Starting phenix.real_space_refine on Mon Aug 25 13:18:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdl_17613/08_2025/8pdl_17613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdl_17613/08_2025/8pdl_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_2025/8pdl_17613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2025/8pdl_17613.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2025/8pdl_17613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdl_17613/08_2025/8pdl_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-2.0-5787/lib/python3.9/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: {'RNA': 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: 3.11, per 1000 atoms: 0.11 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: 2.01 Conformation dependent library (CDL) restraints added in 982.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.53 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: 3.66 Time building geometry restraints manager: 2.70 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: 35483 1.22 - 2.43: 3424 2.43 - 3.65: 479 3.65 - 4.87: 204 4.87 - 6.09: 80 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: 15595 16.10 - 32.19: 1785 32.19 - 48.29: 320 48.29 - 64.39: 130 64.39 - 80.48: 130 Dihedral angle restraints: 17960 sinusoidal: 7800 harmonic: 10160 Sorted by residual: dihedral pdb=" CA TYR M 59 " pdb=" C TYR M 59 " pdb=" N LYS M 60 " pdb=" CA LYS M 60 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR O 59 " pdb=" C TYR O 59 " pdb=" N LYS O 60 " pdb=" CA LYS O 60 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3064 0.046 - 0.091: 1138 0.091 - 0.137: 376 0.137 - 0.183: 72 0.183 - 0.229: 30 Chirality restraints: 4680 Sorted by residual: chirality pdb=" CB VAL G 35 " pdb=" CA VAL G 35 " pdb=" CG1 VAL G 35 " pdb=" CG2 VAL G 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL Q 35 " pdb=" CA VAL Q 35 " pdb=" CG1 VAL Q 35 " pdb=" CG2 VAL Q 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+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: 0.05 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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= 0.357 Angle : 0.831 6.086 39670 Z= 0.466 Chirality : 0.055 0.229 4680 Planarity : 0.009 0.132 4810 Dihedral : 15.938 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 aren 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 covalent geometry : bond 0.00850 (29170) covalent geometry : angle 0.83103 (39670) hydrogen bonds : bond 0.12359 ( 1680) hydrogen bonds : angle 6.22245 ( 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 : 1.185 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: 0.1617 time to fit residues: 83.5301 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 : 0.643 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.197702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.168373 restraints weight = 33639.474| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.64 r_work: 0.3581 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1452 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= 0.144 Angle : 0.545 9.641 39670 Z= 0.288 Chirality : 0.040 0.131 4680 Planarity : 0.005 0.073 4810 Dihedral : 11.960 74.167 4920 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.14 % Allowed : 5.54 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.15), residues: 3470 helix: 1.46 (0.11), residues: 2300 sheet: -1.51 (0.28), residues: 190 loop : -0.06 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 27 TYR 0.019 0.002 TYR G 354 PHE 0.009 0.002 PHE I 224 TRP 0.005 0.001 TRP A 261 HIS 0.003 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00322 (29170) covalent geometry : angle 0.54481 (39670) hydrogen bonds : bond 0.04515 ( 1680) hydrogen bonds : angle 4.51119 ( 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 341 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 0.791 Fit side-chains REVERT: A 337 MET cc_start: 0.7370 (tpp) cc_final: 0.7104 (tmm) REVERT: C 85 ASN cc_start: 0.7707 (m110) cc_final: 0.7389 (m-40) REVERT: C 338 TYR cc_start: 0.7545 (t80) cc_final: 0.7307 (t80) REVERT: E 338 TYR cc_start: 0.7608 (t80) cc_final: 0.7305 (t80) REVERT: G 338 TYR cc_start: 0.7503 (t80) cc_final: 0.7215 (t80) REVERT: I 26 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8374 (mtmm) REVERT: I 46 LEU cc_start: 0.8043 (tp) cc_final: 0.7833 (tp) REVERT: I 337 MET cc_start: 0.7555 (tpp) cc_final: 0.7151 (tmm) REVERT: I 338 TYR cc_start: 0.7566 (t80) cc_final: 0.7334 (t80) REVERT: K 190 VAL cc_start: 0.8432 (t) cc_final: 0.8056 (t) REVERT: K 337 MET cc_start: 0.7360 (tpp) cc_final: 0.7114 (tmm) REVERT: M 85 ASN cc_start: 0.7699 (m110) cc_final: 0.7378 (m-40) REVERT: M 338 TYR cc_start: 0.7555 (t80) cc_final: 0.7325 (t80) REVERT: O 338 TYR cc_start: 0.7616 (t80) cc_final: 0.7314 (t80) REVERT: Q 338 TYR cc_start: 0.7481 (t80) cc_final: 0.7207 (t80) REVERT: S 26 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8378 (mtmm) REVERT: S 46 LEU cc_start: 0.8032 (tp) cc_final: 0.7817 (tp) REVERT: S 216 GLN cc_start: 0.7970 (mt0) cc_final: 0.7753 (mt0) REVERT: S 337 MET cc_start: 0.7539 (tpp) cc_final: 0.7153 (tmm) REVERT: S 338 TYR cc_start: 0.7590 (t80) cc_final: 0.7344 (t80) outliers start: 34 outliers final: 20 residues processed: 329 average time/residue: 0.1600 time to fit residues: 87.2140 Evaluate side-chains 263 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 0.5980 chunk 320 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4128 r_free = 0.4128 target = 0.195697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164775 restraints weight = 33470.984| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.72 r_work: 0.3521 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29170 Z= 0.151 Angle : 0.519 7.312 39670 Z= 0.272 Chirality : 0.040 0.141 4680 Planarity : 0.005 0.057 4810 Dihedral : 11.885 74.149 4920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.78 % Allowed : 7.85 % Favored : 90.37 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 3470 helix: 1.20 (0.11), residues: 2400 sheet: -1.52 (0.28), residues: 190 loop : -0.62 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 27 TYR 0.020 0.002 TYR C 354 PHE 0.009 0.002 PHE C 169 TRP 0.005 0.001 TRP K 261 HIS 0.003 0.001 HIS O 7 Details of bonding type rmsd covalent geometry : bond 0.00348 (29170) covalent geometry : angle 0.51917 (39670) hydrogen bonds : bond 0.04362 ( 1680) hydrogen bonds : angle 4.35812 ( 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 330 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8208 (m110) cc_final: 0.7998 (m110) REVERT: A 113 MET cc_start: 0.4715 (mmm) cc_final: 0.4500 (mmt) REVERT: A 337 MET cc_start: 0.7413 (tpp) cc_final: 0.7169 (tmm) REVERT: A 341 ARG cc_start: 0.5918 (mpt-90) cc_final: 0.5649 (mpt90) REVERT: C 85 ASN cc_start: 0.7876 (m110) cc_final: 0.7507 (m-40) REVERT: C 181 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: C 272 MET cc_start: 0.6774 (mmm) cc_final: 0.6471 (mmp) REVERT: E 337 MET cc_start: 0.7586 (tpp) cc_final: 0.7298 (tmm) REVERT: G 337 MET cc_start: 0.7480 (tpp) cc_final: 0.6860 (tmm) REVERT: G 338 TYR cc_start: 0.7617 (t80) cc_final: 0.7245 (t80) REVERT: I 26 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8487 (mtmm) REVERT: I 337 MET cc_start: 0.7631 (tpp) cc_final: 0.7209 (tmm) REVERT: K 85 ASN cc_start: 0.8210 (m110) cc_final: 0.8001 (m110) REVERT: K 113 MET cc_start: 0.4699 (mmm) cc_final: 0.4487 (mmt) REVERT: K 337 MET cc_start: 0.7423 (tpp) cc_final: 0.7179 (tmm) REVERT: K 341 ARG cc_start: 0.5939 (mpt-90) cc_final: 0.5672 (mpt90) REVERT: M 85 ASN cc_start: 0.7880 (m110) cc_final: 0.7509 (m-40) REVERT: M 272 MET cc_start: 0.6792 (mmm) cc_final: 0.6491 (mmp) REVERT: M 337 MET cc_start: 0.7396 (tpp) cc_final: 0.7104 (tmm) REVERT: O 337 MET cc_start: 0.7537 (tpp) cc_final: 0.7298 (tmm) REVERT: Q 337 MET cc_start: 0.7446 (tpp) cc_final: 0.6843 (tmm) REVERT: Q 338 TYR cc_start: 0.7623 (t80) cc_final: 0.7250 (t80) REVERT: S 26 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8484 (mtmm) REVERT: S 337 MET cc_start: 0.7597 (tpp) cc_final: 0.7203 (tmm) outliers start: 53 outliers final: 23 residues processed: 322 average time/residue: 0.1595 time to fit residues: 83.5947 Evaluate side-chains 281 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain E residue 47 LEU 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 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 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: 4.9990 chunk 195 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 299 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN E 279 GLN O 41 GLN O 85 ASN O 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.197854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170114 restraints weight = 33160.040| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.60 r_work: 0.3548 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1974 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= 0.142 Angle : 0.496 7.171 39670 Z= 0.260 Chirality : 0.039 0.130 4680 Planarity : 0.004 0.049 4810 Dihedral : 11.658 74.130 4920 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.54 % Allowed : 9.43 % Favored : 89.03 % 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 aren not related in a simple way. whole: 0.97 (0.15), residues: 3470 helix: 1.28 (0.11), residues: 2380 sheet: -1.54 (0.29), residues: 190 loop : -0.39 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 27 TYR 0.018 0.002 TYR M 354 PHE 0.010 0.002 PHE A 224 TRP 0.003 0.001 TRP E 123 HIS 0.003 0.001 HIS E 7 Details of bonding type rmsd covalent geometry : bond 0.00327 (29170) covalent geometry : angle 0.49591 (39670) hydrogen bonds : bond 0.04087 ( 1680) hydrogen bonds : angle 4.26155 ( 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 321 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7960 (tp) cc_final: 0.7661 (tt) REVERT: A 337 MET cc_start: 0.7521 (tpp) cc_final: 0.7219 (tmm) REVERT: A 341 ARG cc_start: 0.6013 (mpt-90) cc_final: 0.5795 (mpt90) REVERT: C 85 ASN cc_start: 0.7855 (m110) cc_final: 0.7445 (m110) REVERT: E 23 TYR cc_start: 0.8266 (m-80) cc_final: 0.8047 (m-80) REVERT: E 337 MET cc_start: 0.7444 (tpp) cc_final: 0.7168 (tmm) REVERT: G 272 MET cc_start: 0.7003 (mmm) cc_final: 0.6764 (mmp) REVERT: G 337 MET cc_start: 0.7477 (tpp) cc_final: 0.6928 (tmm) REVERT: G 338 TYR cc_start: 0.7679 (t80) cc_final: 0.7256 (t80) REVERT: I 26 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8478 (mtmm) REVERT: I 337 MET cc_start: 0.7615 (tpp) cc_final: 0.7209 (tmm) REVERT: K 94 LEU cc_start: 0.7965 (tp) cc_final: 0.7667 (tt) REVERT: K 337 MET cc_start: 0.7482 (tpp) cc_final: 0.7218 (tmm) REVERT: K 341 ARG cc_start: 0.6028 (mpt-90) cc_final: 0.5808 (mpt90) REVERT: M 85 ASN cc_start: 0.7869 (m110) cc_final: 0.7463 (m110) REVERT: O 23 TYR cc_start: 0.8261 (m-80) cc_final: 0.8044 (m-80) REVERT: O 337 MET cc_start: 0.7469 (tpp) cc_final: 0.7210 (tmm) REVERT: Q 272 MET cc_start: 0.6976 (mmm) cc_final: 0.6737 (mmp) REVERT: Q 337 MET cc_start: 0.7452 (tpp) cc_final: 0.6913 (tmm) REVERT: Q 338 TYR cc_start: 0.7674 (t80) cc_final: 0.7251 (t80) REVERT: S 26 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8483 (mtmm) REVERT: S 337 MET cc_start: 0.7621 (tpp) cc_final: 0.7215 (tmm) outliers start: 46 outliers final: 22 residues processed: 315 average time/residue: 0.1530 time to fit residues: 78.9476 Evaluate side-chains 286 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 342 VAL Chi-restraints excluded: chain O residue 342 VAL 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: 5.9990 chunk 289 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS E 275 HIS ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN K 306 GLN M 275 HIS O 85 ASN O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.193545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166463 restraints weight = 33171.686| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.56 r_work: 0.3512 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29170 Z= 0.183 Angle : 0.536 7.211 39670 Z= 0.278 Chirality : 0.041 0.256 4680 Planarity : 0.005 0.049 4810 Dihedral : 11.729 74.367 4920 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.64 % Allowed : 10.37 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.15), residues: 3470 helix: 1.34 (0.11), residues: 2320 sheet: -1.61 (0.30), residues: 190 loop : -0.16 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 27 TYR 0.014 0.002 TYR A 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 covalent geometry : bond 0.00437 (29170) covalent geometry : angle 0.53575 (39670) hydrogen bonds : bond 0.04392 ( 1680) hydrogen bonds : angle 4.36275 ( 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 343 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.886 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: A 337 MET cc_start: 0.7620 (tpp) cc_final: 0.7296 (tmm) REVERT: A 341 ARG cc_start: 0.5999 (mpt-90) cc_final: 0.5764 (mpt90) REVERT: C 337 MET cc_start: 0.7616 (mmm) cc_final: 0.7060 (tmm) REVERT: E 94 LEU cc_start: 0.8000 (tp) cc_final: 0.7503 (tt) REVERT: E 337 MET cc_start: 0.7591 (tpp) cc_final: 0.7177 (tmm) REVERT: G 272 MET cc_start: 0.7113 (mmm) cc_final: 0.6888 (mmp) REVERT: G 337 MET cc_start: 0.7594 (tpp) cc_final: 0.7072 (tmm) REVERT: G 338 TYR cc_start: 0.7765 (t80) cc_final: 0.7529 (t80) REVERT: I 26 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8520 (mtmm) REVERT: I 94 LEU cc_start: 0.7900 (tp) cc_final: 0.7335 (tt) REVERT: I 279 GLN cc_start: 0.7515 (mm110) cc_final: 0.7211 (mm-40) REVERT: I 337 MET cc_start: 0.7666 (tpp) cc_final: 0.7252 (tmm) REVERT: I 339 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7326 (ttm170) REVERT: K 337 MET cc_start: 0.7590 (tpp) cc_final: 0.7285 (tmm) REVERT: K 341 ARG cc_start: 0.5995 (mpt-90) cc_final: 0.5765 (mpt90) REVERT: O 94 LEU cc_start: 0.8019 (tp) cc_final: 0.7521 (tt) REVERT: O 337 MET cc_start: 0.7637 (tpp) cc_final: 0.7197 (tmm) REVERT: Q 272 MET cc_start: 0.7084 (mmm) cc_final: 0.6861 (mmp) REVERT: Q 337 MET cc_start: 0.7584 (tpp) cc_final: 0.7072 (tmm) REVERT: Q 338 TYR cc_start: 0.7755 (t80) cc_final: 0.7516 (t80) REVERT: S 26 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8520 (mtmm) REVERT: S 94 LEU cc_start: 0.7889 (tp) cc_final: 0.7340 (tt) REVERT: S 279 GLN cc_start: 0.7523 (mm110) cc_final: 0.7225 (mm-40) REVERT: S 337 MET cc_start: 0.7663 (tpp) cc_final: 0.7247 (tmm) REVERT: S 339 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7324 (ttm170) outliers start: 49 outliers final: 24 residues processed: 335 average time/residue: 0.1691 time to fit residues: 92.0366 Evaluate side-chains 299 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 88 SER 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 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 47 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 338 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 153 optimal weight: 7.9990 chunk 335 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 242 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 279 GLN ** 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 = 0.4152 r_free = 0.4152 target = 0.198053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.170492 restraints weight = 33278.387| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.52 r_work: 0.3617 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2390 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= 0.116 Angle : 0.479 7.594 39670 Z= 0.251 Chirality : 0.038 0.156 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.711 73.963 4920 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.14 % Allowed : 11.48 % Favored : 87.38 % 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 aren not related in a simple way. whole: 1.08 (0.15), residues: 3470 helix: 1.44 (0.11), residues: 2390 sheet: -1.49 (0.32), residues: 190 loop : -0.62 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 27 TYR 0.017 0.001 TYR I 354 PHE 0.009 0.001 PHE C 169 TRP 0.003 0.001 TRP E 123 HIS 0.003 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00261 (29170) covalent geometry : angle 0.47899 (39670) hydrogen bonds : bond 0.03806 ( 1680) hydrogen bonds : angle 4.13970 ( 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 343 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.892 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: A 337 MET cc_start: 0.7518 (tpp) cc_final: 0.7239 (tmm) REVERT: C 55 LYS cc_start: 0.8189 (tttm) cc_final: 0.7918 (tppt) REVERT: C 85 ASN cc_start: 0.7962 (m110) cc_final: 0.7608 (m110) REVERT: C 337 MET cc_start: 0.7425 (mmm) cc_final: 0.6978 (tmm) REVERT: E 94 LEU cc_start: 0.7977 (tp) cc_final: 0.7481 (tt) REVERT: E 337 MET cc_start: 0.7443 (tpp) cc_final: 0.7126 (tmm) REVERT: G 337 MET cc_start: 0.7562 (tpp) cc_final: 0.7041 (tmm) REVERT: G 338 TYR cc_start: 0.7671 (t80) cc_final: 0.7065 (t80) REVERT: I 94 LEU cc_start: 0.7865 (tp) cc_final: 0.7276 (tt) REVERT: I 258 MET cc_start: 0.8279 (mmm) cc_final: 0.7461 (mmm) REVERT: I 337 MET cc_start: 0.7659 (tpp) cc_final: 0.7246 (tmm) REVERT: K 337 MET cc_start: 0.7587 (tpp) cc_final: 0.7267 (tmm) REVERT: M 55 LYS cc_start: 0.8216 (tttm) cc_final: 0.7940 (tppt) REVERT: M 85 ASN cc_start: 0.7969 (m110) cc_final: 0.7618 (m110) REVERT: M 337 MET cc_start: 0.7113 (tpp) cc_final: 0.6744 (tmm) REVERT: O 94 LEU cc_start: 0.7978 (tp) cc_final: 0.7508 (tt) REVERT: O 337 MET cc_start: 0.7466 (tpp) cc_final: 0.7117 (tmm) REVERT: Q 337 MET cc_start: 0.7550 (tpp) cc_final: 0.7029 (tmm) REVERT: Q 338 TYR cc_start: 0.7680 (t80) cc_final: 0.7070 (t80) REVERT: S 94 LEU cc_start: 0.7866 (tp) cc_final: 0.7293 (tt) REVERT: S 258 MET cc_start: 0.8282 (mmm) cc_final: 0.7444 (mmm) REVERT: S 337 MET cc_start: 0.7689 (tpp) cc_final: 0.7243 (tmm) outliers start: 34 outliers final: 18 residues processed: 335 average time/residue: 0.1790 time to fit residues: 97.6568 Evaluate side-chains 285 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 176 ILE 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 178 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 176 ILE 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 178 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: 0.7980 chunk 255 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 344 ASN G 275 HIS I 41 GLN I 150 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN O 344 ASN Q 275 HIS S 150 GLN ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.193718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164639 restraints weight = 33140.890| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.55 r_work: 0.3545 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29170 Z= 0.179 Angle : 0.534 8.787 39670 Z= 0.275 Chirality : 0.041 0.147 4680 Planarity : 0.004 0.047 4810 Dihedral : 11.703 74.333 4920 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.07 % Allowed : 13.05 % Favored : 85.87 % 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 aren not related in a simple way. whole: 1.17 (0.15), residues: 3470 helix: 1.48 (0.11), residues: 2330 sheet: -1.40 (0.32), residues: 190 loop : -0.38 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 27 TYR 0.015 0.002 TYR K 338 PHE 0.012 0.002 PHE O 169 TRP 0.003 0.001 TRP C 261 HIS 0.004 0.001 HIS E 7 Details of bonding type rmsd covalent geometry : bond 0.00425 (29170) covalent geometry : angle 0.53431 (39670) hydrogen bonds : bond 0.04299 ( 1680) hydrogen bonds : angle 4.30955 ( 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 324 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7622 (tpp) cc_final: 0.7318 (tmm) REVERT: C 177 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 258 MET cc_start: 0.8411 (mmm) cc_final: 0.7849 (mmm) REVERT: C 337 MET cc_start: 0.7701 (mmm) cc_final: 0.7122 (tmm) REVERT: E 337 MET cc_start: 0.7578 (tpp) cc_final: 0.7167 (tmm) REVERT: G 337 MET cc_start: 0.7696 (tpp) cc_final: 0.7132 (tmm) REVERT: G 338 TYR cc_start: 0.7721 (t80) cc_final: 0.7470 (t80) REVERT: I 279 GLN cc_start: 0.7521 (mm110) cc_final: 0.7211 (mm-40) REVERT: I 337 MET cc_start: 0.7724 (tpp) cc_final: 0.7304 (tmm) REVERT: K 337 MET cc_start: 0.7634 (tpp) cc_final: 0.7327 (tmm) REVERT: M 55 LYS cc_start: 0.8319 (tttm) cc_final: 0.7977 (tppt) REVERT: M 258 MET cc_start: 0.8400 (mmm) cc_final: 0.7836 (mmm) REVERT: M 337 MET cc_start: 0.7328 (tpp) cc_final: 0.6886 (tmm) REVERT: O 337 MET cc_start: 0.7612 (tpp) cc_final: 0.7152 (tmm) REVERT: Q 113 MET cc_start: 0.5006 (mmt) cc_final: 0.4756 (mmt) REVERT: Q 337 MET cc_start: 0.7630 (tpp) cc_final: 0.7108 (tmm) REVERT: Q 338 TYR cc_start: 0.7716 (t80) cc_final: 0.7474 (t80) REVERT: S 94 LEU cc_start: 0.7976 (tp) cc_final: 0.7411 (tt) REVERT: S 279 GLN cc_start: 0.7527 (mm110) cc_final: 0.7211 (mm-40) REVERT: S 337 MET cc_start: 0.7740 (tpp) cc_final: 0.7313 (tmm) outliers start: 32 outliers final: 22 residues processed: 316 average time/residue: 0.1563 time to fit residues: 81.2025 Evaluate side-chains 295 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR 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 177 GLU Chi-restraints excluded: chain C residue 286 THR 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 I residue 32 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 32 THR 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 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain S residue 32 THR 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: 0.5980 chunk 258 optimal weight: 0.5980 chunk 245 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 45 optimal weight: 0.0870 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 304 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169174 restraints weight = 33155.175| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.59 r_work: 0.3559 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29170 Z= 0.131 Angle : 0.505 9.080 39670 Z= 0.261 Chirality : 0.039 0.171 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.691 74.054 4920 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.97 % Allowed : 13.56 % 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 aren not related in a simple way. whole: 1.12 (0.15), residues: 3470 helix: 1.46 (0.11), residues: 2380 sheet: -1.39 (0.32), residues: 190 loop : -0.56 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 27 TYR 0.018 0.002 TYR I 354 PHE 0.010 0.001 PHE M 169 TRP 0.003 0.001 TRP Q 123 HIS 0.005 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00303 (29170) covalent geometry : angle 0.50519 (39670) hydrogen bonds : bond 0.03956 ( 1680) hydrogen bonds : angle 4.17542 ( 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 309 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8149 (m-40) cc_final: 0.7800 (t0) REVERT: A 337 MET cc_start: 0.7582 (tpp) cc_final: 0.7315 (tmm) REVERT: A 354 TYR cc_start: 0.6573 (t80) cc_final: 0.6362 (t80) REVERT: C 55 LYS cc_start: 0.8223 (tttm) cc_final: 0.7921 (tppt) REVERT: C 258 MET cc_start: 0.8564 (mmm) cc_final: 0.7999 (mmm) REVERT: C 337 MET cc_start: 0.7596 (mmm) cc_final: 0.7057 (tmm) REVERT: E 337 MET cc_start: 0.7553 (tpp) cc_final: 0.7085 (tmm) REVERT: G 337 MET cc_start: 0.7623 (tpp) cc_final: 0.7075 (tmm) REVERT: G 338 TYR cc_start: 0.7596 (t80) cc_final: 0.7021 (t80) REVERT: I 258 MET cc_start: 0.8344 (mmm) cc_final: 0.7238 (mmm) REVERT: I 337 MET cc_start: 0.7698 (tpp) cc_final: 0.7288 (tmm) REVERT: K 85 ASN cc_start: 0.8091 (m-40) cc_final: 0.7790 (t0) REVERT: K 337 MET cc_start: 0.7597 (tpp) cc_final: 0.7309 (tmm) REVERT: K 354 TYR cc_start: 0.6605 (t80) cc_final: 0.6383 (t80) REVERT: M 55 LYS cc_start: 0.8276 (tttm) cc_final: 0.7952 (tppt) REVERT: M 258 MET cc_start: 0.8551 (mmm) cc_final: 0.7989 (mmm) REVERT: M 337 MET cc_start: 0.7309 (tpp) cc_final: 0.6864 (tmm) REVERT: O 337 MET cc_start: 0.7563 (tpp) cc_final: 0.7070 (tmm) REVERT: Q 337 MET cc_start: 0.7641 (tpp) cc_final: 0.7102 (tmm) REVERT: Q 338 TYR cc_start: 0.7612 (t80) cc_final: 0.7029 (t80) REVERT: S 258 MET cc_start: 0.8347 (mmm) cc_final: 0.7225 (mmm) REVERT: S 337 MET cc_start: 0.7703 (tpp) cc_final: 0.7301 (tmm) outliers start: 29 outliers final: 17 residues processed: 305 average time/residue: 0.1534 time to fit residues: 77.4722 Evaluate side-chains 285 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 176 ILE 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 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE 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: 2.9990 chunk 321 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 250 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 190 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.197902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170687 restraints weight = 33071.768| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.56 r_work: 0.3606 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29170 Z= 0.117 Angle : 0.495 8.197 39670 Z= 0.255 Chirality : 0.038 0.147 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.704 73.900 4920 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.94 % Allowed : 13.79 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.15), residues: 3470 helix: 1.58 (0.11), residues: 2380 sheet: -1.37 (0.33), residues: 190 loop : -0.55 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 27 TYR 0.018 0.001 TYR K 338 PHE 0.010 0.001 PHE C 169 TRP 0.004 0.001 TRP G 123 HIS 0.003 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00266 (29170) covalent geometry : angle 0.49533 (39670) hydrogen bonds : bond 0.03747 ( 1680) hydrogen bonds : angle 4.06776 ( 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: 28 poor density : 301 time to evaluate : 0.785 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: A 85 ASN cc_start: 0.7948 (m-40) cc_final: 0.7738 (t0) REVERT: A 337 MET cc_start: 0.7467 (tpp) cc_final: 0.7242 (tmm) REVERT: C 55 LYS cc_start: 0.8183 (tttm) cc_final: 0.7889 (tppt) REVERT: C 85 ASN cc_start: 0.7912 (m110) cc_final: 0.7546 (m110) REVERT: C 258 MET cc_start: 0.8548 (mmm) cc_final: 0.8079 (mmm) REVERT: C 337 MET cc_start: 0.7467 (mmm) cc_final: 0.7030 (tmm) REVERT: E 177 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: G 55 LYS cc_start: 0.8081 (tttm) cc_final: 0.7802 (tppt) REVERT: G 80 GLN cc_start: 0.8466 (tp40) cc_final: 0.8095 (tp40) REVERT: G 337 MET cc_start: 0.7631 (tpp) cc_final: 0.7055 (tmm) REVERT: G 338 TYR cc_start: 0.7463 (t80) cc_final: 0.6860 (t80) REVERT: I 81 GLN cc_start: 0.8344 (tt0) cc_final: 0.8130 (tt0) REVERT: I 85 ASN cc_start: 0.8197 (m110) cc_final: 0.7767 (t0) REVERT: I 258 MET cc_start: 0.8275 (mmm) cc_final: 0.7464 (mmm) REVERT: I 337 MET cc_start: 0.7661 (tpp) cc_final: 0.7264 (tmm) REVERT: K 85 ASN cc_start: 0.8017 (m-40) cc_final: 0.7796 (t0) REVERT: K 337 MET cc_start: 0.7508 (tpp) cc_final: 0.7277 (tmm) REVERT: M 55 LYS cc_start: 0.8202 (tttm) cc_final: 0.7874 (tppt) REVERT: M 85 ASN cc_start: 0.7941 (m110) cc_final: 0.7583 (m110) REVERT: M 258 MET cc_start: 0.8525 (mmm) cc_final: 0.8021 (mmm) REVERT: M 337 MET cc_start: 0.7316 (tpp) cc_final: 0.6808 (tmm) REVERT: Q 55 LYS cc_start: 0.8149 (tttm) cc_final: 0.7854 (tppt) REVERT: Q 80 GLN cc_start: 0.8471 (tp40) cc_final: 0.8108 (tp40) REVERT: Q 337 MET cc_start: 0.7596 (tpp) cc_final: 0.7033 (tmm) REVERT: Q 338 TYR cc_start: 0.7465 (t80) cc_final: 0.6868 (t80) REVERT: S 81 GLN cc_start: 0.8349 (tt0) cc_final: 0.8136 (tt0) REVERT: S 85 ASN cc_start: 0.8228 (m110) cc_final: 0.7791 (t0) REVERT: S 258 MET cc_start: 0.8280 (mmm) cc_final: 0.7455 (mmm) REVERT: S 337 MET cc_start: 0.7677 (tpp) cc_final: 0.7284 (tmm) outliers start: 28 outliers final: 20 residues processed: 317 average time/residue: 0.1635 time to fit residues: 85.3870 Evaluate side-chains 301 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain I residue 42 GLN 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 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 295 MET 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: 0.3980 chunk 201 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 315 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 328 optimal weight: 0.0030 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.197057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.167695 restraints weight = 33030.292| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.57 r_work: 0.3594 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29170 Z= 0.127 Angle : 0.504 8.209 39670 Z= 0.258 Chirality : 0.038 0.146 4680 Planarity : 0.004 0.044 4810 Dihedral : 11.676 73.985 4920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.81 % Allowed : 14.36 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.15), residues: 3470 helix: 1.61 (0.11), residues: 2380 sheet: -1.38 (0.32), residues: 190 loop : -0.55 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 27 TYR 0.021 0.002 TYR S 354 PHE 0.010 0.002 PHE C 169 TRP 0.004 0.001 TRP Q 123 HIS 0.004 0.001 HIS Q 56 Details of bonding type rmsd covalent geometry : bond 0.00294 (29170) covalent geometry : angle 0.50391 (39670) hydrogen bonds : bond 0.03819 ( 1680) hydrogen bonds : angle 4.07949 ( 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 304 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7509 (tpp) cc_final: 0.7256 (tmm) REVERT: C 55 LYS cc_start: 0.8187 (tttm) cc_final: 0.7886 (tppt) REVERT: C 258 MET cc_start: 0.8548 (mmm) cc_final: 0.8070 (mmm) REVERT: C 337 MET cc_start: 0.7547 (mmm) cc_final: 0.7035 (tmm) REVERT: E 177 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: G 55 LYS cc_start: 0.8120 (tttm) cc_final: 0.7860 (tppt) REVERT: G 80 GLN cc_start: 0.8454 (tp40) cc_final: 0.8051 (tp40) REVERT: G 337 MET cc_start: 0.7623 (tpp) cc_final: 0.7047 (tmm) REVERT: G 338 TYR cc_start: 0.7474 (t80) cc_final: 0.6889 (t80) REVERT: I 55 LYS cc_start: 0.7994 (tttm) cc_final: 0.7690 (tppt) REVERT: I 81 GLN cc_start: 0.8351 (tt0) cc_final: 0.8136 (tt0) REVERT: I 258 MET cc_start: 0.8316 (mmm) cc_final: 0.7480 (mmm) REVERT: I 337 MET cc_start: 0.7656 (tpp) cc_final: 0.7270 (tmm) REVERT: K 337 MET cc_start: 0.7589 (tpp) cc_final: 0.7251 (tmm) REVERT: K 354 TYR cc_start: 0.6585 (t80) cc_final: 0.6380 (t80) REVERT: M 55 LYS cc_start: 0.8170 (tttm) cc_final: 0.7839 (tppt) REVERT: M 258 MET cc_start: 0.8526 (mmm) cc_final: 0.8026 (mmm) REVERT: M 337 MET cc_start: 0.7363 (tpp) cc_final: 0.6831 (tmm) REVERT: O 177 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: Q 55 LYS cc_start: 0.8167 (tttm) cc_final: 0.7901 (tppt) REVERT: Q 80 GLN cc_start: 0.8461 (tp40) cc_final: 0.8063 (tp40) REVERT: Q 337 MET cc_start: 0.7587 (tpp) cc_final: 0.7047 (tmm) REVERT: Q 338 TYR cc_start: 0.7474 (t80) cc_final: 0.6909 (t80) REVERT: S 55 LYS cc_start: 0.8009 (tttm) cc_final: 0.7674 (tppt) REVERT: S 81 GLN cc_start: 0.8339 (tt0) cc_final: 0.8123 (tt0) REVERT: S 258 MET cc_start: 0.8316 (mmm) cc_final: 0.7474 (mmm) REVERT: S 337 MET cc_start: 0.7686 (tpp) cc_final: 0.7285 (tmm) outliers start: 24 outliers final: 20 residues processed: 296 average time/residue: 0.1657 time to fit residues: 79.8887 Evaluate side-chains 291 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain I residue 42 GLN 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 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 177 GLU Chi-restraints excluded: chain S residue 42 GLN Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 295 MET 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: 1.9990 chunk 158 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.194384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167790 restraints weight = 33042.537| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.62 r_work: 0.3546 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29170 Z= 0.167 Angle : 0.536 8.013 39670 Z= 0.274 Chirality : 0.040 0.180 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.681 74.246 4920 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.87 % Allowed : 14.70 % Favored : 84.43 % 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 aren not related in a simple way. whole: 1.16 (0.15), residues: 3470 helix: 1.49 (0.11), residues: 2380 sheet: -1.34 (0.32), residues: 190 loop : -0.59 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 27 TYR 0.018 0.002 TYR A 354 PHE 0.012 0.002 PHE M 169 TRP 0.004 0.001 TRP G 123 HIS 0.005 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00396 (29170) covalent geometry : angle 0.53637 (39670) hydrogen bonds : bond 0.04146 ( 1680) hydrogen bonds : angle 4.21381 ( 4950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6280.76 seconds wall clock time: 108 minutes 38.09 seconds (6518.09 seconds total)