Starting phenix.real_space_refine on Sat Aug 8 23:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdm_17614/08_2026/8pdm_17614.map" } resolution = 3.3 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= 0.037 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: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 121 5.16 5 C 19602 2.51 5 N 5445 2.21 5 O 6226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31471 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 4.22, per 1000 atoms: 0.13 Number of scatterers: 31471 At special positions: 0 Unit cell: (199.5, 200.55, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 77 15.00 O 6226 8.00 N 5445 7.00 C 19602 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 22 sheets defined 68.4% alpha, 2.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 361 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 361 Processing helix chain 'K' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 361 Processing helix chain 'M' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR M 13 " --> pdb=" O SER M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU M 46 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 141 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 175 through 191 removed outlier: 4.032A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR O 13 " --> pdb=" O SER O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU O 46 " --> pdb=" O GLN O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 141 Processing helix chain 'O' and resid 156 through 170 Processing helix chain 'O' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG O 189 " --> pdb=" O ARG O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 198 Processing helix chain 'O' and resid 202 through 217 Processing helix chain 'O' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER O 222 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 251 Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG O 260 " --> pdb=" O GLN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 274 Processing helix chain 'O' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY O 300 " --> pdb=" O PRO O 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 297 through 300' Processing helix chain 'O' and resid 318 through 332 Processing helix chain 'O' and resid 344 through 361 Processing helix chain 'Q' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR Q 13 " --> pdb=" O SER Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 141 Processing helix chain 'Q' and resid 156 through 170 Processing helix chain 'Q' and resid 175 through 191 removed outlier: 4.034A pdb=" N ARG Q 189 " --> pdb=" O ARG Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 198 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER Q 222 " --> pdb=" O VAL Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 251 Processing helix chain 'Q' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG Q 260 " --> pdb=" O GLN Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 274 Processing helix chain 'Q' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY Q 300 " --> pdb=" O PRO Q 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 297 through 300' Processing helix chain 'Q' and resid 318 through 332 Processing helix chain 'Q' and resid 344 through 361 Processing helix chain 'S' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR S 13 " --> pdb=" O SER S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU S 46 " --> pdb=" O GLN S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 141 Processing helix chain 'S' and resid 156 through 170 Processing helix chain 'S' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'U' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR U 13 " --> pdb=" O SER U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU U 46 " --> pdb=" O GLN U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 75 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'U' and resid 120 through 141 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'U' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG U 189 " --> pdb=" O ARG U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 198 Processing helix chain 'U' and resid 202 through 217 Processing helix chain 'U' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER U 222 " --> pdb=" O VAL U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 251 Processing helix chain 'U' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG U 260 " --> pdb=" O GLN U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 274 Processing helix chain 'U' and resid 275 through 296 removed outlier: 4.527A pdb=" N LYS U 283 " --> pdb=" O GLN U 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY U 300 " --> pdb=" O PRO U 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 297 through 300' Processing helix chain 'U' and resid 318 through 332 Processing helix chain 'U' and resid 344 through 361 Processing sheet with id=1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'M' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG M 96 " --> pdb=" O ASP M 115 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR O 33 " --> pdb=" O VAL O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'O' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG O 96 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Q' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR Q 33 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG Q 96 " --> pdb=" O ASP Q 115 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'S' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'U' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR U 33 " --> pdb=" O VAL U 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'U' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG U 96 " --> pdb=" O ASP U 115 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 3.64 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: 10136 1.34 - 1.45: 4378 1.45 - 1.57: 17210 1.57 - 1.69: 154 1.69 - 1.80: 209 Bond restraints: 32087 Sorted by residual: bond pdb=" CB VAL U 325 " pdb=" CG1 VAL U 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CB VAL O 325 " pdb=" CG1 VAL O 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.53e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CB VAL M 325 " pdb=" CG1 VAL M 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 bond pdb=" CB VAL I 325 " pdb=" CG1 VAL I 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 32082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 39728 1.18 - 2.37: 2981 2.37 - 3.55: 677 3.55 - 4.74: 202 4.74 - 5.92: 49 Bond angle restraints: 43637 Sorted by residual: angle pdb=" CA TYR O 61 " pdb=" CB TYR O 61 " pdb=" CG TYR O 61 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR K 61 " pdb=" CB TYR K 61 " pdb=" CG TYR K 61 " ideal model delta sigma weight residual 113.90 118.65 -4.75 1.80e+00 3.09e-01 6.96e+00 angle pdb=" CA TYR S 61 " pdb=" CB TYR S 61 " pdb=" CG TYR S 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.93e+00 angle pdb=" CA TYR I 61 " pdb=" CB TYR I 61 " pdb=" CG TYR I 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.92e+00 angle pdb=" CA TYR E 61 " pdb=" CB TYR E 61 " pdb=" CG TYR E 61 " ideal model delta sigma weight residual 113.90 118.63 -4.73 1.80e+00 3.09e-01 6.92e+00 ... (remaining 43632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17346 16.60 - 33.20: 1795 33.20 - 49.80: 296 49.80 - 66.40: 176 66.40 - 83.00: 143 Dihedral angle restraints: 19756 sinusoidal: 8580 harmonic: 11176 Sorted by residual: dihedral pdb=" C4' C N 74 " pdb=" C3' C N 74 " pdb=" C2' C N 74 " pdb=" C1' C N 74 " ideal model delta sinusoidal sigma weight residual 36.34 -34.31 70.65 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" C4' C D 74 " pdb=" C3' C D 74 " pdb=" C2' C D 74 " pdb=" C1' C D 74 " ideal model delta sinusoidal sigma weight residual 36.35 -34.29 70.63 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" C4' C P 74 " pdb=" C3' C P 74 " pdb=" C2' C P 74 " pdb=" C1' C P 74 " ideal model delta sinusoidal sigma weight residual 36.35 -34.29 70.63 1 3.10e+00 1.04e-01 6.68e+02 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4020 0.059 - 0.118: 930 0.118 - 0.177: 121 0.177 - 0.236: 56 0.236 - 0.294: 21 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C2' C V 74 " pdb=" C3' C V 74 " pdb=" O2' C V 74 " pdb=" C1' C V 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' C T 74 " pdb=" C3' C T 74 " pdb=" O2' C T 74 " pdb=" C1' C T 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' C F 74 " pdb=" C3' C F 74 " pdb=" O2' C F 74 " pdb=" C1' C F 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 5145 not shown) Planarity restraints: 5291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY S 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLY S 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY S 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS S 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY G 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY G 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY Q 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY Q 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 229 " 0.018 2.00e-02 2.50e+03 ... (remaining 5288 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.36: 121 1.36 - 2.25: 352 2.25 - 3.13: 26184 3.13 - 4.02: 84872 4.02 - 4.90: 156081 Warning: very small nonbonded interaction distances. Nonbonded interactions: 267610 Sorted by model distance: nonbonded pdb=" C3' C J 77 " pdb=" OP1 C L 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C F 77 " pdb=" OP1 C H 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C T 77 " pdb=" OP1 C V 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C R 77 " pdb=" OP1 C T 71 " model vdw 0.481 3.470 nonbonded pdb=" OP1 C B 71 " pdb=" C3' C V 77 " model vdw 0.481 3.470 ... (remaining 267605 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 29.490 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.022 1.151 32098 Z= 2.146 Angle : 0.764 5.921 43637 Z= 0.417 Chirality : 0.056 0.294 5148 Planarity : 0.006 0.052 5291 Dihedral : 16.019 82.999 12584 Min Nonbonded Distance : 0.481 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.75 (0.13), residues: 3817 helix: 1.00 (0.10), residues: 2464 sheet: -1.19 (0.33), residues: 165 loop : -0.11 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 208 TYR 0.027 0.003 TYR E 61 PHE 0.013 0.003 PHE U 214 TRP 0.013 0.002 TRP I 261 HIS 0.003 0.001 HIS U 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (32087) covalent geometry : angle 0.76411 / 0.42 (43637) hydrogen bonds : bond 0.11926 / 8.08 ( 1826) hydrogen bonds : angle 5.93484 / 4.13 ( 5379) Misc. bond : bond 1.15083 / 64.77 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7370 (ttp-110) REVERT: G 138 LEU cc_start: 0.8331 (mp) cc_final: 0.8064 (mp) REVERT: I 53 TYR cc_start: 0.6244 (p90) cc_final: 0.6003 (p90) REVERT: I 138 LEU cc_start: 0.8393 (mp) cc_final: 0.8159 (mp) REVERT: I 249 MET cc_start: 0.7609 (mmm) cc_final: 0.7024 (mmm) REVERT: K 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8360 (mp) REVERT: M 39 SER cc_start: 0.8582 (m) cc_final: 0.8338 (p) REVERT: M 84 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: M 249 MET cc_start: 0.7274 (mmm) cc_final: 0.6836 (mmm) REVERT: O 7 HIS cc_start: 0.7683 (t70) cc_final: 0.7453 (t70) REVERT: Q 138 LEU cc_start: 0.8545 (mp) cc_final: 0.8305 (mp) REVERT: S 249 MET cc_start: 0.7544 (mmm) cc_final: 0.7133 (mmm) REVERT: U 39 SER cc_start: 0.8580 (m) cc_final: 0.8319 (p) REVERT: U 138 LEU cc_start: 0.8580 (mp) cc_final: 0.8334 (mp) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.2208 time to fit residues: 185.7654 Evaluate side-chains 390 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 148 GLN A 306 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 306 GLN E 80 GLN E 306 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 306 GLN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN I 80 GLN I 306 GLN ** I 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 306 GLN ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN M 148 GLN M 306 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 148 GLN O 306 GLN ** O 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN Q 148 GLN Q 306 GLN ** Q 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN S 306 GLN ** S 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 306 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139332 restraints weight = 43167.805| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.33 r_work: 0.3411 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32098 Z= 0.162 Angle : 0.761 12.391 43637 Z= 0.342 Chirality : 0.062 0.736 5148 Planarity : 0.009 0.173 5291 Dihedral : 14.067 159.355 5412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.37 % Allowed : 6.62 % Favored : 92.01 % 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: 1.20 (0.14), residues: 3817 helix: 1.36 (0.11), residues: 2519 sheet: -0.69 (0.34), residues: 165 loop : -0.11 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 78 TYR 0.024 0.002 TYR Q 23 PHE 0.025 0.002 PHE G 348 TRP 0.003 0.001 TRP E 261 HIS 0.007 0.001 HIS O 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (32087) covalent geometry : angle 0.76064 / 0.34 (43637) hydrogen bonds : bond 0.04810 / 3.22 ( 1826) hydrogen bonds : angle 4.55320 / 3.16 ( 5379) Misc. bond : bond 0.00369 / 0.21 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 488 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8792 (tp40) cc_final: 0.8011 (tt0) REVERT: A 249 MET cc_start: 0.7761 (mmm) cc_final: 0.7491 (mmm) REVERT: C 80 GLN cc_start: 0.8905 (tp40) cc_final: 0.8222 (tt0) REVERT: C 115 ASP cc_start: 0.6611 (t70) cc_final: 0.6388 (t70) REVERT: C 249 MET cc_start: 0.7659 (mmm) cc_final: 0.7410 (mmm) REVERT: E 53 TYR cc_start: 0.6929 (p90) cc_final: 0.6584 (p90) REVERT: E 80 GLN cc_start: 0.8782 (tp40) cc_final: 0.8052 (tt0) REVERT: E 290 ASP cc_start: 0.8276 (m-30) cc_final: 0.7987 (m-30) REVERT: G 80 GLN cc_start: 0.8778 (tp40) cc_final: 0.8099 (tt0) REVERT: G 138 LEU cc_start: 0.8488 (mp) cc_final: 0.8116 (mp) REVERT: I 53 TYR cc_start: 0.6626 (p90) cc_final: 0.6167 (p90) REVERT: I 80 GLN cc_start: 0.8818 (tp40) cc_final: 0.8164 (tt0) REVERT: I 115 ASP cc_start: 0.6435 (t70) cc_final: 0.6146 (t70) REVERT: I 138 LEU cc_start: 0.8369 (mp) cc_final: 0.8167 (mp) REVERT: I 249 MET cc_start: 0.7841 (mmm) cc_final: 0.7512 (mmm) REVERT: K 80 GLN cc_start: 0.8925 (tp40) cc_final: 0.8181 (tt0) REVERT: K 138 LEU cc_start: 0.8446 (mp) cc_final: 0.8245 (mp) REVERT: M 80 GLN cc_start: 0.8826 (tp40) cc_final: 0.8085 (tt0) REVERT: M 115 ASP cc_start: 0.6369 (t70) cc_final: 0.5868 (t70) REVERT: O 80 GLN cc_start: 0.8804 (tp40) cc_final: 0.8059 (tt0) REVERT: O 249 MET cc_start: 0.7721 (mmm) cc_final: 0.7464 (mmm) REVERT: Q 80 GLN cc_start: 0.8839 (tp40) cc_final: 0.8130 (tt0) REVERT: Q 138 LEU cc_start: 0.8439 (mp) cc_final: 0.8199 (mp) REVERT: Q 200 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7085 (mtm-85) REVERT: S 50 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7545 (tp30) REVERT: S 80 GLN cc_start: 0.8965 (tp40) cc_final: 0.8242 (tt0) REVERT: S 249 MET cc_start: 0.7816 (mmm) cc_final: 0.7548 (mmm) REVERT: U 80 GLN cc_start: 0.8810 (tp40) cc_final: 0.8086 (tt0) REVERT: U 138 LEU cc_start: 0.8713 (mp) cc_final: 0.8392 (mp) outliers start: 45 outliers final: 9 residues processed: 499 average time/residue: 0.2198 time to fit residues: 168.3930 Evaluate side-chains 427 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 418 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 10 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 149 optimal weight: 0.2980 chunk 337 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 335 optimal weight: 0.6980 chunk 341 optimal weight: 0.9990 chunk 102 optimal weight: 0.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 284 GLN K 148 GLN M 148 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 284 GLN Q 284 GLN S 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142541 restraints weight = 42826.783| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.33 r_work: 0.3445 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32098 Z= 0.128 Angle : 0.633 11.315 43637 Z= 0.291 Chirality : 0.046 0.317 5148 Planarity : 0.007 0.437 5291 Dihedral : 14.467 177.435 5412 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.16 % Allowed : 10.56 % Favored : 88.29 % 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: 1.41 (0.14), residues: 3817 helix: 1.62 (0.11), residues: 2508 sheet: -1.51 (0.31), residues: 209 loop : -0.00 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG U 78 TYR 0.025 0.001 TYR A 23 PHE 0.029 0.002 PHE K 348 TRP 0.002 0.000 TRP E 261 HIS 0.009 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (32087) covalent geometry : angle 0.63303 / 0.29 (43637) hydrogen bonds : bond 0.04106 / 2.73 ( 1826) hydrogen bonds : angle 4.28914 / 2.98 ( 5379) Misc. bond : bond 0.00082 / 0.04 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 474 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8738 (tp40) cc_final: 0.8030 (tt0) REVERT: C 80 GLN cc_start: 0.8840 (tp40) cc_final: 0.8159 (tt0) REVERT: C 249 MET cc_start: 0.7659 (mmm) cc_final: 0.7331 (mmm) REVERT: C 338 TYR cc_start: 0.7138 (t80) cc_final: 0.6897 (t80) REVERT: E 80 GLN cc_start: 0.8745 (tp40) cc_final: 0.8050 (tt0) REVERT: E 290 ASP cc_start: 0.8228 (m-30) cc_final: 0.7734 (m-30) REVERT: G 80 GLN cc_start: 0.8744 (tp40) cc_final: 0.8126 (tt0) REVERT: G 138 LEU cc_start: 0.8312 (mp) cc_final: 0.7939 (mp) REVERT: G 175 THR cc_start: 0.8341 (m) cc_final: 0.8122 (p) REVERT: I 53 TYR cc_start: 0.6715 (p90) cc_final: 0.6374 (p90) REVERT: I 80 GLN cc_start: 0.8730 (tp40) cc_final: 0.8123 (tt0) REVERT: I 128 ASP cc_start: 0.7442 (t70) cc_final: 0.7171 (t0) REVERT: I 138 LEU cc_start: 0.8362 (mp) cc_final: 0.8111 (mp) REVERT: K 80 GLN cc_start: 0.8902 (tp40) cc_final: 0.8216 (tt0) REVERT: K 138 LEU cc_start: 0.8457 (mp) cc_final: 0.8227 (mp) REVERT: K 175 THR cc_start: 0.8277 (m) cc_final: 0.8024 (p) REVERT: K 347 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7641 (mm) REVERT: M 80 GLN cc_start: 0.8721 (tp40) cc_final: 0.8094 (tt0) REVERT: M 128 ASP cc_start: 0.7732 (t70) cc_final: 0.7395 (t0) REVERT: O 80 GLN cc_start: 0.8732 (tp40) cc_final: 0.7996 (tt0) REVERT: O 128 ASP cc_start: 0.7521 (t70) cc_final: 0.7267 (t0) REVERT: O 249 MET cc_start: 0.7664 (mmm) cc_final: 0.7347 (mmm) REVERT: Q 80 GLN cc_start: 0.8752 (tp40) cc_final: 0.8109 (tt0) REVERT: Q 138 LEU cc_start: 0.8564 (mp) cc_final: 0.8241 (mp) REVERT: Q 346 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7805 (tt0) REVERT: S 80 GLN cc_start: 0.8791 (tp40) cc_final: 0.8099 (tt0) REVERT: S 249 MET cc_start: 0.7663 (mmm) cc_final: 0.7303 (mmm) REVERT: S 347 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8209 (mt) REVERT: U 80 GLN cc_start: 0.8619 (tp40) cc_final: 0.8036 (tt0) REVERT: U 138 LEU cc_start: 0.8684 (mp) cc_final: 0.8366 (mp) REVERT: U 151 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7097 (ptp-170) outliers start: 38 outliers final: 10 residues processed: 486 average time/residue: 0.2228 time to fit residues: 165.4434 Evaluate side-chains 430 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 417 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain U residue 23 TYR Chi-restraints excluded: chain U residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 354 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 276 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 232 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 153 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 275 HIS ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141914 restraints weight = 42523.411| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.32 r_work: 0.3428 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32098 Z= 0.137 Angle : 0.604 12.015 43637 Z= 0.283 Chirality : 0.045 0.368 5148 Planarity : 0.014 0.421 5291 Dihedral : 13.107 179.034 5412 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 12.05 % Favored : 86.18 % 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: 1.42 (0.14), residues: 3817 helix: 1.63 (0.11), residues: 2519 sheet: -1.40 (0.32), residues: 209 loop : -0.07 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG I 78 TYR 0.028 0.002 TYR S 23 PHE 0.030 0.002 PHE C 348 TRP 0.003 0.001 TRP A 261 HIS 0.007 0.001 HIS S 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (32087) covalent geometry : angle 0.60360 / 0.28 (43637) hydrogen bonds : bond 0.04025 / 2.68 ( 1826) hydrogen bonds : angle 4.21551 / 2.93 ( 5379) Misc. bond : bond 0.00436 / 0.25 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 437 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8745 (tp40) cc_final: 0.8061 (tt0) REVERT: A 249 MET cc_start: 0.7559 (mmm) cc_final: 0.7276 (mmm) REVERT: C 80 GLN cc_start: 0.8900 (tp40) cc_final: 0.8213 (tt0) REVERT: C 249 MET cc_start: 0.7688 (mmm) cc_final: 0.7375 (mmm) REVERT: C 338 TYR cc_start: 0.7026 (t80) cc_final: 0.6787 (t80) REVERT: C 344 ASN cc_start: 0.6619 (t0) cc_final: 0.5832 (t0) REVERT: E 80 GLN cc_start: 0.8757 (tp40) cc_final: 0.8127 (tt0) REVERT: E 128 ASP cc_start: 0.7613 (t70) cc_final: 0.7363 (t0) REVERT: G 50 GLU cc_start: 0.7797 (tp30) cc_final: 0.7548 (mm-30) REVERT: G 80 GLN cc_start: 0.8728 (tp40) cc_final: 0.8181 (tt0) REVERT: G 138 LEU cc_start: 0.8370 (mp) cc_final: 0.7894 (mp) REVERT: G 200 ARG cc_start: 0.7318 (ptp90) cc_final: 0.7109 (mtm-85) REVERT: I 53 TYR cc_start: 0.6783 (p90) cc_final: 0.6576 (p90) REVERT: I 80 GLN cc_start: 0.8642 (tp40) cc_final: 0.8127 (tt0) REVERT: I 128 ASP cc_start: 0.7550 (t70) cc_final: 0.7321 (t0) REVERT: I 138 LEU cc_start: 0.8173 (mp) cc_final: 0.7886 (mp) REVERT: K 51 ILE cc_start: 0.8414 (mt) cc_final: 0.8101 (mt) REVERT: K 80 GLN cc_start: 0.8785 (tp40) cc_final: 0.8113 (tt0) REVERT: K 138 LEU cc_start: 0.8525 (mp) cc_final: 0.8232 (mp) REVERT: K 347 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7916 (mt) REVERT: M 80 GLN cc_start: 0.8586 (tp40) cc_final: 0.8037 (tt0) REVERT: O 80 GLN cc_start: 0.8656 (tp40) cc_final: 0.7999 (tt0) REVERT: O 249 MET cc_start: 0.7722 (mmm) cc_final: 0.7404 (mmm) REVERT: Q 80 GLN cc_start: 0.8745 (tp40) cc_final: 0.8078 (tt0) REVERT: Q 138 LEU cc_start: 0.8581 (mp) cc_final: 0.8258 (mp) REVERT: S 80 GLN cc_start: 0.8794 (tp40) cc_final: 0.8173 (tt0) REVERT: S 249 MET cc_start: 0.7693 (mmm) cc_final: 0.7331 (mmm) REVERT: S 344 ASN cc_start: 0.6287 (t0) cc_final: 0.5320 (t0) REVERT: U 80 GLN cc_start: 0.8627 (tp40) cc_final: 0.7996 (tt0) REVERT: U 113 MET cc_start: 0.4741 (mtp) cc_final: 0.4312 (mtm) REVERT: U 138 LEU cc_start: 0.8623 (mp) cc_final: 0.8234 (mp) REVERT: U 151 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7129 (ptp-170) outliers start: 58 outliers final: 36 residues processed: 456 average time/residue: 0.2153 time to fit residues: 150.4540 Evaluate side-chains 441 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 403 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 275 optimal weight: 0.4980 chunk 353 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 187 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN O 275 HIS Q 344 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141921 restraints weight = 42726.823| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.33 r_work: 0.3427 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32098 Z= 0.134 Angle : 0.596 12.173 43637 Z= 0.276 Chirality : 0.046 0.382 5148 Planarity : 0.012 0.443 5291 Dihedral : 13.072 179.692 5412 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.23 % Allowed : 12.78 % Favored : 84.99 % 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: 1.52 (0.14), residues: 3817 helix: 1.69 (0.11), residues: 2530 sheet: -0.33 (0.37), residues: 165 loop : -0.26 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG O 78 TYR 0.022 0.002 TYR M 23 PHE 0.031 0.002 PHE C 348 TRP 0.004 0.001 TRP Q 261 HIS 0.024 0.002 HIS O 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (32087) covalent geometry : angle 0.59576 / 0.28 (43637) hydrogen bonds : bond 0.03949 / 2.63 ( 1826) hydrogen bonds : angle 4.16448 / 2.90 ( 5379) Misc. bond : bond 0.00357 / 0.23 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 413 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8766 (tp40) cc_final: 0.8016 (tt0) REVERT: A 249 MET cc_start: 0.7629 (mmm) cc_final: 0.7393 (mmm) REVERT: C 80 GLN cc_start: 0.8900 (tp40) cc_final: 0.8211 (tt0) REVERT: C 249 MET cc_start: 0.7749 (mmm) cc_final: 0.7413 (mmm) REVERT: E 80 GLN cc_start: 0.8766 (tp40) cc_final: 0.8021 (tt0) REVERT: G 80 GLN cc_start: 0.8756 (tp40) cc_final: 0.8198 (tt0) REVERT: G 138 LEU cc_start: 0.8390 (mp) cc_final: 0.8016 (mp) REVERT: I 80 GLN cc_start: 0.8686 (tp40) cc_final: 0.8149 (tt0) REVERT: I 128 ASP cc_start: 0.7538 (t70) cc_final: 0.7307 (t0) REVERT: I 138 LEU cc_start: 0.8146 (mp) cc_final: 0.7836 (mp) REVERT: K 80 GLN cc_start: 0.8811 (tp40) cc_final: 0.8138 (tt0) REVERT: K 138 LEU cc_start: 0.8489 (mp) cc_final: 0.8150 (mp) REVERT: K 347 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7822 (mt) REVERT: M 80 GLN cc_start: 0.8575 (tp40) cc_final: 0.8022 (tt0) REVERT: O 80 GLN cc_start: 0.8700 (tp40) cc_final: 0.8042 (tt0) REVERT: O 249 MET cc_start: 0.7696 (mmm) cc_final: 0.7360 (mmm) REVERT: Q 80 GLN cc_start: 0.8750 (tp40) cc_final: 0.8112 (tt0) REVERT: Q 138 LEU cc_start: 0.8555 (mp) cc_final: 0.8221 (mp) REVERT: S 80 GLN cc_start: 0.8785 (tp40) cc_final: 0.8183 (tt0) REVERT: S 249 MET cc_start: 0.7717 (mmm) cc_final: 0.7378 (mmm) REVERT: U 80 GLN cc_start: 0.8627 (tp40) cc_final: 0.7957 (tt0) REVERT: U 113 MET cc_start: 0.4836 (mtp) cc_final: 0.4389 (mtm) REVERT: U 138 LEU cc_start: 0.8543 (mp) cc_final: 0.8140 (mp) REVERT: U 151 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7292 (ptp-170) outliers start: 73 outliers final: 49 residues processed: 441 average time/residue: 0.2068 time to fit residues: 140.7433 Evaluate side-chains 434 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 383 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 290 ASP Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 358 LEU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 223 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 364 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 148 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 344 ASN S 148 GLN S 275 HIS U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139093 restraints weight = 42661.390| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.32 r_work: 0.3366 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32098 Z= 0.185 Angle : 0.642 12.515 43637 Z= 0.299 Chirality : 0.047 0.418 5148 Planarity : 0.007 0.206 5291 Dihedral : 13.104 179.822 5412 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.23 % Allowed : 13.45 % Favored : 84.32 % 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: 1.47 (0.14), residues: 3817 helix: 1.66 (0.11), residues: 2530 sheet: -0.24 (0.37), residues: 165 loop : -0.33 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG M 78 TYR 0.026 0.002 TYR I 23 PHE 0.032 0.003 PHE C 348 TRP 0.009 0.001 TRP S 261 HIS 0.018 0.001 HIS O 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (32087) covalent geometry : angle 0.64209 / 0.30 (43637) hydrogen bonds : bond 0.04308 / 2.87 ( 1826) hydrogen bonds : angle 4.29037 / 2.99 ( 5379) Misc. bond : bond 0.00349 / 0.19 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 401 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8789 (tp40) cc_final: 0.8031 (tt0) REVERT: C 80 GLN cc_start: 0.8943 (tp40) cc_final: 0.8240 (tt0) REVERT: C 249 MET cc_start: 0.7748 (mmm) cc_final: 0.7435 (mmm) REVERT: E 80 GLN cc_start: 0.8757 (tp40) cc_final: 0.8063 (tt0) REVERT: E 249 MET cc_start: 0.8103 (mmm) cc_final: 0.7848 (mmm) REVERT: G 80 GLN cc_start: 0.8783 (tp40) cc_final: 0.8245 (tt0) REVERT: G 138 LEU cc_start: 0.8367 (mp) cc_final: 0.7999 (mp) REVERT: G 200 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: I 80 GLN cc_start: 0.8745 (tp40) cc_final: 0.8185 (tt0) REVERT: I 128 ASP cc_start: 0.7572 (t70) cc_final: 0.7334 (t0) REVERT: I 138 LEU cc_start: 0.8223 (mp) cc_final: 0.8015 (mp) REVERT: I 151 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7412 (ptp-170) REVERT: K 51 ILE cc_start: 0.7980 (mt) cc_final: 0.7601 (mt) REVERT: K 80 GLN cc_start: 0.8867 (tp40) cc_final: 0.8224 (tt0) REVERT: K 138 LEU cc_start: 0.8452 (mp) cc_final: 0.8172 (mp) REVERT: K 347 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7685 (mt) REVERT: M 80 GLN cc_start: 0.8710 (tp40) cc_final: 0.8100 (tt0) REVERT: O 80 GLN cc_start: 0.8754 (tp40) cc_final: 0.8135 (tt0) REVERT: O 249 MET cc_start: 0.7725 (mmm) cc_final: 0.7438 (mmm) REVERT: O 347 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7326 (mt) REVERT: Q 80 GLN cc_start: 0.8801 (tp40) cc_final: 0.8160 (tt0) REVERT: Q 138 LEU cc_start: 0.8637 (mp) cc_final: 0.8386 (mp) REVERT: S 80 GLN cc_start: 0.8861 (tp40) cc_final: 0.8191 (tt0) REVERT: S 249 MET cc_start: 0.7747 (mmm) cc_final: 0.7436 (mmm) REVERT: U 80 GLN cc_start: 0.8738 (tp40) cc_final: 0.8093 (tt0) REVERT: U 113 MET cc_start: 0.4877 (mtp) cc_final: 0.4422 (mtm) REVERT: U 138 LEU cc_start: 0.8359 (mp) cc_final: 0.8018 (mp) REVERT: U 151 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7423 (ptp-170) outliers start: 73 outliers final: 56 residues processed: 430 average time/residue: 0.2073 time to fit residues: 136.9226 Evaluate side-chains 438 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 378 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 298 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 305 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 329 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS U 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.168722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136993 restraints weight = 43217.871| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.71 r_work: 0.3323 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32098 Z= 0.141 Angle : 0.614 12.891 43637 Z= 0.283 Chirality : 0.047 0.424 5148 Planarity : 0.006 0.169 5291 Dihedral : 13.108 179.335 5412 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.10 % Allowed : 14.70 % Favored : 83.19 % 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: 1.56 (0.14), residues: 3817 helix: 1.74 (0.11), residues: 2541 sheet: -0.32 (0.36), residues: 165 loop : -0.30 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 78 TYR 0.019 0.001 TYR M 23 PHE 0.032 0.003 PHE C 348 TRP 0.004 0.001 TRP Q 261 HIS 0.012 0.001 HIS O 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (32087) covalent geometry : angle 0.61405 / 0.28 (43637) hydrogen bonds : bond 0.04000 / 2.67 ( 1826) hydrogen bonds : angle 4.18505 / 2.91 ( 5379) Misc. bond : bond 0.00276 / 0.15 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 397 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8706 (tp40) cc_final: 0.7965 (tt0) REVERT: A 200 ARG cc_start: 0.7197 (ptp90) cc_final: 0.6915 (mtm110) REVERT: C 80 GLN cc_start: 0.8856 (tp40) cc_final: 0.8152 (tt0) REVERT: C 249 MET cc_start: 0.7537 (mmm) cc_final: 0.7192 (mmm) REVERT: E 80 GLN cc_start: 0.8745 (tp40) cc_final: 0.8042 (tt0) REVERT: G 80 GLN cc_start: 0.8716 (tp40) cc_final: 0.8152 (tt0) REVERT: G 138 LEU cc_start: 0.8338 (mp) cc_final: 0.8029 (mp) REVERT: I 80 GLN cc_start: 0.8677 (tp40) cc_final: 0.8101 (tt0) REVERT: I 128 ASP cc_start: 0.7495 (t70) cc_final: 0.7273 (t0) REVERT: I 138 LEU cc_start: 0.8185 (mp) cc_final: 0.7969 (mp) REVERT: I 151 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7218 (ptp-170) REVERT: I 249 MET cc_start: 0.7495 (mmm) cc_final: 0.7168 (mmm) REVERT: K 51 ILE cc_start: 0.7731 (mt) cc_final: 0.7436 (mt) REVERT: K 80 GLN cc_start: 0.8732 (tp40) cc_final: 0.8056 (tt0) REVERT: K 113 MET cc_start: 0.4142 (OUTLIER) cc_final: 0.3661 (mtm) REVERT: K 138 LEU cc_start: 0.8392 (mp) cc_final: 0.8111 (mp) REVERT: K 344 ASN cc_start: 0.6761 (t0) cc_final: 0.5814 (t0) REVERT: K 347 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7689 (mm) REVERT: M 80 GLN cc_start: 0.8609 (tp40) cc_final: 0.7998 (tt0) REVERT: O 80 GLN cc_start: 0.8676 (tp40) cc_final: 0.8039 (tt0) REVERT: O 151 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6998 (mtt90) REVERT: O 249 MET cc_start: 0.7678 (mmm) cc_final: 0.7381 (mmm) REVERT: Q 80 GLN cc_start: 0.8707 (tp40) cc_final: 0.8103 (tt0) REVERT: Q 138 LEU cc_start: 0.8557 (mp) cc_final: 0.8307 (mp) REVERT: Q 250 GLN cc_start: 0.8086 (mt0) cc_final: 0.7834 (mt0) REVERT: Q 339 ARG cc_start: 0.7038 (tpp-160) cc_final: 0.6753 (mmp80) REVERT: S 80 GLN cc_start: 0.8761 (tp40) cc_final: 0.8086 (tt0) REVERT: S 249 MET cc_start: 0.7557 (mmm) cc_final: 0.7247 (mmm) REVERT: U 78 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7029 (tpp-160) REVERT: U 80 GLN cc_start: 0.8582 (tp40) cc_final: 0.7944 (tt0) REVERT: U 113 MET cc_start: 0.4788 (mtp) cc_final: 0.4364 (mtm) REVERT: U 138 LEU cc_start: 0.8288 (mp) cc_final: 0.7945 (mp) REVERT: U 151 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7335 (ptp-170) outliers start: 69 outliers final: 52 residues processed: 424 average time/residue: 0.2112 time to fit residues: 137.1967 Evaluate side-chains 441 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 385 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 23 TYR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 275 HIS Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 324 optimal weight: 0.9980 chunk 188 optimal weight: 0.0370 chunk 352 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 108 optimal weight: 0.0470 chunk 181 optimal weight: 0.6980 chunk 348 optimal weight: 0.7980 chunk 259 optimal weight: 0.5980 chunk 175 optimal weight: 0.0770 chunk 218 optimal weight: 5.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 117 HIS G 275 HIS I 117 HIS ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140537 restraints weight = 42863.153| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.66 r_work: 0.3381 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 32098 Z= 0.107 Angle : 0.595 14.242 43637 Z= 0.272 Chirality : 0.045 0.385 5148 Planarity : 0.006 0.150 5291 Dihedral : 13.065 178.987 5412 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.56 % Allowed : 15.74 % Favored : 82.70 % 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: 1.82 (0.14), residues: 3817 helix: 1.96 (0.11), residues: 2541 sheet: -0.39 (0.35), residues: 165 loop : -0.25 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 78 TYR 0.016 0.001 TYR M 23 PHE 0.032 0.002 PHE I 348 TRP 0.007 0.001 TRP Q 261 HIS 0.026 0.001 HIS O 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (32087) covalent geometry : angle 0.59467 / 0.27 (43637) hydrogen bonds : bond 0.03633 / 2.42 ( 1826) hydrogen bonds : angle 4.03994 / 2.81 ( 5379) Misc. bond : bond 0.00260 / 0.15 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 416 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8671 (tp40) cc_final: 0.7970 (tt0) REVERT: A 175 THR cc_start: 0.8330 (m) cc_final: 0.8103 (p) REVERT: A 200 ARG cc_start: 0.7138 (ptp90) cc_final: 0.6891 (mtm-85) REVERT: A 249 MET cc_start: 0.7598 (tpp) cc_final: 0.7380 (mmm) REVERT: C 80 GLN cc_start: 0.8788 (tp40) cc_final: 0.8137 (tt0) REVERT: C 249 MET cc_start: 0.7497 (mmm) cc_final: 0.7164 (mmm) REVERT: E 80 GLN cc_start: 0.8684 (tp40) cc_final: 0.8025 (tt0) REVERT: E 249 MET cc_start: 0.7902 (mmm) cc_final: 0.7693 (mmm) REVERT: E 339 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6736 (mmt-90) REVERT: G 80 GLN cc_start: 0.8661 (tp40) cc_final: 0.8115 (tt0) REVERT: G 138 LEU cc_start: 0.8381 (mp) cc_final: 0.8038 (mp) REVERT: G 249 MET cc_start: 0.6976 (mmm) cc_final: 0.6740 (tpt) REVERT: I 80 GLN cc_start: 0.8582 (tp40) cc_final: 0.8087 (tt0) REVERT: I 128 ASP cc_start: 0.7533 (t70) cc_final: 0.7327 (t0) REVERT: I 138 LEU cc_start: 0.8243 (mp) cc_final: 0.7934 (mp) REVERT: I 151 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7125 (ptp-170) REVERT: I 249 MET cc_start: 0.7423 (mmm) cc_final: 0.7105 (mmm) REVERT: K 51 ILE cc_start: 0.7452 (mt) cc_final: 0.7155 (mt) REVERT: K 80 GLN cc_start: 0.8687 (tp40) cc_final: 0.8042 (tt0) REVERT: K 113 MET cc_start: 0.3786 (mtp) cc_final: 0.3387 (mtm) REVERT: K 138 LEU cc_start: 0.8355 (mp) cc_final: 0.7979 (mp) REVERT: K 339 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.7034 (mmt-90) REVERT: K 347 LEU cc_start: 0.8417 (mm) cc_final: 0.8144 (mt) REVERT: M 80 GLN cc_start: 0.8487 (tp40) cc_final: 0.7986 (tt0) REVERT: M 339 ARG cc_start: 0.7238 (tpp-160) cc_final: 0.6995 (mmt-90) REVERT: O 80 GLN cc_start: 0.8586 (tp40) cc_final: 0.7989 (tt0) REVERT: O 249 MET cc_start: 0.7528 (mmm) cc_final: 0.7179 (mmm) REVERT: Q 80 GLN cc_start: 0.8639 (tp40) cc_final: 0.8070 (tt0) REVERT: Q 138 LEU cc_start: 0.8588 (mp) cc_final: 0.8333 (mp) REVERT: S 80 GLN cc_start: 0.8702 (tp40) cc_final: 0.8092 (tt0) REVERT: S 249 MET cc_start: 0.7480 (mmm) cc_final: 0.7161 (mmm) REVERT: S 339 ARG cc_start: 0.7215 (tpp-160) cc_final: 0.7002 (mmt-90) REVERT: U 78 ARG cc_start: 0.7761 (mmm160) cc_final: 0.7005 (tpp-160) REVERT: U 80 GLN cc_start: 0.8529 (tp40) cc_final: 0.7907 (tt0) REVERT: U 138 LEU cc_start: 0.8304 (mp) cc_final: 0.7959 (mp) REVERT: U 151 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7329 (ptp-170) outliers start: 51 outliers final: 38 residues processed: 441 average time/residue: 0.2118 time to fit residues: 144.3759 Evaluate side-chains 434 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 394 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 23 TYR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 275 HIS Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 116 optimal weight: 1.9990 chunk 169 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 273 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 374 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS C 117 HIS G 275 HIS I 117 HIS ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138127 restraints weight = 43014.450| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.77 r_work: 0.3322 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32098 Z= 0.142 Angle : 0.618 15.507 43637 Z= 0.285 Chirality : 0.045 0.384 5148 Planarity : 0.006 0.155 5291 Dihedral : 13.025 179.999 5412 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.59 % Allowed : 16.29 % Favored : 82.12 % 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: 1.79 (0.14), residues: 3817 helix: 1.92 (0.11), residues: 2541 sheet: -0.34 (0.35), residues: 165 loop : -0.23 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 78 TYR 0.017 0.002 TYR M 23 PHE 0.032 0.003 PHE K 348 TRP 0.004 0.001 TRP G 261 HIS 0.008 0.001 HIS O 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32087) covalent geometry : angle 0.61829 / 0.28 (43637) hydrogen bonds : bond 0.03871 / 2.58 ( 1826) hydrogen bonds : angle 4.13513 / 2.87 ( 5379) Misc. bond : bond 0.00255 / 0.14 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 393 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8721 (tp40) cc_final: 0.8017 (tt0) REVERT: A 84 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7716 (ttp-110) REVERT: A 249 MET cc_start: 0.7679 (tpp) cc_final: 0.7449 (mmm) REVERT: C 80 GLN cc_start: 0.8836 (tp40) cc_final: 0.8144 (tt0) REVERT: C 249 MET cc_start: 0.7573 (mmm) cc_final: 0.7203 (mmm) REVERT: E 80 GLN cc_start: 0.8728 (tp40) cc_final: 0.8052 (tt0) REVERT: E 249 MET cc_start: 0.7984 (mmm) cc_final: 0.7758 (mmm) REVERT: E 339 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6912 (mmt-90) REVERT: G 80 GLN cc_start: 0.8749 (tp40) cc_final: 0.8182 (tt0) REVERT: G 138 LEU cc_start: 0.8329 (mp) cc_final: 0.7984 (mp) REVERT: G 200 ARG cc_start: 0.7335 (ptp90) cc_final: 0.7019 (mtm-85) REVERT: G 339 ARG cc_start: 0.7188 (tpp-160) cc_final: 0.6843 (mmt-90) REVERT: I 80 GLN cc_start: 0.8676 (tp40) cc_final: 0.8111 (tt0) REVERT: I 128 ASP cc_start: 0.7491 (t70) cc_final: 0.7285 (t0) REVERT: I 138 LEU cc_start: 0.8230 (mp) cc_final: 0.7974 (mp) REVERT: I 151 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7170 (ptp-170) REVERT: I 249 MET cc_start: 0.7540 (mmm) cc_final: 0.7180 (mmm) REVERT: K 51 ILE cc_start: 0.7722 (mt) cc_final: 0.7426 (mt) REVERT: K 80 GLN cc_start: 0.8746 (tp40) cc_final: 0.8083 (tt0) REVERT: K 113 MET cc_start: 0.3672 (mtp) cc_final: 0.3269 (mtm) REVERT: K 138 LEU cc_start: 0.8419 (mp) cc_final: 0.8095 (mp) REVERT: K 339 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.7053 (mmt-90) REVERT: M 80 GLN cc_start: 0.8544 (tp40) cc_final: 0.8026 (tt0) REVERT: M 339 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.7111 (mmt-90) REVERT: O 80 GLN cc_start: 0.8633 (tp40) cc_final: 0.7991 (tt0) REVERT: O 135 MET cc_start: 0.7054 (ttm) cc_final: 0.6542 (ttt) REVERT: O 249 MET cc_start: 0.7677 (mmm) cc_final: 0.7354 (mmm) REVERT: Q 80 GLN cc_start: 0.8715 (tp40) cc_final: 0.8077 (tt0) REVERT: Q 138 LEU cc_start: 0.8519 (mp) cc_final: 0.8236 (mp) REVERT: S 80 GLN cc_start: 0.8778 (tp40) cc_final: 0.8115 (tt0) REVERT: S 249 MET cc_start: 0.7589 (mmm) cc_final: 0.7255 (mmm) REVERT: U 78 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7206 (tpp-160) REVERT: U 80 GLN cc_start: 0.8588 (tp40) cc_final: 0.7946 (tt0) REVERT: U 138 LEU cc_start: 0.8250 (mp) cc_final: 0.7903 (mp) REVERT: U 151 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7339 (ptp-170) outliers start: 52 outliers final: 45 residues processed: 422 average time/residue: 0.2113 time to fit residues: 136.4496 Evaluate side-chains 430 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 383 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 275 HIS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 182 optimal weight: 0.8980 chunk 382 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 372 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS C 117 HIS G 275 HIS I 117 HIS ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142487 restraints weight = 42625.189| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.29 r_work: 0.3437 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32098 Z= 0.123 Angle : 0.613 14.827 43637 Z= 0.281 Chirality : 0.045 0.373 5148 Planarity : 0.005 0.149 5291 Dihedral : 13.023 179.554 5412 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.62 % Allowed : 16.11 % Favored : 82.28 % 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: 1.83 (0.14), residues: 3817 helix: 1.95 (0.11), residues: 2541 sheet: -0.33 (0.35), residues: 165 loop : -0.20 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG S 78 TYR 0.016 0.001 TYR M 23 PHE 0.033 0.002 PHE C 348 TRP 0.004 0.000 TRP Q 261 HIS 0.011 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (32087) covalent geometry : angle 0.61349 / 0.28 (43637) hydrogen bonds : bond 0.03769 / 2.50 ( 1826) hydrogen bonds : angle 4.10180 / 2.84 ( 5379) Misc. bond : bond 0.00253 / 0.14 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 401 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8767 (tp40) cc_final: 0.8075 (tt0) REVERT: A 84 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7650 (ttp-110) REVERT: A 200 ARG cc_start: 0.7245 (ptp90) cc_final: 0.7004 (mtm-85) REVERT: A 249 MET cc_start: 0.7683 (tpp) cc_final: 0.7457 (mmm) REVERT: A 339 ARG cc_start: 0.7159 (tpp-160) cc_final: 0.6880 (mmt-90) REVERT: C 80 GLN cc_start: 0.8871 (tp40) cc_final: 0.8195 (tt0) REVERT: C 117 HIS cc_start: 0.7815 (t-90) cc_final: 0.7488 (t70) REVERT: C 249 MET cc_start: 0.7632 (mmm) cc_final: 0.7272 (mmm) REVERT: E 80 GLN cc_start: 0.8724 (tp40) cc_final: 0.8082 (tt0) REVERT: E 339 ARG cc_start: 0.7228 (tpp-160) cc_final: 0.6948 (mmt-90) REVERT: G 80 GLN cc_start: 0.8811 (tp40) cc_final: 0.8195 (tt0) REVERT: G 138 LEU cc_start: 0.8421 (mp) cc_final: 0.8065 (mp) REVERT: G 200 ARG cc_start: 0.7282 (ptp90) cc_final: 0.6954 (mtm-85) REVERT: I 80 GLN cc_start: 0.8688 (tp40) cc_final: 0.8154 (tt0) REVERT: I 138 LEU cc_start: 0.8216 (mp) cc_final: 0.7969 (mp) REVERT: I 151 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7168 (ptp-170) REVERT: I 249 MET cc_start: 0.7579 (mmm) cc_final: 0.7247 (mmm) REVERT: K 51 ILE cc_start: 0.7635 (mt) cc_final: 0.7400 (mt) REVERT: K 80 GLN cc_start: 0.8860 (tp40) cc_final: 0.8183 (tt0) REVERT: K 113 MET cc_start: 0.3737 (mtp) cc_final: 0.3342 (mtm) REVERT: K 138 LEU cc_start: 0.8466 (mp) cc_final: 0.8160 (mp) REVERT: K 339 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.7086 (mmt-90) REVERT: M 80 GLN cc_start: 0.8588 (tp40) cc_final: 0.8077 (tt0) REVERT: M 339 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.7141 (mmt-90) REVERT: O 80 GLN cc_start: 0.8675 (tp40) cc_final: 0.8060 (tt0) REVERT: O 249 MET cc_start: 0.7597 (mmm) cc_final: 0.7280 (mmm) REVERT: O 339 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.7012 (mmt-90) REVERT: Q 80 GLN cc_start: 0.8733 (tp40) cc_final: 0.8144 (tt0) REVERT: Q 138 LEU cc_start: 0.8514 (mp) cc_final: 0.8245 (mp) REVERT: S 80 GLN cc_start: 0.8815 (tp40) cc_final: 0.8163 (tt0) REVERT: S 249 MET cc_start: 0.7675 (mmm) cc_final: 0.7369 (mmm) REVERT: U 50 GLU cc_start: 0.7792 (tp30) cc_final: 0.7583 (tp30) REVERT: U 78 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7273 (tpp-160) REVERT: U 80 GLN cc_start: 0.8659 (tp40) cc_final: 0.8011 (tt0) REVERT: U 138 LEU cc_start: 0.8275 (mp) cc_final: 0.7932 (mp) REVERT: U 151 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7408 (ptp-170) REVERT: U 339 ARG cc_start: 0.7204 (tpp-160) cc_final: 0.6962 (mmt-90) outliers start: 53 outliers final: 46 residues processed: 427 average time/residue: 0.2082 time to fit residues: 135.1852 Evaluate side-chains 438 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 390 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 23 TYR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 275 HIS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 19 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 384 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 383 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS E 117 HIS G 275 HIS I 117 HIS ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141576 restraints weight = 42855.803| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.32 r_work: 0.3417 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32098 Z= 0.140 Angle : 0.630 16.533 43637 Z= 0.289 Chirality : 0.046 0.380 5148 Planarity : 0.005 0.141 5291 Dihedral : 13.024 179.833 5412 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.65 % Allowed : 16.23 % Favored : 82.12 % 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: 1.80 (0.14), residues: 3817 helix: 1.90 (0.11), residues: 2541 sheet: -0.31 (0.35), residues: 165 loop : -0.16 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 78 TYR 0.016 0.001 TYR M 23 PHE 0.033 0.003 PHE S 348 TRP 0.004 0.001 TRP A 261 HIS 0.008 0.001 HIS O 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (32087) covalent geometry : angle 0.63043 / 0.29 (43637) hydrogen bonds : bond 0.03872 / 2.58 ( 1826) hydrogen bonds : angle 4.14628 / 2.87 ( 5379) Misc. bond : bond 0.00253 / 0.14 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7129.42 seconds wall clock time: 123 minutes 31.94 seconds (7411.94 seconds total)