Starting phenix.real_space_refine on Sat Aug 8 12:50:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2026/8pdl_17613.cif" } resolution = 3.1 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= -0.001 sd= 0.042 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 70 5.49 5 S 110 5.16 5 C 17820 2.51 5 N 4950 2.21 5 O 5660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.03s 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: 28610 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, D, F, H, J, L, N, P, R, T Time building chain proxies: 3.39, per 1000 atoms: 0.12 Number of scatterers: 28610 At special positions: 0 Unit cell: (192.15, 183.75, 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 110 16.00 P 70 15.00 O 5660 8.00 N 4950 7.00 C 17820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6520 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 20 sheets defined 70.1% alpha, 2.3% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.716A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.872A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.715A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.870A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.698A 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: 3.631A 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: 4.716A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.949A 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: 3.698A 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: 3.630A 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: 4.716A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.715A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.870A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing sheet with id=1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.715A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.715A 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: 6.218A 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: 3.713A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 2.76 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: 9128 1.34 - 1.45: 4086 1.45 - 1.57: 15636 1.57 - 1.69: 130 1.69 - 1.80: 190 Bond restraints: 29170 Sorted by residual: bond pdb=" CB VAL A 325 " pdb=" CG1 VAL A 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" CB VAL K 325 " pdb=" CG1 VAL K 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" CB VAL G 325 " pdb=" CG1 VAL G 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL Q 325 " pdb=" CG1 VAL Q 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 ... (remaining 29165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 35283 1.22 - 2.43: 3504 2.43 - 3.65: 549 3.65 - 4.87: 244 4.87 - 6.09: 90 Bond angle restraints: 39670 Sorted by residual: angle pdb=" CA PRO C 319 " pdb=" N PRO C 319 " pdb=" CD PRO C 319 " ideal model delta sigma weight residual 112.00 106.36 5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" CA PRO M 319 " pdb=" N PRO M 319 " pdb=" CD PRO M 319 " ideal model delta sigma weight residual 112.00 106.36 5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" CA PRO Q 319 " pdb=" N PRO Q 319 " pdb=" CD PRO Q 319 " ideal model delta sigma weight residual 112.00 106.38 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" CA PRO K 319 " pdb=" N PRO K 319 " pdb=" CD PRO K 319 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA PRO A 319 " pdb=" N PRO A 319 " pdb=" CD PRO A 319 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 ... (remaining 39665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 15485 16.10 - 32.19: 1835 32.19 - 48.29: 340 48.29 - 64.39: 160 64.39 - 80.48: 140 Dihedral angle restraints: 17960 sinusoidal: 7800 harmonic: 10160 Sorted by residual: 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 -36.59 72.94 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' C T 74 " pdb=" C3' C T 74 " pdb=" C2' C T 74 " pdb=" C1' C T 74 " ideal model delta sinusoidal sigma weight residual 36.35 -36.56 72.90 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' C J 74 " pdb=" C3' C J 74 " pdb=" C2' C J 74 " pdb=" C1' C J 74 " ideal model delta sinusoidal sigma weight residual 36.34 -36.56 72.90 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 17957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3615 0.063 - 0.127: 817 0.127 - 0.190: 153 0.190 - 0.254: 65 0.254 - 0.317: 30 Chirality restraints: 4680 Sorted by residual: chirality pdb=" P C N 71 " pdb=" OP1 C N 71 " pdb=" OP2 C N 71 " pdb=" O5' C N 71 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" P C D 71 " pdb=" OP1 C D 71 " pdb=" OP2 C D 71 " pdb=" O5' C D 71 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" P C R 71 " pdb=" OP1 C R 71 " pdb=" OP2 C R 71 " pdb=" O5' C R 71 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 4677 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS I 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO I 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO I 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 319 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS S 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO S 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO S 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 319 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS K 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO K 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO K 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO K 319 " -0.070 5.00e-02 4.00e+02 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.72: 70 1.72 - 2.51: 280 2.51 - 3.31: 35121 3.31 - 4.10: 72945 4.10 - 4.90: 137796 Warning: very small nonbonded interaction distances. Nonbonded interactions: 246212 Sorted by model distance: nonbonded pdb=" P C B 71 " pdb=" O3' C T 77 " model vdw 0.922 3.400 nonbonded pdb=" O3' C J 77 " pdb=" P C L 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C H 77 " pdb=" P C J 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C R 77 " pdb=" P C T 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C B 77 " pdb=" P C D 71 " model vdw 0.922 3.400 ... (remaining 246207 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: 0.10 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' } 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' } 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.560 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.009 0.062 29170 Z= 0.356 Angle : 0.859 6.086 39670 Z= 0.466 Chirality : 0.064 0.317 4680 Planarity : 0.009 0.132 4810 Dihedral : 16.532 80.482 11440 Min Nonbonded Distance : 0.922 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.63 (0.14), residues: 3470 helix: 0.97 (0.11), residues: 2240 sheet: -1.09 (0.35), residues: 150 loop : -0.33 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 208 TYR 0.036 0.003 TYR M 198 PHE 0.017 0.004 PHE M 244 TRP 0.023 0.003 TRP E 261 HIS 0.008 0.002 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.36 (29170) covalent geometry : angle 0.85930 / 0.47 (39670) hydrogen bonds : bond 0.12359 / 8.41 ( 1680) hydrogen bonds : angle 6.22245 / 4.40 ( 4950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.007 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: G 13 TYR cc_start: 0.9080 (m-10) cc_final: 0.8865 (m-10) REVERT: I 208 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7726 (tpt170) REVERT: Q 13 TYR cc_start: 0.9080 (m-10) cc_final: 0.8866 (m-10) REVERT: S 208 ARG cc_start: 0.7931 (tpt90) cc_final: 0.7719 (tpt170) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1769 time to fit residues: 91.7829 Evaluate side-chains 264 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN C 306 GLN E 306 GLN G 306 GLN I 306 GLN K 306 GLN M 306 GLN O 306 GLN Q 306 GLN S 306 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.199854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.170536 restraints weight = 33596.502| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.50 r_work: 0.3606 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29170 Z= 0.149 Angle : 0.690 9.530 39670 Z= 0.317 Chirality : 0.054 0.519 4680 Planarity : 0.005 0.072 4810 Dihedral : 12.635 73.674 4920 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.07 % Allowed : 5.64 % Favored : 93.29 % 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: 1.23 (0.15), residues: 3470 helix: 1.45 (0.11), residues: 2300 sheet: -1.52 (0.28), residues: 190 loop : -0.05 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 27 TYR 0.019 0.002 TYR C 354 PHE 0.009 0.002 PHE I 224 TRP 0.005 0.001 TRP A 261 HIS 0.004 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (29170) covalent geometry : angle 0.69016 / 0.32 (39670) hydrogen bonds : bond 0.04542 / 3.07 ( 1680) hydrogen bonds : angle 4.49783 / 3.15 ( 4950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 0.672 Fit side-chains REVERT: A 190 VAL cc_start: 0.8369 (t) cc_final: 0.8021 (t) REVERT: A 337 MET cc_start: 0.7430 (tpp) cc_final: 0.7121 (tmm) REVERT: C 85 ASN cc_start: 0.7686 (m110) cc_final: 0.7365 (m-40) REVERT: E 338 TYR cc_start: 0.7616 (t80) cc_final: 0.7383 (t80) REVERT: E 341 ARG cc_start: 0.6142 (mpt-90) cc_final: 0.5917 (mpt90) REVERT: G 338 TYR cc_start: 0.7490 (t80) cc_final: 0.7273 (t80) REVERT: I 26 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8383 (mtmm) REVERT: I 46 LEU cc_start: 0.8087 (tp) cc_final: 0.7868 (tp) REVERT: I 337 MET cc_start: 0.7508 (tpp) cc_final: 0.7114 (tmm) REVERT: K 190 VAL cc_start: 0.8364 (t) cc_final: 0.8011 (t) REVERT: K 337 MET cc_start: 0.7394 (tpp) cc_final: 0.7118 (tmm) REVERT: M 85 ASN cc_start: 0.7693 (m110) cc_final: 0.7372 (m-40) REVERT: O 338 TYR cc_start: 0.7634 (t80) cc_final: 0.7403 (t80) REVERT: O 341 ARG cc_start: 0.6103 (mpt-90) cc_final: 0.5882 (mpt90) REVERT: Q 338 TYR cc_start: 0.7474 (t80) cc_final: 0.7261 (t80) REVERT: S 26 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8381 (mtmm) REVERT: S 46 LEU cc_start: 0.8071 (tp) cc_final: 0.7850 (tp) REVERT: S 216 GLN cc_start: 0.7979 (mt0) cc_final: 0.7759 (mt0) REVERT: S 337 MET cc_start: 0.7517 (tpp) cc_final: 0.7107 (tmm) outliers start: 32 outliers final: 20 residues processed: 337 average time/residue: 0.1516 time to fit residues: 83.7929 Evaluate side-chains 272 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 218 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 320 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN I 85 ASN K 85 ASN S 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165688 restraints weight = 33756.971| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.63 r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29170 Z= 0.222 Angle : 0.652 7.638 39670 Z= 0.314 Chirality : 0.050 0.348 4680 Planarity : 0.005 0.058 4810 Dihedral : 12.751 103.593 4920 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.81 % Allowed : 8.02 % Favored : 90.17 % 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: 0.86 (0.14), residues: 3470 helix: 1.16 (0.11), residues: 2300 sheet: -1.61 (0.27), residues: 190 loop : -0.19 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 27 TYR 0.016 0.002 TYR M 354 PHE 0.012 0.002 PHE C 169 TRP 0.006 0.001 TRP A 261 HIS 0.005 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (29170) covalent geometry : angle 0.65191 / 0.31 (39670) hydrogen bonds : bond 0.04954 / 3.35 ( 1680) hydrogen bonds : angle 4.59283 / 3.22 ( 4950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 0.918 Fit side-chains REVERT: A 85 ASN cc_start: 0.8191 (m110) cc_final: 0.7975 (m110) REVERT: A 113 MET cc_start: 0.4772 (mmm) cc_final: 0.4498 (mmt) REVERT: A 337 MET cc_start: 0.7688 (tpp) cc_final: 0.7295 (tmm) REVERT: C 272 MET cc_start: 0.6863 (mmm) cc_final: 0.6630 (mmp) REVERT: C 337 MET cc_start: 0.7575 (tpp) cc_final: 0.7241 (tmm) REVERT: E 80 GLN cc_start: 0.8758 (tp40) cc_final: 0.8511 (tp40) REVERT: E 181 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: E 337 MET cc_start: 0.7778 (tpp) cc_final: 0.7464 (tmm) REVERT: E 341 ARG cc_start: 0.6454 (mpt-90) cc_final: 0.6193 (mpt90) REVERT: G 337 MET cc_start: 0.7718 (tpp) cc_final: 0.7091 (tmm) REVERT: I 46 LEU cc_start: 0.8147 (tp) cc_final: 0.7931 (tp) REVERT: I 337 MET cc_start: 0.7710 (tpp) cc_final: 0.7289 (tmm) REVERT: K 85 ASN cc_start: 0.8181 (m110) cc_final: 0.7966 (m110) REVERT: K 113 MET cc_start: 0.4789 (mmm) cc_final: 0.4526 (mmt) REVERT: K 337 MET cc_start: 0.7700 (tpp) cc_final: 0.7336 (tmm) REVERT: M 272 MET cc_start: 0.6878 (mmm) cc_final: 0.6650 (mmp) REVERT: M 337 MET cc_start: 0.7733 (tpp) cc_final: 0.7293 (tmm) REVERT: O 80 GLN cc_start: 0.8752 (tp40) cc_final: 0.8504 (tp40) REVERT: O 181 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: O 337 MET cc_start: 0.7812 (tpp) cc_final: 0.7471 (tmm) REVERT: O 341 ARG cc_start: 0.6433 (mpt-90) cc_final: 0.6176 (mpt90) REVERT: Q 337 MET cc_start: 0.7749 (tpp) cc_final: 0.7108 (tmm) REVERT: S 46 LEU cc_start: 0.8116 (tp) cc_final: 0.7897 (tp) REVERT: S 337 MET cc_start: 0.7720 (tpp) cc_final: 0.7285 (tmm) outliers start: 54 outliers final: 26 residues processed: 311 average time/residue: 0.1679 time to fit residues: 84.4948 Evaluate side-chains 273 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 181 GLU Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 166 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 299 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 ASN E 279 GLN O 85 ASN O 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.195300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168215 restraints weight = 33532.479| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.59 r_work: 0.3548 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29170 Z= 0.149 Angle : 0.582 7.433 39670 Z= 0.275 Chirality : 0.047 0.337 4680 Planarity : 0.004 0.051 4810 Dihedral : 12.972 113.994 4920 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.78 % Allowed : 9.63 % Favored : 88.59 % 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: 0.65 (0.14), residues: 3470 helix: 1.09 (0.11), residues: 2400 sheet: -1.61 (0.29), residues: 190 loop : -0.74 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 27 TYR 0.016 0.002 TYR C 354 PHE 0.010 0.002 PHE C 169 TRP 0.003 0.001 TRP E 123 HIS 0.004 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (29170) covalent geometry : angle 0.58156 / 0.27 (39670) hydrogen bonds : bond 0.04205 / 2.84 ( 1680) hydrogen bonds : angle 4.34455 / 3.04 ( 4950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7974 (tp) cc_final: 0.7659 (tt) REVERT: A 113 MET cc_start: 0.4693 (mmm) cc_final: 0.4424 (mmt) REVERT: A 337 MET cc_start: 0.7656 (tpp) cc_final: 0.7296 (tmm) REVERT: C 85 ASN cc_start: 0.7955 (m110) cc_final: 0.7539 (m110) REVERT: C 337 MET cc_start: 0.7417 (tpp) cc_final: 0.7017 (tmm) REVERT: E 94 LEU cc_start: 0.7853 (tp) cc_final: 0.7408 (tt) REVERT: E 113 MET cc_start: 0.4905 (mmm) cc_final: 0.4689 (mmt) REVERT: E 337 MET cc_start: 0.7681 (tpp) cc_final: 0.7199 (tmm) REVERT: E 341 ARG cc_start: 0.6534 (mpt-90) cc_final: 0.6325 (mpt90) REVERT: G 337 MET cc_start: 0.7767 (tpp) cc_final: 0.7152 (tmm) REVERT: I 337 MET cc_start: 0.7722 (tpp) cc_final: 0.7236 (tmm) REVERT: K 94 LEU cc_start: 0.7979 (tp) cc_final: 0.7665 (tt) REVERT: K 113 MET cc_start: 0.4698 (mmm) cc_final: 0.4437 (mmt) REVERT: K 337 MET cc_start: 0.7708 (tpp) cc_final: 0.7347 (tmm) REVERT: M 85 ASN cc_start: 0.7927 (m110) cc_final: 0.7511 (m110) REVERT: M 337 MET cc_start: 0.7564 (tpp) cc_final: 0.7063 (tmm) REVERT: O 94 LEU cc_start: 0.7846 (tp) cc_final: 0.7404 (tt) REVERT: O 113 MET cc_start: 0.4782 (mmm) cc_final: 0.4568 (mmt) REVERT: O 337 MET cc_start: 0.7684 (tpp) cc_final: 0.7222 (tmm) REVERT: O 341 ARG cc_start: 0.6541 (mpt-90) cc_final: 0.6337 (mpt90) REVERT: Q 272 MET cc_start: 0.7090 (mmm) cc_final: 0.6827 (mmp) REVERT: Q 337 MET cc_start: 0.7746 (tpp) cc_final: 0.7121 (tmm) REVERT: S 337 MET cc_start: 0.7672 (tpp) cc_final: 0.7228 (tmm) outliers start: 53 outliers final: 28 residues processed: 327 average time/residue: 0.1531 time to fit residues: 83.2015 Evaluate side-chains 283 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 34 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 275 HIS C 275 HIS E 85 ASN E 275 HIS G 41 GLN G 275 HIS G 279 GLN K 85 ASN K 275 HIS M 275 HIS O 85 ASN O 275 HIS Q 41 GLN ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 279 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.193398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166524 restraints weight = 33452.795| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.58 r_work: 0.3526 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29170 Z= 0.181 Angle : 0.598 7.273 39670 Z= 0.286 Chirality : 0.048 0.347 4680 Planarity : 0.005 0.049 4810 Dihedral : 13.116 130.200 4920 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.81 % Allowed : 10.07 % Favored : 88.12 % 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: 0.94 (0.15), residues: 3470 helix: 1.25 (0.11), residues: 2320 sheet: -1.65 (0.30), residues: 190 loop : -0.23 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 221 TYR 0.016 0.002 TYR Q 354 PHE 0.012 0.002 PHE M 169 TRP 0.003 0.001 TRP A 261 HIS 0.004 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (29170) covalent geometry : angle 0.59833 / 0.29 (39670) hydrogen bonds : bond 0.04408 / 2.98 ( 1680) hydrogen bonds : angle 4.38104 / 3.07 ( 4950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4607 (mmm) cc_final: 0.4363 (mmt) REVERT: A 337 MET cc_start: 0.7791 (tpp) cc_final: 0.7355 (tmm) REVERT: C 181 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: C 337 MET cc_start: 0.7557 (tpp) cc_final: 0.7078 (tmm) REVERT: E 113 MET cc_start: 0.4935 (mmm) cc_final: 0.4726 (mmt) REVERT: E 337 MET cc_start: 0.7692 (tpp) cc_final: 0.7194 (tmm) REVERT: G 181 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: G 337 MET cc_start: 0.7797 (tpp) cc_final: 0.7201 (tmm) REVERT: I 94 LEU cc_start: 0.7893 (tp) cc_final: 0.7338 (tt) REVERT: I 337 MET cc_start: 0.7747 (tpp) cc_final: 0.7259 (tmm) REVERT: K 113 MET cc_start: 0.4622 (mmm) cc_final: 0.4384 (mmt) REVERT: K 337 MET cc_start: 0.7829 (tpp) cc_final: 0.7397 (tmm) REVERT: M 181 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: M 337 MET cc_start: 0.7697 (tpp) cc_final: 0.7137 (tmm) REVERT: O 113 MET cc_start: 0.4921 (mmm) cc_final: 0.4707 (mmt) REVERT: O 337 MET cc_start: 0.7703 (tpp) cc_final: 0.7191 (tmm) REVERT: Q 181 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: Q 272 MET cc_start: 0.7014 (mmm) cc_final: 0.6811 (mmp) REVERT: Q 337 MET cc_start: 0.7726 (tpp) cc_final: 0.7142 (tmm) REVERT: S 94 LEU cc_start: 0.7890 (tp) cc_final: 0.7346 (tt) REVERT: S 337 MET cc_start: 0.7730 (tpp) cc_final: 0.7262 (tmm) outliers start: 54 outliers final: 28 residues processed: 332 average time/residue: 0.1755 time to fit residues: 95.8807 Evaluate side-chains 300 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 181 GLU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 338 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 335 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN I 279 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 275 HIS S 150 GLN S 279 GLN ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.194707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165681 restraints weight = 33479.349| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.60 r_work: 0.3554 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29170 Z= 0.146 Angle : 0.572 8.108 39670 Z= 0.270 Chirality : 0.047 0.310 4680 Planarity : 0.004 0.046 4810 Dihedral : 13.085 133.382 4920 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.41 % Allowed : 11.38 % Favored : 87.21 % 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: 0.89 (0.15), residues: 3470 helix: 1.27 (0.11), residues: 2380 sheet: -1.68 (0.30), residues: 190 loop : -0.56 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 27 TYR 0.017 0.002 TYR Q 354 PHE 0.010 0.002 PHE C 169 TRP 0.003 0.001 TRP G 123 HIS 0.003 0.001 HIS O 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (29170) covalent geometry : angle 0.57194 / 0.27 (39670) hydrogen bonds : bond 0.04092 / 2.77 ( 1680) hydrogen bonds : angle 4.24107 / 2.97 ( 4950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4775 (mmm) cc_final: 0.4536 (mmt) REVERT: A 337 MET cc_start: 0.7739 (tpp) cc_final: 0.7332 (tmm) REVERT: C 177 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: C 181 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: C 337 MET cc_start: 0.7543 (tpp) cc_final: 0.7097 (tmm) REVERT: E 81 GLN cc_start: 0.8574 (tt0) cc_final: 0.8236 (tt0) REVERT: E 113 MET cc_start: 0.4695 (mmm) cc_final: 0.4494 (mmt) REVERT: E 337 MET cc_start: 0.7653 (tpp) cc_final: 0.7188 (tmm) REVERT: G 337 MET cc_start: 0.7754 (tpp) cc_final: 0.7193 (tmm) REVERT: I 94 LEU cc_start: 0.7888 (tp) cc_final: 0.7326 (tt) REVERT: I 258 MET cc_start: 0.8344 (mmm) cc_final: 0.7386 (mmm) REVERT: I 337 MET cc_start: 0.7713 (tpp) cc_final: 0.7244 (tmm) REVERT: K 113 MET cc_start: 0.4786 (mmm) cc_final: 0.4561 (mmt) REVERT: K 337 MET cc_start: 0.7700 (tpp) cc_final: 0.7303 (tmm) REVERT: M 177 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: M 181 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: M 337 MET cc_start: 0.7675 (tpp) cc_final: 0.7143 (tmm) REVERT: O 81 GLN cc_start: 0.8561 (tt0) cc_final: 0.8241 (tt0) REVERT: O 113 MET cc_start: 0.4662 (mmm) cc_final: 0.4458 (mmt) REVERT: O 337 MET cc_start: 0.7653 (tpp) cc_final: 0.7188 (tmm) REVERT: Q 337 MET cc_start: 0.7769 (tpp) cc_final: 0.7174 (tmm) REVERT: S 94 LEU cc_start: 0.7887 (tp) cc_final: 0.7336 (tt) REVERT: S 258 MET cc_start: 0.8353 (mmm) cc_final: 0.7414 (mmm) REVERT: S 337 MET cc_start: 0.7700 (tpp) cc_final: 0.7238 (tmm) outliers start: 42 outliers final: 22 residues processed: 319 average time/residue: 0.1677 time to fit residues: 89.1237 Evaluate side-chains 292 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 181 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 268 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN Q 85 ASN ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.192052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163783 restraints weight = 33395.836| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.64 r_work: 0.3508 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29170 Z= 0.203 Angle : 0.618 9.042 39670 Z= 0.295 Chirality : 0.049 0.338 4680 Planarity : 0.005 0.047 4810 Dihedral : 13.135 135.302 4920 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.81 % Allowed : 12.45 % Favored : 85.74 % 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: 0.95 (0.15), residues: 3470 helix: 1.29 (0.11), residues: 2320 sheet: -1.73 (0.31), residues: 190 loop : -0.32 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 27 TYR 0.015 0.002 TYR I 354 PHE 0.014 0.002 PHE O 169 TRP 0.004 0.001 TRP M 261 HIS 0.004 0.001 HIS O 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (29170) covalent geometry : angle 0.61816 / 0.30 (39670) hydrogen bonds : bond 0.04510 / 3.05 ( 1680) hydrogen bonds : angle 4.40634 / 3.08 ( 4950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8163 (tp) cc_final: 0.7952 (tp) REVERT: A 113 MET cc_start: 0.4733 (mmm) cc_final: 0.4448 (mmt) REVERT: A 337 MET cc_start: 0.7725 (tpp) cc_final: 0.7327 (tmm) REVERT: C 177 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: C 181 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: C 258 MET cc_start: 0.8478 (mmm) cc_final: 0.7947 (mmm) REVERT: C 337 MET cc_start: 0.7778 (tpp) cc_final: 0.7180 (tmm) REVERT: E 113 MET cc_start: 0.5067 (mmm) cc_final: 0.4816 (mmt) REVERT: E 337 MET cc_start: 0.7745 (tpp) cc_final: 0.7215 (tmm) REVERT: G 337 MET cc_start: 0.7822 (tpp) cc_final: 0.7232 (tmm) REVERT: I 337 MET cc_start: 0.7827 (tpp) cc_final: 0.7289 (tmm) REVERT: K 46 LEU cc_start: 0.8179 (tp) cc_final: 0.7966 (tp) REVERT: K 113 MET cc_start: 0.4731 (mmm) cc_final: 0.4451 (mmt) REVERT: K 337 MET cc_start: 0.7788 (tpp) cc_final: 0.7353 (tmm) REVERT: M 177 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: M 181 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: M 258 MET cc_start: 0.8452 (mmm) cc_final: 0.7910 (mmm) REVERT: M 337 MET cc_start: 0.7865 (tpp) cc_final: 0.7225 (tmm) REVERT: O 113 MET cc_start: 0.5072 (mmm) cc_final: 0.4816 (mmt) REVERT: O 337 MET cc_start: 0.7782 (tpp) cc_final: 0.7211 (tmm) REVERT: Q 337 MET cc_start: 0.7764 (tpp) cc_final: 0.7203 (tmm) REVERT: S 337 MET cc_start: 0.7790 (tpp) cc_final: 0.7275 (tmm) outliers start: 54 outliers final: 30 residues processed: 328 average time/residue: 0.1526 time to fit residues: 82.1065 Evaluate side-chains 298 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 181 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 286 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 144 optimal weight: 0.6980 chunk 258 optimal weight: 0.2980 chunk 245 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 304 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 GLN ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.166753 restraints weight = 33408.751| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.59 r_work: 0.3563 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29170 Z= 0.137 Angle : 0.574 8.082 39670 Z= 0.269 Chirality : 0.047 0.300 4680 Planarity : 0.004 0.045 4810 Dihedral : 13.077 132.971 4920 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.61 % Allowed : 12.92 % Favored : 85.47 % 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: 1.02 (0.15), residues: 3470 helix: 1.40 (0.11), residues: 2380 sheet: -1.62 (0.32), residues: 190 loop : -0.61 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 27 TYR 0.019 0.002 TYR M 354 PHE 0.010 0.002 PHE M 169 TRP 0.003 0.001 TRP G 123 HIS 0.003 0.001 HIS M 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (29170) covalent geometry : angle 0.57410 / 0.27 (39670) hydrogen bonds : bond 0.04008 / 2.72 ( 1680) hydrogen bonds : angle 4.20527 / 2.94 ( 4950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4673 (mmm) cc_final: 0.4392 (mmt) REVERT: A 177 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 337 MET cc_start: 0.7645 (tpp) cc_final: 0.7253 (tmm) REVERT: C 177 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: C 258 MET cc_start: 0.8597 (mmm) cc_final: 0.8068 (mmm) REVERT: C 337 MET cc_start: 0.7680 (tpp) cc_final: 0.7160 (tmm) REVERT: E 80 GLN cc_start: 0.8612 (tp40) cc_final: 0.8006 (tp40) REVERT: E 81 GLN cc_start: 0.8502 (tt0) cc_final: 0.8151 (tt0) REVERT: E 113 MET cc_start: 0.4899 (mmm) cc_final: 0.4646 (mmt) REVERT: E 337 MET cc_start: 0.7652 (tpp) cc_final: 0.7148 (tmm) REVERT: G 337 MET cc_start: 0.7722 (tpp) cc_final: 0.7198 (tmm) REVERT: I 337 MET cc_start: 0.7724 (tpp) cc_final: 0.7250 (tmm) REVERT: K 46 LEU cc_start: 0.8143 (tp) cc_final: 0.7941 (tp) REVERT: K 113 MET cc_start: 0.4672 (mmm) cc_final: 0.4402 (mmt) REVERT: K 177 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: K 337 MET cc_start: 0.7700 (tpp) cc_final: 0.7286 (tmm) REVERT: M 177 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: M 258 MET cc_start: 0.8585 (mmm) cc_final: 0.8060 (mmm) REVERT: M 337 MET cc_start: 0.7776 (tpp) cc_final: 0.7199 (tmm) REVERT: O 80 GLN cc_start: 0.8600 (tp40) cc_final: 0.7996 (tp40) REVERT: O 81 GLN cc_start: 0.8496 (tt0) cc_final: 0.8139 (tt0) REVERT: O 113 MET cc_start: 0.4974 (mmm) cc_final: 0.4723 (mmt) REVERT: O 337 MET cc_start: 0.7721 (tpp) cc_final: 0.7148 (tmm) REVERT: Q 337 MET cc_start: 0.7773 (tpp) cc_final: 0.7219 (tmm) REVERT: S 337 MET cc_start: 0.7706 (tpp) cc_final: 0.7236 (tmm) outliers start: 48 outliers final: 26 residues processed: 334 average time/residue: 0.1412 time to fit residues: 78.8522 Evaluate side-chains 310 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 177 GLU Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 198 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 321 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 190 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN I 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.168036 restraints weight = 33262.110| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.58 r_work: 0.3559 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29170 Z= 0.140 Angle : 0.578 7.852 39670 Z= 0.272 Chirality : 0.046 0.285 4680 Planarity : 0.004 0.045 4810 Dihedral : 13.057 133.322 4920 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.97 % Allowed : 13.93 % Favored : 85.10 % 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: 1.06 (0.15), residues: 3470 helix: 1.43 (0.11), residues: 2380 sheet: -1.70 (0.31), residues: 190 loop : -0.58 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 27 TYR 0.020 0.002 TYR I 354 PHE 0.011 0.002 PHE M 169 TRP 0.004 0.001 TRP Q 123 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (29170) covalent geometry : angle 0.57754 / 0.27 (39670) hydrogen bonds : bond 0.03968 / 2.69 ( 1680) hydrogen bonds : angle 4.18605 / 2.93 ( 4950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4644 (mmm) cc_final: 0.4375 (mmt) REVERT: A 337 MET cc_start: 0.7711 (tpp) cc_final: 0.7270 (tmm) REVERT: C 55 LYS cc_start: 0.8271 (tttm) cc_final: 0.7944 (tppt) REVERT: C 258 MET cc_start: 0.8612 (mmm) cc_final: 0.8139 (mmm) REVERT: C 337 MET cc_start: 0.7703 (tpp) cc_final: 0.7158 (tmm) REVERT: E 80 GLN cc_start: 0.8630 (tp40) cc_final: 0.8026 (tp40) REVERT: E 81 GLN cc_start: 0.8511 (tt0) cc_final: 0.8145 (tt0) REVERT: E 113 MET cc_start: 0.4973 (mmm) cc_final: 0.4728 (mmt) REVERT: E 337 MET cc_start: 0.7644 (tpp) cc_final: 0.7079 (tmm) REVERT: G 80 GLN cc_start: 0.8506 (tp40) cc_final: 0.7914 (tp40) REVERT: G 337 MET cc_start: 0.7729 (tpp) cc_final: 0.7198 (tmm) REVERT: I 80 GLN cc_start: 0.8374 (tp40) cc_final: 0.8066 (tp40) REVERT: I 337 MET cc_start: 0.7722 (tpp) cc_final: 0.7249 (tmm) REVERT: K 113 MET cc_start: 0.4633 (mmm) cc_final: 0.4377 (mmt) REVERT: K 337 MET cc_start: 0.7697 (tpp) cc_final: 0.7290 (tmm) REVERT: M 55 LYS cc_start: 0.8294 (tttm) cc_final: 0.7944 (tppt) REVERT: M 258 MET cc_start: 0.8594 (mmm) cc_final: 0.8117 (mmm) REVERT: M 337 MET cc_start: 0.7753 (tpp) cc_final: 0.7182 (tmm) REVERT: M 354 TYR cc_start: 0.6859 (t80) cc_final: 0.6655 (t80) REVERT: O 80 GLN cc_start: 0.8623 (tp40) cc_final: 0.8020 (tp40) REVERT: O 81 GLN cc_start: 0.8506 (tt0) cc_final: 0.8135 (tt0) REVERT: O 113 MET cc_start: 0.4985 (mmm) cc_final: 0.4743 (mmt) REVERT: O 337 MET cc_start: 0.7696 (tpp) cc_final: 0.7081 (tmm) REVERT: Q 80 GLN cc_start: 0.8510 (tp40) cc_final: 0.7925 (tp40) REVERT: Q 337 MET cc_start: 0.7796 (tpp) cc_final: 0.7221 (tmm) REVERT: S 80 GLN cc_start: 0.8365 (tp40) cc_final: 0.8057 (tp40) REVERT: S 337 MET cc_start: 0.7677 (tpp) cc_final: 0.7232 (tmm) outliers start: 29 outliers final: 29 residues processed: 325 average time/residue: 0.1393 time to fit residues: 75.5720 Evaluate side-chains 305 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 330 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 199 optimal weight: 1.9990 chunk 328 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 GLN ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.198100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169477 restraints weight = 33181.531| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.60 r_work: 0.3584 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29170 Z= 0.123 Angle : 0.571 8.393 39670 Z= 0.266 Chirality : 0.046 0.267 4680 Planarity : 0.004 0.044 4810 Dihedral : 13.018 132.220 4920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.01 % Allowed : 13.96 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 3470 helix: 1.54 (0.11), residues: 2390 sheet: -1.66 (0.31), residues: 190 loop : -0.70 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 27 TYR 0.021 0.001 TYR C 354 PHE 0.010 0.001 PHE A 169 TRP 0.004 0.001 TRP S 123 HIS 0.003 0.001 HIS O 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (29170) covalent geometry : angle 0.57094 / 0.27 (39670) hydrogen bonds : bond 0.03769 / 2.56 ( 1680) hydrogen bonds : angle 4.09687 / 2.87 ( 4950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4452 (mmm) cc_final: 0.4179 (mmt) REVERT: A 337 MET cc_start: 0.7581 (tpp) cc_final: 0.7206 (tmm) REVERT: C 55 LYS cc_start: 0.8241 (tttm) cc_final: 0.7917 (tppt) REVERT: C 258 MET cc_start: 0.8571 (mmm) cc_final: 0.8126 (mmm) REVERT: C 337 MET cc_start: 0.7668 (tpp) cc_final: 0.7123 (tmm) REVERT: E 81 GLN cc_start: 0.8488 (tt0) cc_final: 0.8139 (tt0) REVERT: E 113 MET cc_start: 0.4791 (mmm) cc_final: 0.4581 (mmt) REVERT: E 337 MET cc_start: 0.7615 (tpp) cc_final: 0.7055 (tmm) REVERT: G 55 LYS cc_start: 0.8031 (tttm) cc_final: 0.7742 (tppt) REVERT: G 80 GLN cc_start: 0.8527 (tp40) cc_final: 0.8024 (tp40) REVERT: G 337 MET cc_start: 0.7763 (tpp) cc_final: 0.7203 (tmm) REVERT: I 80 GLN cc_start: 0.8340 (tp40) cc_final: 0.8037 (tp40) REVERT: I 337 MET cc_start: 0.7608 (tpp) cc_final: 0.7185 (tmm) REVERT: K 113 MET cc_start: 0.4468 (mmm) cc_final: 0.4202 (mmt) REVERT: K 337 MET cc_start: 0.7616 (tpp) cc_final: 0.7230 (tmm) REVERT: M 55 LYS cc_start: 0.8289 (tttm) cc_final: 0.7933 (tppt) REVERT: M 258 MET cc_start: 0.8542 (mmm) cc_final: 0.8083 (mmm) REVERT: M 337 MET cc_start: 0.7601 (tpp) cc_final: 0.7129 (tmm) REVERT: O 81 GLN cc_start: 0.8507 (tt0) cc_final: 0.8158 (tt0) REVERT: O 113 MET cc_start: 0.4793 (mmm) cc_final: 0.4577 (mmt) REVERT: O 337 MET cc_start: 0.7689 (tpp) cc_final: 0.7072 (tmm) REVERT: Q 55 LYS cc_start: 0.8133 (tttm) cc_final: 0.7826 (tppt) REVERT: Q 80 GLN cc_start: 0.8516 (tp40) cc_final: 0.8025 (tp40) REVERT: Q 85 ASN cc_start: 0.8394 (m-40) cc_final: 0.8193 (m110) REVERT: Q 337 MET cc_start: 0.7752 (tpp) cc_final: 0.7189 (tmm) REVERT: S 80 GLN cc_start: 0.8334 (tp40) cc_final: 0.8040 (tp40) REVERT: S 337 MET cc_start: 0.7666 (tpp) cc_final: 0.7209 (tmm) outliers start: 30 outliers final: 28 residues processed: 324 average time/residue: 0.1690 time to fit residues: 90.0389 Evaluate side-chains 297 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 305 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 114 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 296 optimal weight: 0.0670 chunk 279 optimal weight: 7.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166923 restraints weight = 33223.347| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.65 r_work: 0.3574 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29170 Z= 0.125 Angle : 0.571 8.192 39670 Z= 0.267 Chirality : 0.045 0.262 4680 Planarity : 0.004 0.043 4810 Dihedral : 13.005 132.656 4920 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.91 % Allowed : 14.60 % Favored : 84.50 % 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 (0.15), residues: 3470 helix: 1.58 (0.11), residues: 2390 sheet: -1.61 (0.31), residues: 190 loop : -0.70 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 27 TYR 0.021 0.001 TYR I 354 PHE 0.010 0.001 PHE C 169 TRP 0.003 0.001 TRP E 123 HIS 0.004 0.001 HIS Q 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (29170) covalent geometry : angle 0.57110 / 0.27 (39670) hydrogen bonds : bond 0.03796 / 2.57 ( 1680) hydrogen bonds : angle 4.08146 / 2.85 ( 4950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6386.87 seconds wall clock time: 110 minutes 34.45 seconds (6634.45 seconds total)