and resid 138 through 149 Processing helix chain 'b' and resid 8 through 21 removed outlier: 3.778A pdb=" N LYS b 12 " --> pdb=" O ASP b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 61 removed outlier: 3.602A pdb=" N PHE b 53 " --> pdb=" O PRO b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 removed outlier: 4.642A pdb=" N ARG b 115 " --> pdb=" O ALA b 111 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA b 116 " --> pdb=" O SER b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 137 Processing helix chain 'b' and resid 138 through 149 Processing helix chain 'c' and resid 8 through 21 removed outlier: 3.778A pdb=" N LYS c 12 " --> pdb=" O ASP c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.601A pdb=" N PHE c 53 " --> pdb=" O PRO c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 122 removed outlier: 4.641A pdb=" N ARG c 115 " --> pdb=" O ALA c 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA c 116 " --> pdb=" O SER c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 137 Processing helix chain 'c' and resid 138 through 149 Processing helix chain 'd' and resid 8 through 21 removed outlier: 3.778A pdb=" N LYS d 12 " --> pdb=" O ASP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 61 removed outlier: 3.601A pdb=" N PHE d 53 " --> pdb=" O PRO d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 122 removed outlier: 4.642A pdb=" N ARG d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 Processing helix chain 'd' and resid 138 through 149 Processing helix chain 'e' and resid 8 through 21 removed outlier: 3.778A pdb=" N LYS e 12 " --> pdb=" O ASP e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 61 removed outlier: 3.602A pdb=" N PHE e 53 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 removed outlier: 4.641A pdb=" N ARG e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA e 116 " --> pdb=" O SER e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 137 Processing helix chain 'e' and resid 138 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.621A pdb=" N LEU A 10 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR A 108 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS A 12 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.532A pdb=" N ASN A 299 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.620A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.533A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.621A pdb=" N LEU C 10 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR C 108 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS C 12 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 171 through 172 removed outlier: 6.534A pdb=" N ASN C 299 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.620A pdb=" N LEU D 10 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR D 108 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N CYS D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 6.534A pdb=" N ASN D 299 " --> pdb=" O ILE D 332 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 240 through 243 Processing sheet with id=AC3, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.620A pdb=" N LEU E 10 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR E 108 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS E 12 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC5, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AC6, first strand: chain 'E' and resid 171 through 172 removed outlier: 6.535A pdb=" N ASN E 299 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 240 through 243 Processing sheet with id=AC8, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.142A pdb=" N LYS a 6 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL a 40 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL a 40 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LYS a 30 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE a 127 " --> pdb=" O VAL a 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.143A pdb=" N LYS b 6 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL b 40 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL b 40 " --> pdb=" O LYS b 30 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS b 30 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE b 127 " --> pdb=" O VAL b 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.142A pdb=" N LYS c 6 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL c 40 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL c 40 " --> pdb=" O LYS c 30 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LYS c 30 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE c 127 " --> pdb=" O VAL c 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.142A pdb=" N LYS d 6 " --> pdb=" O ILE d 38 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N VAL d 40 " --> pdb=" O LYS d 6 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL d 40 " --> pdb=" O LYS d 30 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS d 30 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE d 127 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 6 through 7 removed outlier: 7.142A pdb=" N LYS e 6 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL e 40 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL e 40 " --> pdb=" O LYS e 30 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS e 30 " --> pdb=" O VAL e 40 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE e 127 " --> pdb=" O VAL e 92 " (cutoff:3.500A) 1075 hydrogen bonds defined for protein. 2700 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: 4.74 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6786 1.34 - 1.46: 3637 1.46 - 1.58: 10507 1.58 - 1.69: 15 1.69 - 1.81: 260 Bond restraints: 21205 Sorted by residual: bond pdb=" C4 ADP A 400 " pdb=" C5 ADP A 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" C4 ADP D 400 " pdb=" C5 ADP D 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.91e-01 bond pdb=" C4 ADP B 400 " pdb=" C5 ADP B 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.82e-01 bond pdb=" C4 ADP C 400 " pdb=" C5 ADP C 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.77e-01 ... (remaining 21200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 28095 1.18 - 2.36: 438 2.36 - 3.54: 162 3.54 - 4.72: 30 4.72 - 5.91: 30 Bond angle restraints: 28755 Sorted by residual: angle pdb=" C VAL E 32 " pdb=" N PHE E 33 " pdb=" CA PHE E 33 " ideal model delta sigma weight residual 122.90 118.78 4.12 2.07e+00 2.33e-01 3.97e+00 angle pdb=" O2B ADP D 400 " pdb=" PB ADP D 400 " pdb=" O3B ADP D 400 " ideal model delta sigma weight residual 119.90 113.99 5.91 3.00e+00 1.11e-01 3.87e+00 angle pdb=" O2B ADP E 400 " pdb=" PB ADP E 400 " pdb=" O3B ADP E 400 " ideal model delta sigma weight residual 119.90 114.04 5.86 3.00e+00 1.11e-01 3.82e+00 angle pdb=" C VAL A 32 " pdb=" N PHE A 33 " pdb=" CA PHE A 33 " ideal model delta sigma weight residual 122.90 118.87 4.03 2.07e+00 2.33e-01 3.78e+00 angle pdb=" C VAL B 32 " pdb=" N PHE B 33 " pdb=" CA PHE B 33 " ideal model delta sigma weight residual 122.90 118.87 4.03 2.07e+00 2.33e-01 3.78e+00 ... (remaining 28750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 12456 16.98 - 33.97: 419 33.97 - 50.95: 65 50.95 - 67.93: 5 67.93 - 84.91: 10 Dihedral angle restraints: 12955 sinusoidal: 5235 harmonic: 7720 Sorted by residual: dihedral pdb=" CA LEU D 67 " pdb=" C LEU D 67 " pdb=" N THR D 68 " pdb=" CA THR D 68 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CA LEU A 67 " pdb=" C LEU A 67 " pdb=" N THR A 68 " pdb=" CA THR A 68 " ideal model delta harmonic sigma weight residual 180.00 164.49 15.51 0 5.00e+00 4.00e-02 9.62e+00 dihedral pdb=" CA LEU C 67 " pdb=" C LEU C 67 " pdb=" N THR C 68 " pdb=" CA THR C 68 " ideal model delta harmonic sigma weight residual 180.00 164.54 15.46 0 5.00e+00 4.00e-02 9.56e+00 ... (remaining 12952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1888 0.027 - 0.055: 786 0.055 - 0.082: 230 0.082 - 0.110: 239 0.110 - 0.137: 52 Chirality restraints: 3195 Sorted by residual: chirality pdb=" CA ILE A 167 " pdb=" N ILE A 167 " pdb=" C ILE A 167 " pdb=" CB ILE A 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL A 32 " pdb=" N VAL A 32 " pdb=" C VAL A 32 " pdb=" CB VAL A 32 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE E 167 " pdb=" N ILE E 167 " pdb=" C ILE E 167 " pdb=" CB ILE E 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 3192 not shown) Planarity restraints: 3700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 344 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C GLY D 344 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY D 344 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY D 345 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 165 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 166 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO B 166 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.016 5.00e-02 4.00e+02 ... (remaining 3697 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 35 2.59 - 3.17: 18092 3.17 - 3.75: 34279 3.75 - 4.32: 49511 4.32 - 4.90: 79991 Nonbonded interactions: 181908 Sorted by model distance: nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.018 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.019 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.020 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.020 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.020 2.170 ... (remaining 181903 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 73.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.870 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.210 Find NCS groups from input model: 0.230 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:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 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 : 0.002 0.021 21205 Z= 0.098 Angle : 0.474 5.905 28755 Z= 0.244 Chirality : 0.042 0.137 3195 Planarity : 0.003 0.029 3700 Dihedral : 9.069 84.914 8015 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.88 % Allowed : 2.88 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.17), residues: 2620 helix: 1.60 (0.17), residues: 1015 sheet: 0.68 (0.23), residues: 515 loop : 2.25 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.011 0.001 TYR b 69 PHE 0.012 0.001 PHE b 29 TRP 0.006 0.001 TRP A 81 HIS 0.002 0.001 HIS c 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.10 (21205) covalent geometry : angle 0.47385 / 0.24 (28755) hydrogen bonds : bond 0.14566 / 9.34 ( 1065) hydrogen bonds : angle 6.51849 / 4.77 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 0.953 Fit side-chains REVERT: A 49 MET cc_start: 0.7460 (ptm) cc_final: 0.6860 (mmt) REVERT: B 49 MET cc_start: 0.7358 (ptm) cc_final: 0.6927 (mmt) REVERT: C 49 MET cc_start: 0.7261 (ptm) cc_final: 0.7002 (ptp) REVERT: D 49 MET cc_start: 0.7223 (ptm) cc_final: 0.6988 (ptp) REVERT: E 49 MET cc_start: 0.7235 (ptm) cc_final: 0.7015 (ptp) REVERT: a 65 LYS cc_start: 0.7604 (mppt) cc_final: 0.7216 (tptt) REVERT: b 65 LYS cc_start: 0.7574 (mppt) cc_final: 0.7118 (tptt) REVERT: c 65 LYS cc_start: 0.7612 (mppt) cc_final: 0.6967 (tptt) outliers start: 20 outliers final: 7 residues processed: 262 average time/residue: 0.7553 time to fit residues: 221.2761 Evaluate side-chains 210 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 371 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.3980 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN B 248 GLN C 248 GLN D 51 GLN D 248 GLN D 355 GLN E 248 GLN a 47 ASN a 96 GLN b 47 ASN b 96 GLN c 23 GLN c 47 ASN c 96 GLN d 23 GLN d 47 ASN d 96 GLN e 23 GLN e 47 ASN e 96 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040685 restraints weight = 169547.030| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.73 r_work: 0.2496 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2497 r_free = 0.2497 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9449 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21205 Z= 0.201 Angle : 0.577 7.457 28755 Z= 0.294 Chirality : 0.047 0.177 3195 Planarity : 0.004 0.037 3700 Dihedral : 6.632 91.525 2979 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.80 % Allowed : 5.18 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.17), residues: 2620 helix: 1.41 (0.17), residues: 1055 sheet: 0.70 (0.23), residues: 505 loop : 2.08 (0.22), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 374 TYR 0.018 0.002 TYR c 69 PHE 0.015 0.002 PHE b 29 TRP 0.013 0.002 TRP D 342 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (21205) covalent geometry : angle 0.57670 / 0.29 (28755) hydrogen bonds : bond 0.04938 / 3.26 ( 1065) hydrogen bonds : angle 5.21157 / 3.78 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.976 Fit side-chains REVERT: A 49 MET cc_start: 0.7491 (ptm) cc_final: 0.6481 (mmt) REVERT: B 49 MET cc_start: 0.7533 (ptm) cc_final: 0.6728 (mmt) REVERT: C 49 MET cc_start: 0.7242 (ptm) cc_final: 0.6973 (ptp) REVERT: D 49 MET cc_start: 0.7217 (ptm) cc_final: 0.6908 (ptp) REVERT: E 41 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7761 (ttm-80) REVERT: E 49 MET cc_start: 0.7225 (ptm) cc_final: 0.6901 (ptp) REVERT: E 70 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9052 (mttp) REVERT: a 101 ASN cc_start: 0.9238 (p0) cc_final: 0.9026 (p0) REVERT: b 65 LYS cc_start: 0.8467 (mppt) cc_final: 0.7119 (tptt) REVERT: d 8 ASP cc_start: 0.8691 (t0) cc_final: 0.8455 (t0) REVERT: e 8 ASP cc_start: 0.8792 (t0) cc_final: 0.8525 (t0) outliers start: 18 outliers final: 7 residues processed: 213 average time/residue: 0.7000 time to fit residues: 167.7688 Evaluate side-chains 205 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 353 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [121, 205, 27, 0, 2, 179, 1, 195, 16, 221, 86] chunk 121 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 179 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 128 GLN b 23 GLN b 47 ASN c 23 GLN c 47 ASN d 23 GLN d 47 ASN e 23 GLN e 47 ASN e 96 GLN e 128 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.041805 restraints weight = 189943.409| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.83 r_work: 0.2537 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9423 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21205 Z= 0.117 Angle : 0.512 6.603 28755 Z= 0.256 Chirality : 0.044 0.162 3195 Planarity : 0.004 0.037 3700 Dihedral : 6.104 77.006 2975 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.62 % Allowed : 5.44 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.18), residues: 2620 helix: 1.56 (0.17), residues: 1055 sheet: 0.72 (0.23), residues: 505 loop : 2.10 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 374 TYR 0.012 0.001 TYR c 69 PHE 0.014 0.001 PHE c 29 TRP 0.010 0.001 TRP D 342 HIS 0.002 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21205) covalent geometry : angle 0.51190 / 0.26 (28755) hydrogen bonds : bond 0.03827 / 2.54 ( 1065) hydrogen bonds : angle 4.84852 / 3.53 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.898 Fit side-chains REVERT: A 41 ARG cc_start: 0.7468 (ttp80) cc_final: 0.7116 (ttm110) REVERT: A 49 MET cc_start: 0.7468 (ptm) cc_final: 0.6457 (mmt) REVERT: B 49 MET cc_start: 0.7418 (ptm) cc_final: 0.6738 (mmt) REVERT: C 49 MET cc_start: 0.7244 (ptm) cc_final: 0.7033 (ptp) REVERT: D 49 MET cc_start: 0.7163 (ptm) cc_final: 0.6915 (ptp) REVERT: E 49 MET cc_start: 0.7178 (ptm) cc_final: 0.6873 (ptp) REVERT: a 65 LYS cc_start: 0.8430 (mppt) cc_final: 0.7186 (tptt) REVERT: b 65 LYS cc_start: 0.8426 (mppt) cc_final: 0.7135 (tptt) REVERT: c 1 MET cc_start: 0.6678 (mtt) cc_final: 0.6134 (mpt) REVERT: e 8 ASP cc_start: 0.8817 (t0) cc_final: 0.8487 (t0) outliers start: 14 outliers final: 9 residues processed: 208 average time/residue: 0.6941 time to fit residues: 162.4187 Evaluate side-chains 206 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain a residue 134 MET Chi-restraints excluded: chain e residue 134 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [61, 182, 37, 217, 126, 22, 258, 206, 198, 190, 219] chunk 61 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 219 optimal weight: 0.0870 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN c 23 GLN d 23 GLN d 47 ASN e 23 GLN e 47 ASN e 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.040167 restraints weight = 179418.161| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.74 r_work: 0.2483 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9457 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21205 Z= 0.206 Angle : 0.569 7.336 28755 Z= 0.290 Chirality : 0.047 0.178 3195 Planarity : 0.004 0.038 3700 Dihedral : 6.629 89.105 2975 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.71 % Allowed : 5.75 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2620 helix: 1.48 (0.17), residues: 1055 sheet: 0.64 (0.22), residues: 505 loop : 1.90 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 374 TYR 0.015 0.001 TYR c 69 PHE 0.016 0.002 PHE b 29 TRP 0.012 0.002 TRP D 342 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (21205) covalent geometry : angle 0.56947 / 0.29 (28755) hydrogen bonds : bond 0.04794 / 3.18 ( 1065) hydrogen bonds : angle 4.96707 / 3.60 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.049 Fit side-chains REVERT: A 41 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7121 (ttm110) REVERT: A 49 MET cc_start: 0.7444 (ptm) cc_final: 0.6556 (mmt) REVERT: B 49 MET cc_start: 0.7482 (ptm) cc_final: 0.6846 (mmt) REVERT: C 49 MET cc_start: 0.7188 (ptm) cc_final: 0.6966 (ptp) REVERT: D 49 MET cc_start: 0.7179 (ptm) cc_final: 0.6896 (ptp) REVERT: E 41 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7832 (ttm-80) REVERT: E 49 MET cc_start: 0.7206 (ptm) cc_final: 0.6856 (ptp) REVERT: E 70 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9062 (mttp) REVERT: a 1 MET cc_start: 0.6569 (mtt) cc_final: 0.6020 (mpt) REVERT: b 65 LYS cc_start: 0.8536 (mppt) cc_final: 0.7187 (tptt) REVERT: c 1 MET cc_start: 0.6771 (mtt) cc_final: 0.5898 (mpt) REVERT: e 8 ASP cc_start: 0.8836 (t0) cc_final: 0.8487 (t0) outliers start: 16 outliers final: 8 residues processed: 202 average time/residue: 0.7230 time to fit residues: 164.1708 Evaluate side-chains 198 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [85, 192, 202, 248, 66, 152, 187, 51, 189, 38, 190] chunk 85 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN c 23 GLN d 23 GLN d 47 ASN e 23 GLN e 47 ASN e 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.039907 restraints weight = 198815.437| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.95 r_work: 0.2470 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9468 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21205 Z= 0.202 Angle : 0.569 7.342 28755 Z= 0.290 Chirality : 0.047 0.178 3195 Planarity : 0.004 0.040 3700 Dihedral : 6.670 88.685 2975 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.66 % Allowed : 6.06 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.17), residues: 2620 helix: 1.46 (0.17), residues: 1055 sheet: 0.59 (0.22), residues: 505 loop : 1.81 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 374 TYR 0.014 0.001 TYR c 69 PHE 0.016 0.002 PHE b 29 TRP 0.012 0.002 TRP D 342 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (21205) covalent geometry : angle 0.56874 / 0.29 (28755) hydrogen bonds : bond 0.04746 / 3.15 ( 1065) hydrogen bonds : angle 4.92925 / 3.57 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.914 Fit side-chains REVERT: A 41 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7083 (ttm110) REVERT: A 49 MET cc_start: 0.7383 (ptm) cc_final: 0.6599 (mmt) REVERT: B 49 MET cc_start: 0.7436 (ptm) cc_final: 0.6885 (mmt) REVERT: C 41 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7668 (ttm-80) REVERT: C 49 MET cc_start: 0.7150 (ptm) cc_final: 0.6934 (ptp) REVERT: D 49 MET cc_start: 0.7105 (ptm) cc_final: 0.6789 (ptp) REVERT: E 41 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7809 (ttm-80) REVERT: E 46 MET cc_start: 0.5086 (mmm) cc_final: 0.4869 (mmm) REVERT: E 49 MET cc_start: 0.7150 (ptm) cc_final: 0.6792 (ptp) REVERT: a 1 MET cc_start: 0.6598 (mtt) cc_final: 0.5828 (mpt) REVERT: b 65 LYS cc_start: 0.8577 (mppt) cc_final: 0.7231 (tptt) REVERT: b 115 ARG cc_start: 0.9083 (ttp-170) cc_final: 0.8855 (ttp-170) REVERT: c 1 MET cc_start: 0.6735 (mtt) cc_final: 0.6178 (mpt) REVERT: e 8 ASP cc_start: 0.8854 (t0) cc_final: 0.8477 (t0) outliers start: 15 outliers final: 7 residues processed: 201 average time/residue: 0.7066 time to fit residues: 159.2241 Evaluate side-chains 196 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [202, 119, 200, 234, 76, 31, 51, 88, 131, 180, 222] chunk 202 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN d 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.039972 restraints weight = 194162.951| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.92 r_work: 0.2472 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2472 r_free = 0.2472 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9469 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21205 Z= 0.190 Angle : 0.562 7.671 28755 Z= 0.286 Chirality : 0.046 0.177 3195 Planarity : 0.004 0.039 3700 Dihedral : 6.633 87.236 2975 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.66 % Allowed : 6.02 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.17), residues: 2620 helix: 1.49 (0.17), residues: 1055 sheet: 0.58 (0.22), residues: 505 loop : 1.78 (0.21), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 115 TYR 0.014 0.001 TYR c 69 PHE 0.015 0.002 PHE b 29 TRP 0.013 0.002 TRP D 342 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (21205) covalent geometry : angle 0.56190 / 0.29 (28755) hydrogen bonds : bond 0.04616 / 3.06 ( 1065) hydrogen bonds : angle 4.88120 / 3.54 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.956 Fit side-chains REVERT: A 41 ARG cc_start: 0.7436 (ttp80) cc_final: 0.7069 (ttm110) REVERT: A 49 MET cc_start: 0.7374 (ptm) cc_final: 0.6563 (mmt) REVERT: B 41 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7670 (ttm110) REVERT: B 49 MET cc_start: 0.7401 (ptm) cc_final: 0.6887 (mmt) REVERT: C 46 MET cc_start: 0.4919 (mmm) cc_final: 0.4704 (mmm) REVERT: C 49 MET cc_start: 0.7082 (ptm) cc_final: 0.6879 (ptp) REVERT: D 49 MET cc_start: 0.7058 (ptm) cc_final: 0.6833 (ptp) REVERT: E 41 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7812 (ttm-80) REVERT: E 46 MET cc_start: 0.5074 (mmm) cc_final: 0.4846 (mmm) REVERT: E 49 MET cc_start: 0.7133 (ptm) cc_final: 0.6799 (ptp) REVERT: a 1 MET cc_start: 0.6587 (mtt) cc_final: 0.6088 (mpt) REVERT: b 65 LYS cc_start: 0.8566 (mppt) cc_final: 0.7192 (tptt) REVERT: b 115 ARG cc_start: 0.9086 (ttp-170) cc_final: 0.8864 (ttp-170) REVERT: c 1 MET cc_start: 0.6775 (mtt) cc_final: 0.6229 (mpt) REVERT: e 8 ASP cc_start: 0.8855 (t0) cc_final: 0.8488 (t0) outliers start: 15 outliers final: 8 residues processed: 200 average time/residue: 0.7059 time to fit residues: 158.8692 Evaluate side-chains 198 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 353 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [149, 152, 137, 22, 41, 67, 71, 2, 194, 139, 40] chunk 149 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.060651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.041110 restraints weight = 203568.705| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.95 r_work: 0.2513 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9436 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 : 0.003 0.030 21205 Z= 0.123 Angle : 0.521 8.038 28755 Z= 0.261 Chirality : 0.044 0.163 3195 Planarity : 0.004 0.040 3700 Dihedral : 6.179 76.175 2975 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.66 % Allowed : 6.06 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.17), residues: 2620 helix: 1.59 (0.17), residues: 1055 sheet: 0.63 (0.23), residues: 505 loop : 1.86 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 115 TYR 0.012 0.001 TYR d 15 PHE 0.014 0.001 PHE c 29 TRP 0.013 0.002 TRP E 342 HIS 0.002 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (21205) covalent geometry : angle 0.52078 / 0.26 (28755) hydrogen bonds : bond 0.03789 / 2.52 ( 1065) hydrogen bonds : angle 4.68612 / 3.41 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.883 Fit side-chains REVERT: A 41 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7082 (ttm110) REVERT: A 49 MET cc_start: 0.7271 (ptm) cc_final: 0.6514 (mmt) REVERT: B 49 MET cc_start: 0.7313 (ptm) cc_final: 0.6825 (mmt) REVERT: C 41 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7770 (ttm-80) REVERT: C 46 MET cc_start: 0.4943 (mmm) cc_final: 0.4678 (mmm) REVERT: C 49 MET cc_start: 0.7089 (ptm) cc_final: 0.6876 (ptp) REVERT: D 49 MET cc_start: 0.7028 (ptm) cc_final: 0.6762 (ptp) REVERT: E 41 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7777 (ttm-80) REVERT: E 46 MET cc_start: 0.5079 (mmm) cc_final: 0.4868 (mmm) REVERT: E 49 MET cc_start: 0.7127 (ptm) cc_final: 0.6803 (ptp) REVERT: a 1 MET cc_start: 0.6562 (mtt) cc_final: 0.5792 (mpt) REVERT: a 65 LYS cc_start: 0.8461 (mppt) cc_final: 0.7267 (tptt) REVERT: b 65 LYS cc_start: 0.8471 (mppt) cc_final: 0.7102 (tptt) REVERT: b 115 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8804 (ttp-170) REVERT: c 1 MET cc_start: 0.6741 (mtt) cc_final: 0.5920 (mpt) REVERT: e 8 ASP cc_start: 0.8831 (t0) cc_final: 0.8458 (t0) outliers start: 15 outliers final: 12 residues processed: 200 average time/residue: 0.7254 time to fit residues: 162.4550 Evaluate side-chains 204 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain d residue 134 MET Chi-restraints excluded: chain e residue 134 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [59, 46, 230, 121, 139, 140, 4, 105, 69, 177, 227] chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.041837 restraints weight = 193505.451| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.91 r_work: 0.2541 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9422 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21205 Z= 0.105 Angle : 0.511 8.864 28755 Z= 0.254 Chirality : 0.043 0.148 3195 Planarity : 0.004 0.048 3700 Dihedral : 5.880 69.341 2975 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.53 % Allowed : 6.33 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.17), residues: 2620 helix: 1.65 (0.17), residues: 1055 sheet: 0.67 (0.23), residues: 505 loop : 1.93 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 41 TYR 0.011 0.001 TYR d 15 PHE 0.014 0.001 PHE c 29 TRP 0.012 0.002 TRP E 342 HIS 0.004 0.000 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (21205) covalent geometry : angle 0.51139 / 0.25 (28755) hydrogen bonds : bond 0.03428 / 2.28 ( 1065) hydrogen bonds : angle 4.56211 / 3.32 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.979 Fit side-chains REVERT: A 41 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7149 (ttm110) REVERT: A 49 MET cc_start: 0.7173 (ptm) cc_final: 0.6514 (mmt) REVERT: B 49 MET cc_start: 0.7163 (ptm) cc_final: 0.6733 (mmt) REVERT: C 46 MET cc_start: 0.4957 (mmm) cc_final: 0.4674 (mmm) REVERT: D 49 MET cc_start: 0.7011 (ptm) cc_final: 0.6733 (ptp) REVERT: E 49 MET cc_start: 0.7096 (ptm) cc_final: 0.6781 (ptp) REVERT: a 1 MET cc_start: 0.6559 (mtt) cc_final: 0.5760 (mpt) REVERT: a 65 LYS cc_start: 0.8375 (mppt) cc_final: 0.7222 (tptt) REVERT: b 65 LYS cc_start: 0.8388 (mppt) cc_final: 0.7054 (tptt) REVERT: c 1 MET cc_start: 0.6726 (mtt) cc_final: 0.5881 (mpt) REVERT: c 65 LYS cc_start: 0.8404 (mppt) cc_final: 0.7005 (tptt) REVERT: e 8 ASP cc_start: 0.8823 (t0) cc_final: 0.8437 (t0) outliers start: 12 outliers final: 9 residues processed: 206 average time/residue: 0.7037 time to fit residues: 163.1104 Evaluate side-chains 206 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain e residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [67, 106, 215, 206, 220, 56, 222, 219, 213, 130, 212] chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.039868 restraints weight = 211693.955| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 4.03 r_work: 0.2469 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9471 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21205 Z= 0.195 Angle : 0.578 8.663 28755 Z= 0.292 Chirality : 0.046 0.176 3195 Planarity : 0.004 0.065 3700 Dihedral : 6.568 87.775 2975 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.53 % Allowed : 6.68 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.17), residues: 2620 helix: 1.51 (0.17), residues: 1055 sheet: 0.61 (0.22), residues: 505 loop : 1.84 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 41 TYR 0.014 0.001 TYR d 15 PHE 0.015 0.001 PHE b 29 TRP 0.012 0.002 TRP D 342 HIS 0.004 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (21205) covalent geometry : angle 0.57754 / 0.29 (28755) hydrogen bonds : bond 0.04640 / 3.08 ( 1065) hydrogen bonds : angle 4.82489 / 3.50 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.856 Fit side-chains REVERT: A 41 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7110 (ttm110) REVERT: A 49 MET cc_start: 0.7164 (ptm) cc_final: 0.6480 (mmt) REVERT: B 46 MET cc_start: 0.4572 (mmm) cc_final: 0.4266 (mmm) REVERT: B 49 MET cc_start: 0.7167 (ptm) cc_final: 0.6737 (mmt) REVERT: C 46 MET cc_start: 0.4968 (mmm) cc_final: 0.4697 (mmm) REVERT: D 49 MET cc_start: 0.6942 (ptm) cc_final: 0.6680 (ptp) REVERT: E 41 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7908 (ttm-80) REVERT: E 46 MET cc_start: 0.4682 (mmm) cc_final: 0.3833 (mmt) REVERT: E 49 MET cc_start: 0.6979 (ptm) cc_final: 0.6675 (ptp) REVERT: a 1 MET cc_start: 0.6565 (mtt) cc_final: 0.6022 (mpt) REVERT: a 65 LYS cc_start: 0.8471 (mppt) cc_final: 0.7294 (tptt) REVERT: b 65 LYS cc_start: 0.8473 (mppt) cc_final: 0.7127 (tptt) REVERT: c 1 MET cc_start: 0.6751 (mtt) cc_final: 0.6224 (mpt) REVERT: c 65 LYS cc_start: 0.8500 (mppt) cc_final: 0.7103 (tptt) REVERT: e 8 ASP cc_start: 0.8856 (t0) cc_final: 0.8463 (t0) outliers start: 12 outliers final: 7 residues processed: 202 average time/residue: 0.7044 time to fit residues: 159.3371 Evaluate side-chains 201 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [126, 216, 137, 21, 146, 125, 81, 103, 4, 218, 187] chunk 126 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 146 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN c 23 GLN d 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.041074 restraints weight = 184228.174| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.76 r_work: 0.2514 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9438 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21205 Z= 0.133 Angle : 0.544 9.393 28755 Z= 0.272 Chirality : 0.045 0.168 3195 Planarity : 0.004 0.043 3700 Dihedral : 6.280 79.920 2975 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.49 % Allowed : 6.68 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.17), residues: 2620 helix: 1.56 (0.17), residues: 1055 sheet: 0.63 (0.23), residues: 505 loop : 1.89 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 41 TYR 0.013 0.001 TYR d 15 PHE 0.014 0.001 PHE c 29 TRP 0.013 0.002 TRP E 342 HIS 0.002 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (21205) covalent geometry : angle 0.54376 / 0.27 (28755) hydrogen bonds : bond 0.03948 / 2.62 ( 1065) hydrogen bonds : angle 4.67772 / 3.40 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.921 Fit side-chains REVERT: A 41 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7189 (ttm110) REVERT: A 46 MET cc_start: 0.4485 (mmm) cc_final: 0.4184 (mmm) REVERT: A 49 MET cc_start: 0.7119 (ptm) cc_final: 0.6445 (mmt) REVERT: B 46 MET cc_start: 0.4490 (mmm) cc_final: 0.4181 (mmm) REVERT: B 49 MET cc_start: 0.7165 (ptm) cc_final: 0.6737 (mmt) REVERT: C 46 MET cc_start: 0.4934 (mmm) cc_final: 0.4653 (mmm) REVERT: D 46 MET cc_start: 0.4379 (mmm) cc_final: 0.3900 (mmm) REVERT: D 49 MET cc_start: 0.6951 (ptm) cc_final: 0.6708 (ptp) REVERT: E 41 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: E 46 MET cc_start: 0.4490 (mmm) cc_final: 0.3661 (mmt) REVERT: E 49 MET cc_start: 0.7018 (ptm) cc_final: 0.6725 (ptp) REVERT: a 1 MET cc_start: 0.6571 (mtt) cc_final: 0.6023 (mpt) REVERT: a 65 LYS cc_start: 0.8418 (mppt) cc_final: 0.7256 (tptt) REVERT: b 65 LYS cc_start: 0.8423 (mppt) cc_final: 0.7090 (tptt) REVERT: c 1 MET cc_start: 0.6745 (mtt) cc_final: 0.6205 (mpt) REVERT: c 65 LYS cc_start: 0.8449 (mppt) cc_final: 0.7043 (tptt) REVERT: e 8 ASP cc_start: 0.8842 (t0) cc_final: 0.8443 (t0) REVERT: e 115 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8564 (ttp80) outliers start: 11 outliers final: 9 residues processed: 200 average time/residue: 0.7071 time to fit residues: 158.5747 Evaluate side-chains 202 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain e residue 115 ARG Chi-restraints excluded: chain e residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [217, 124, 189, 220, 67, 35, 214, 75, 253, 223, 249] chunk 217 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 23 GLN d 47 ASN e 23 GLN e 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.040305 restraints weight = 173018.468| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.75 r_work: 0.2487 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9459 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21205 Z= 0.176 Angle : 0.568 8.646 28755 Z= 0.286 Chirality : 0.046 0.172 3195 Planarity : 0.004 0.046 3700 Dihedral : 6.479 84.411 2975 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.53 % Allowed : 6.68 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.17), residues: 2620 helix: 1.51 (0.17), residues: 1055 sheet: 0.61 (0.22), residues: 505 loop : 1.87 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 41 TYR 0.014 0.001 TYR d 15 PHE 0.015 0.001 PHE b 29 TRP 0.012 0.002 TRP D 342 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (21205) covalent geometry : angle 0.56790 / 0.29 (28755) hydrogen bonds : bond 0.04472 / 2.97 ( 1065) hydrogen bonds : angle 4.78383 / 3.47 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14975.64 seconds wall clock time: 254 minutes 22.36 seconds (15262.36 seconds total)