Starting phenix.real_space_refine on Mon May 26 12:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdl_17613/05_2025/8pdl_17613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdl_17613/05_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_17613/05_2025/8pdl_17613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdl_17613/05_2025/8pdl_17613.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdl_17613/05_2025/8pdl_17613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdl_17613/05_2025/8pdl_17613.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.38, per 1000 atoms: 0.33 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: 6.82 Conformation dependent library (CDL) restraints added in 3.4 seconds 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6520 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 20 sheets defined 70.1% alpha, 2.3% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 8.99 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: 9.15 Time building geometry restraints manager: 7.95 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: 0.24 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.230 Set scattering table: 0.250 Process input model: 57.240 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (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 TRP 0.023 0.003 TRP E 261 HIS 0.008 0.002 HIS C 7 PHE 0.017 0.004 PHE M 244 TYR 0.036 0.003 TYR M 198 ARG 0.008 0.001 ARG O 208 Details of bonding type rmsd hydrogen bonds : bond 0.12359 ( 1680) hydrogen bonds : angle 6.22245 ( 4950) covalent geometry : bond 0.00850 (29170) covalent geometry : angle 0.83103 (39670) *********************** 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 : 2.888 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: 0.7718 (tpt170) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.4059 time to fit residues: 208.5810 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 : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 178 optimal weight: 0.0000 chunk 141 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 317 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.200066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170200 restraints weight = 33287.065| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.53 r_work: 0.3557 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1437 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= 0.137 Angle : 0.542 9.348 39670 Z= 0.288 Chirality : 0.040 0.127 4680 Planarity : 0.005 0.072 4810 Dihedral : 11.962 74.055 4920 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.07 % Allowed : 5.57 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.15), residues: 3470 helix: 1.48 (0.11), residues: 2300 sheet: -1.52 (0.28), residues: 190 loop : -0.01 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.004 0.001 HIS G 275 PHE 0.010 0.002 PHE I 224 TYR 0.019 0.002 TYR G 354 ARG 0.004 0.001 ARG O 27 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 1680) hydrogen bonds : angle 4.50506 ( 4950) covalent geometry : bond 0.00303 (29170) covalent geometry : angle 0.54228 (39670) *********************** 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 336 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 2.841 Fit side-chains REVERT: A 337 MET cc_start: 0.7348 (tpp) cc_final: 0.7100 (tmm) REVERT: C 85 ASN cc_start: 0.7685 (m110) cc_final: 0.7373 (m-40) REVERT: C 338 TYR cc_start: 0.7523 (t80) cc_final: 0.7311 (t80) REVERT: E 338 TYR cc_start: 0.7575 (t80) cc_final: 0.7285 (t80) REVERT: G 338 TYR cc_start: 0.7473 (t80) cc_final: 0.7196 (t80) REVERT: I 26 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8350 (mtmm) REVERT: I 46 LEU cc_start: 0.8074 (tp) cc_final: 0.7857 (tp) REVERT: I 337 MET cc_start: 0.7548 (tpp) cc_final: 0.7134 (tmm) REVERT: I 338 TYR cc_start: 0.7526 (t80) cc_final: 0.7289 (t80) REVERT: K 190 VAL cc_start: 0.8426 (t) cc_final: 0.8058 (t) REVERT: K 337 MET cc_start: 0.7371 (tpp) cc_final: 0.7121 (tmm) REVERT: M 85 ASN cc_start: 0.7686 (m110) cc_final: 0.7372 (m-40) REVERT: M 338 TYR cc_start: 0.7532 (t80) cc_final: 0.7326 (t80) REVERT: O 338 TYR cc_start: 0.7596 (t80) cc_final: 0.7304 (t80) REVERT: Q 338 TYR cc_start: 0.7441 (t80) cc_final: 0.7188 (t80) REVERT: S 26 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8365 (mtmm) REVERT: S 46 LEU cc_start: 0.8064 (tp) cc_final: 0.7844 (tp) REVERT: S 216 GLN cc_start: 0.7977 (mt0) cc_final: 0.7771 (mt0) REVERT: S 337 MET cc_start: 0.7550 (tpp) cc_final: 0.7138 (tmm) REVERT: S 338 TYR cc_start: 0.7552 (t80) cc_final: 0.7294 (t80) outliers start: 32 outliers final: 20 residues processed: 326 average time/residue: 0.3660 time to fit residues: 195.9803 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 : 2.805 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 261 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 315 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 247 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.197385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166975 restraints weight = 33402.992| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.64 r_work: 0.3576 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1778 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= 0.133 Angle : 0.502 7.392 39670 Z= 0.264 Chirality : 0.039 0.124 4680 Planarity : 0.005 0.055 4810 Dihedral : 11.904 73.990 4920 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.88 % Allowed : 6.85 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3470 helix: 1.29 (0.11), residues: 2400 sheet: -1.48 (0.28), residues: 190 loop : -0.56 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 261 HIS 0.003 0.001 HIS O 7 PHE 0.009 0.001 PHE M 169 TYR 0.019 0.002 TYR C 354 ARG 0.004 0.000 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 1680) hydrogen bonds : angle 4.29727 ( 4950) covalent geometry : bond 0.00303 (29170) covalent geometry : angle 0.50169 (39670) *********************** 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 323 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4679 (mmm) cc_final: 0.4470 (mmt) REVERT: C 85 ASN cc_start: 0.7788 (m110) cc_final: 0.7414 (m-40) REVERT: C 272 MET cc_start: 0.6690 (mmm) cc_final: 0.6454 (mmp) REVERT: C 341 ARG cc_start: 0.5908 (mpt-90) cc_final: 0.5704 (mpt90) REVERT: E 23 TYR cc_start: 0.8283 (m-80) cc_final: 0.8018 (m-80) REVERT: E 337 MET cc_start: 0.7501 (tpp) cc_final: 0.7257 (tmm) REVERT: G 338 TYR cc_start: 0.7539 (t80) cc_final: 0.7046 (t80) REVERT: I 26 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8440 (mtmm) REVERT: I 337 MET cc_start: 0.7560 (tpp) cc_final: 0.7161 (tmm) REVERT: K 113 MET cc_start: 0.4672 (mmm) cc_final: 0.4463 (mmt) REVERT: K 341 ARG cc_start: 0.5909 (mpt-90) cc_final: 0.5628 (mpt90) REVERT: M 85 ASN cc_start: 0.7797 (m110) cc_final: 0.7427 (m-40) REVERT: M 272 MET cc_start: 0.6720 (mmm) cc_final: 0.6484 (mmp) REVERT: M 337 MET cc_start: 0.7363 (tpp) cc_final: 0.7111 (tmm) REVERT: M 341 ARG cc_start: 0.5912 (mpt-90) cc_final: 0.5704 (mpt90) REVERT: O 23 TYR cc_start: 0.8265 (m-80) cc_final: 0.7999 (m-80) REVERT: Q 338 TYR cc_start: 0.7538 (t80) cc_final: 0.7039 (t80) REVERT: S 26 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8455 (mtmm) REVERT: S 216 GLN cc_start: 0.8056 (mt0) cc_final: 0.7853 (mt0) REVERT: S 337 MET cc_start: 0.7524 (tpp) cc_final: 0.7153 (tmm) outliers start: 56 outliers final: 24 residues processed: 315 average time/residue: 0.3492 time to fit residues: 182.9693 Evaluate side-chains 270 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.871 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 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 132 optimal weight: 0.5980 chunk 234 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 330 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN E 85 ASN O 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167930 restraints weight = 33589.428| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.59 r_work: 0.3577 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1971 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= 0.138 Angle : 0.503 11.006 39670 Z= 0.261 Chirality : 0.039 0.123 4680 Planarity : 0.004 0.048 4810 Dihedral : 11.666 74.069 4920 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.41 % Allowed : 8.62 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3470 helix: 1.32 (0.11), residues: 2400 sheet: -1.56 (0.29), residues: 190 loop : -0.56 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.003 0.001 HIS O 7 PHE 0.010 0.002 PHE M 169 TYR 0.018 0.002 TYR C 354 ARG 0.003 0.000 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 1680) hydrogen bonds : angle 4.23619 ( 4950) covalent geometry : bond 0.00319 (29170) covalent geometry : angle 0.50277 (39670) *********************** 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 310 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.862 Fit side-chains REVERT: C 85 ASN cc_start: 0.7817 (m110) cc_final: 0.7413 (m110) REVERT: E 23 TYR cc_start: 0.8230 (m-80) cc_final: 0.7959 (m-80) REVERT: E 337 MET cc_start: 0.7398 (tpp) cc_final: 0.7161 (tmm) REVERT: G 272 MET cc_start: 0.7249 (mmm) cc_final: 0.6969 (mmp) REVERT: G 338 TYR cc_start: 0.7579 (t80) cc_final: 0.7080 (t80) REVERT: I 26 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8461 (mtmm) REVERT: I 337 MET cc_start: 0.7536 (tpp) cc_final: 0.7120 (tmm) REVERT: K 338 TYR cc_start: 0.7538 (t80) cc_final: 0.7322 (t80) REVERT: M 85 ASN cc_start: 0.7836 (m110) cc_final: 0.7433 (m110) REVERT: M 337 MET cc_start: 0.7266 (tpp) cc_final: 0.7022 (tmm) REVERT: O 23 TYR cc_start: 0.8220 (m-80) cc_final: 0.7945 (m-80) REVERT: Q 272 MET cc_start: 0.7230 (mmm) cc_final: 0.6958 (mmp) REVERT: Q 338 TYR cc_start: 0.7589 (t80) cc_final: 0.7082 (t80) REVERT: S 26 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8459 (mtmm) REVERT: S 337 MET cc_start: 0.7540 (tpp) cc_final: 0.7136 (tmm) outliers start: 42 outliers final: 24 residues processed: 304 average time/residue: 0.3611 time to fit residues: 182.8684 Evaluate side-chains 279 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE 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 47 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain 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 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 328 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS M 275 HIS O 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167502 restraints weight = 33294.737| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.63 r_work: 0.3567 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29170 Z= 0.142 Angle : 0.495 7.150 39670 Z= 0.258 Chirality : 0.040 0.235 4680 Planarity : 0.004 0.047 4810 Dihedral : 11.691 74.121 4920 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.74 % Allowed : 9.70 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3470 helix: 1.39 (0.11), residues: 2380 sheet: -1.61 (0.30), residues: 190 loop : -0.42 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 261 HIS 0.003 0.001 HIS O 7 PHE 0.010 0.002 PHE C 169 TYR 0.017 0.002 TYR A 354 ARG 0.003 0.000 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 1680) hydrogen bonds : angle 4.19605 ( 4950) covalent geometry : bond 0.00332 (29170) covalent geometry : angle 0.49533 (39670) *********************** 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 344 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 292 time to evaluate : 3.029 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: A 337 MET cc_start: 0.7455 (tpp) cc_final: 0.7012 (tmm) REVERT: C 85 ASN cc_start: 0.7998 (m110) cc_final: 0.7640 (m110) REVERT: C 337 MET cc_start: 0.7586 (mmm) cc_final: 0.6992 (tmm) REVERT: E 23 TYR cc_start: 0.8308 (m-80) cc_final: 0.8095 (m-80) REVERT: E 337 MET cc_start: 0.7505 (tpp) cc_final: 0.7110 (tmm) REVERT: G 272 MET cc_start: 0.7157 (mmm) cc_final: 0.6956 (mmp) REVERT: G 337 MET cc_start: 0.7485 (tpp) cc_final: 0.6967 (tmm) REVERT: G 338 TYR cc_start: 0.7660 (t80) cc_final: 0.7147 (t80) REVERT: G 344 ASN cc_start: 0.5319 (OUTLIER) cc_final: 0.5093 (t0) REVERT: I 258 MET cc_start: 0.8408 (mmm) cc_final: 0.7892 (mmm) REVERT: I 337 MET cc_start: 0.7603 (tpp) cc_final: 0.7169 (tmm) REVERT: K 337 MET cc_start: 0.7518 (tpp) cc_final: 0.7048 (tmm) REVERT: M 85 ASN cc_start: 0.8013 (m110) cc_final: 0.7660 (m110) REVERT: M 337 MET cc_start: 0.7421 (tpp) cc_final: 0.7037 (tmm) REVERT: O 23 TYR cc_start: 0.8277 (m-80) cc_final: 0.8062 (m-80) REVERT: O 337 MET cc_start: 0.7500 (tpp) cc_final: 0.6959 (tmm) REVERT: Q 272 MET cc_start: 0.7147 (mmm) cc_final: 0.6946 (mmp) REVERT: Q 337 MET cc_start: 0.7464 (tpp) cc_final: 0.6956 (tmm) REVERT: Q 338 TYR cc_start: 0.7680 (t80) cc_final: 0.7168 (t80) REVERT: Q 344 ASN cc_start: 0.5317 (OUTLIER) cc_final: 0.5094 (t0) REVERT: S 258 MET cc_start: 0.8411 (mmm) cc_final: 0.7913 (mmm) REVERT: S 337 MET cc_start: 0.7567 (tpp) cc_final: 0.7168 (tmm) outliers start: 52 outliers final: 21 residues processed: 336 average time/residue: 0.3682 time to fit residues: 203.2870 Evaluate side-chains 291 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 3.082 ------------------------------------------------------------------------------- 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 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 G residue 344 ASN 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 47 LEU 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 Q residue 344 ASN 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 145 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 298 optimal weight: 0.0270 chunk 192 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 279 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 85 ASN O 85 ASN O 279 GLN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169234 restraints weight = 33287.128| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.55 r_work: 0.3578 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29170 Z= 0.146 Angle : 0.500 7.872 39670 Z= 0.259 Chirality : 0.039 0.167 4680 Planarity : 0.004 0.047 4810 Dihedral : 11.657 74.126 4920 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.24 % Allowed : 11.48 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3470 helix: 1.43 (0.11), residues: 2380 sheet: -1.57 (0.31), residues: 190 loop : -0.44 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 123 HIS 0.004 0.001 HIS E 7 PHE 0.011 0.002 PHE C 169 TYR 0.016 0.002 TYR G 354 ARG 0.003 0.000 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1680) hydrogen bonds : angle 4.21067 ( 4950) covalent geometry : bond 0.00341 (29170) covalent geometry : angle 0.49976 (39670) *********************** 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 329 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 3.041 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: A 337 MET cc_start: 0.7473 (tpp) cc_final: 0.7116 (tmm) REVERT: C 85 ASN cc_start: 0.7943 (m110) cc_final: 0.7608 (m110) REVERT: C 258 MET cc_start: 0.8323 (mmm) cc_final: 0.7787 (mmm) REVERT: C 337 MET cc_start: 0.7586 (mmm) cc_final: 0.7035 (tmm) REVERT: E 94 LEU cc_start: 0.7791 (tp) cc_final: 0.7345 (tt) REVERT: E 337 MET cc_start: 0.7504 (tpp) cc_final: 0.7136 (tmm) REVERT: G 80 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: G 337 MET cc_start: 0.7593 (tpp) cc_final: 0.7056 (tmm) REVERT: G 338 TYR cc_start: 0.7706 (t80) cc_final: 0.7092 (t80) REVERT: I 94 LEU cc_start: 0.7891 (tp) cc_final: 0.7325 (tt) REVERT: I 337 MET cc_start: 0.7667 (tpp) cc_final: 0.7275 (tmm) REVERT: K 337 MET cc_start: 0.7451 (tpp) cc_final: 0.7100 (tmm) REVERT: M 85 ASN cc_start: 0.7935 (m110) cc_final: 0.7602 (m110) REVERT: M 258 MET cc_start: 0.8311 (mmm) cc_final: 0.7770 (mmm) REVERT: M 337 MET cc_start: 0.7418 (tpp) cc_final: 0.7044 (tmm) REVERT: O 55 LYS cc_start: 0.7902 (tttm) cc_final: 0.7694 (tppt) REVERT: O 94 LEU cc_start: 0.7799 (tp) cc_final: 0.7350 (tt) REVERT: O 337 MET cc_start: 0.7542 (tpp) cc_final: 0.7094 (tmm) REVERT: Q 337 MET cc_start: 0.7555 (tpp) cc_final: 0.7047 (tmm) REVERT: Q 338 TYR cc_start: 0.7731 (t80) cc_final: 0.7126 (t80) REVERT: Q 344 ASN cc_start: 0.5508 (OUTLIER) cc_final: 0.5297 (t0) REVERT: S 94 LEU cc_start: 0.7888 (tp) cc_final: 0.7311 (tt) REVERT: S 337 MET cc_start: 0.7652 (tpp) cc_final: 0.7259 (tmm) outliers start: 37 outliers final: 26 residues processed: 317 average time/residue: 0.3623 time to fit residues: 191.0744 Evaluate side-chains 300 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN 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 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 80 GLN 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 80 GLN Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 344 ASN 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 240 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 306 GLN E 85 ASN E 275 HIS E 344 ASN G 275 HIS K 85 ASN K 306 GLN O 85 ASN O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 275 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.192251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165268 restraints weight = 33267.372| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.62 r_work: 0.3514 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29170 Z= 0.219 Angle : 0.568 8.798 39670 Z= 0.292 Chirality : 0.042 0.168 4680 Planarity : 0.005 0.047 4810 Dihedral : 11.714 74.596 4920 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.34 % Allowed : 12.25 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3470 helix: 1.32 (0.11), residues: 2330 sheet: -1.55 (0.32), residues: 190 loop : -0.38 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 261 HIS 0.005 0.001 HIS E 7 PHE 0.013 0.002 PHE O 169 TYR 0.014 0.002 TYR Q 354 ARG 0.005 0.000 ARG I 27 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 1680) hydrogen bonds : angle 4.41305 ( 4950) covalent geometry : bond 0.00524 (29170) covalent geometry : angle 0.56780 (39670) *********************** 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 328 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7682 (tpp) cc_final: 0.7267 (tmm) REVERT: A 338 TYR cc_start: 0.7965 (t80) cc_final: 0.7516 (t80) REVERT: C 337 MET cc_start: 0.7777 (mmm) cc_final: 0.7123 (tmm) REVERT: E 94 LEU cc_start: 0.7920 (tp) cc_final: 0.7530 (tt) REVERT: E 337 MET cc_start: 0.7649 (tpp) cc_final: 0.7173 (tmm) REVERT: G 80 GLN cc_start: 0.8601 (tp40) cc_final: 0.8226 (tp40) REVERT: G 337 MET cc_start: 0.7697 (tpp) cc_final: 0.7102 (tmm) REVERT: G 338 TYR cc_start: 0.7783 (t80) cc_final: 0.7530 (t80) REVERT: I 337 MET cc_start: 0.7779 (tpp) cc_final: 0.7340 (tmm) REVERT: K 337 MET cc_start: 0.7630 (tpp) cc_final: 0.7215 (tmm) REVERT: K 338 TYR cc_start: 0.8007 (t80) cc_final: 0.7504 (t80) REVERT: M 337 MET cc_start: 0.7684 (tpp) cc_final: 0.7117 (tmm) REVERT: Q 337 MET cc_start: 0.7663 (tpp) cc_final: 0.7094 (tmm) REVERT: Q 338 TYR cc_start: 0.7762 (t80) cc_final: 0.7532 (t80) REVERT: Q 344 ASN cc_start: 0.5642 (OUTLIER) cc_final: 0.5436 (t0) REVERT: S 94 LEU cc_start: 0.7996 (tp) cc_final: 0.7422 (tt) REVERT: S 279 GLN cc_start: 0.7557 (mm110) cc_final: 0.7225 (mm-40) REVERT: S 337 MET cc_start: 0.7791 (tpp) cc_final: 0.7328 (tmm) outliers start: 40 outliers final: 24 residues processed: 321 average time/residue: 0.3634 time to fit residues: 192.1474 Evaluate side-chains 299 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 135 MET Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 344 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 120 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 270 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 290 optimal weight: 0.2980 chunk 125 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN G 279 GLN G 306 GLN K 80 GLN O 344 ASN Q 279 GLN Q 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.196911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169524 restraints weight = 33271.334| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.52 r_work: 0.3599 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2491 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= 0.122 Angle : 0.492 8.957 39670 Z= 0.255 Chirality : 0.039 0.128 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.688 74.003 4920 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.11 % Allowed : 12.45 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3470 helix: 1.49 (0.11), residues: 2380 sheet: -1.45 (0.33), residues: 190 loop : -0.52 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 123 HIS 0.003 0.001 HIS E 7 PHE 0.009 0.001 PHE M 169 TYR 0.020 0.002 TYR I 354 ARG 0.002 0.000 ARG S 27 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1680) hydrogen bonds : angle 4.14011 ( 4950) covalent geometry : bond 0.00275 (29170) covalent geometry : angle 0.49239 (39670) *********************** 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 330 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8171 (m-40) cc_final: 0.7727 (t0) REVERT: A 337 MET cc_start: 0.7539 (tpp) cc_final: 0.7164 (tmm) REVERT: C 85 ASN cc_start: 0.7983 (m110) cc_final: 0.7605 (m110) REVERT: C 337 MET cc_start: 0.7428 (mmm) cc_final: 0.7004 (tmm) REVERT: E 337 MET cc_start: 0.7535 (tpp) cc_final: 0.7052 (tmm) REVERT: G 80 GLN cc_start: 0.8578 (tp40) cc_final: 0.8197 (tp40) REVERT: G 337 MET cc_start: 0.7620 (tpp) cc_final: 0.7070 (tmm) REVERT: G 338 TYR cc_start: 0.7683 (t80) cc_final: 0.7049 (t80) REVERT: I 85 ASN cc_start: 0.8179 (m110) cc_final: 0.7797 (t0) REVERT: I 337 MET cc_start: 0.7712 (tpp) cc_final: 0.7284 (tmm) REVERT: K 85 ASN cc_start: 0.8193 (m-40) cc_final: 0.7738 (t0) REVERT: K 337 MET cc_start: 0.7497 (tpp) cc_final: 0.7162 (tmm) REVERT: M 85 ASN cc_start: 0.7967 (m110) cc_final: 0.7595 (m110) REVERT: M 337 MET cc_start: 0.7558 (tpp) cc_final: 0.7109 (tmm) REVERT: Q 337 MET cc_start: 0.7647 (tpp) cc_final: 0.7078 (tmm) REVERT: Q 338 TYR cc_start: 0.7692 (t80) cc_final: 0.7007 (t80) REVERT: S 337 MET cc_start: 0.7693 (tpp) cc_final: 0.7271 (tmm) outliers start: 33 outliers final: 18 residues processed: 321 average time/residue: 0.3608 time to fit residues: 191.1335 Evaluate side-chains 294 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 2.858 ------------------------------------------------------------------------------- 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 I residue 176 ILE Chi-restraints excluded: chain I residue 295 MET 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 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 68 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 259 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN G 41 GLN I 150 GLN M 80 GLN O 85 ASN S 41 GLN S 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.195220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.168699 restraints weight = 33078.783| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.67 r_work: 0.3548 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2520 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= 0.148 Angle : 0.523 10.007 39670 Z= 0.267 Chirality : 0.039 0.244 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.681 74.138 4920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 13.66 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3470 helix: 1.45 (0.11), residues: 2380 sheet: -1.46 (0.32), residues: 190 loop : -0.52 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 123 HIS 0.004 0.001 HIS O 7 PHE 0.011 0.002 PHE C 169 TYR 0.014 0.002 TYR S 23 ARG 0.003 0.000 ARG I 27 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1680) hydrogen bonds : angle 4.19015 ( 4950) covalent geometry : bond 0.00347 (29170) covalent geometry : angle 0.52261 (39670) *********************** 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 320 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7628 (tpp) cc_final: 0.7218 (tmm) REVERT: A 338 TYR cc_start: 0.7897 (t80) cc_final: 0.7356 (t80) REVERT: C 55 LYS cc_start: 0.8245 (tttm) cc_final: 0.7892 (tppt) REVERT: C 337 MET cc_start: 0.7589 (mmm) cc_final: 0.7086 (tmm) REVERT: G 80 GLN cc_start: 0.8568 (tp40) cc_final: 0.8145 (tp40) REVERT: G 337 MET cc_start: 0.7668 (tpp) cc_final: 0.7078 (tmm) REVERT: G 338 TYR cc_start: 0.7681 (t80) cc_final: 0.7038 (t80) REVERT: I 279 GLN cc_start: 0.7421 (mm110) cc_final: 0.7108 (mm-40) REVERT: I 337 MET cc_start: 0.7745 (tpp) cc_final: 0.7357 (tmm) REVERT: K 85 ASN cc_start: 0.8184 (m-40) cc_final: 0.7772 (t0) REVERT: K 337 MET cc_start: 0.7598 (tpp) cc_final: 0.7219 (tmm) REVERT: M 55 LYS cc_start: 0.8272 (tttm) cc_final: 0.7924 (tppt) REVERT: M 337 MET cc_start: 0.7517 (tpp) cc_final: 0.7110 (tmm) REVERT: Q 337 MET cc_start: 0.7694 (tpp) cc_final: 0.7109 (tmm) REVERT: Q 338 TYR cc_start: 0.7707 (t80) cc_final: 0.7022 (t80) REVERT: S 279 GLN cc_start: 0.7429 (mm110) cc_final: 0.7117 (mm-40) REVERT: S 337 MET cc_start: 0.7773 (tpp) cc_final: 0.7350 (tmm) outliers start: 21 outliers final: 18 residues processed: 317 average time/residue: 0.3612 time to fit residues: 188.3540 Evaluate side-chains 295 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 277 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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 I residue 176 ILE Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 83 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 297 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 G 41 GLN I 41 GLN I 344 ASN K 344 ASN M 344 ASN S 85 ASN S 344 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.168382 restraints weight = 32973.577| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.66 r_work: 0.3540 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29170 Z= 0.153 Angle : 0.535 9.857 39670 Z= 0.273 Chirality : 0.040 0.232 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.679 74.142 4920 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.87 % Allowed : 13.69 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3470 helix: 1.44 (0.11), residues: 2380 sheet: -1.54 (0.32), residues: 190 loop : -0.53 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 123 HIS 0.005 0.001 HIS M 117 PHE 0.011 0.002 PHE M 169 TYR 0.021 0.002 TYR C 354 ARG 0.003 0.000 ARG S 27 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 1680) hydrogen bonds : angle 4.22471 ( 4950) covalent geometry : bond 0.00361 (29170) covalent geometry : angle 0.53539 (39670) ********************** 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 312 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 2.886 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: A 337 MET cc_start: 0.7603 (tpp) cc_final: 0.7194 (tmm) REVERT: A 338 TYR cc_start: 0.7883 (t80) cc_final: 0.7373 (t80) REVERT: C 55 LYS cc_start: 0.8264 (tttm) cc_final: 0.7902 (tppt) REVERT: C 337 MET cc_start: 0.7585 (mmm) cc_final: 0.7070 (tmm) REVERT: C 354 TYR cc_start: 0.6836 (t80) cc_final: 0.6585 (t80) REVERT: E 177 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: G 80 GLN cc_start: 0.8560 (tp40) cc_final: 0.8131 (tp40) REVERT: G 337 MET cc_start: 0.7722 (tpp) cc_final: 0.7090 (tmm) REVERT: G 338 TYR cc_start: 0.7696 (t80) cc_final: 0.7049 (t80) REVERT: I 279 GLN cc_start: 0.7441 (mm110) cc_final: 0.7117 (mm-40) REVERT: I 337 MET cc_start: 0.7789 (tpp) cc_final: 0.7365 (tmm) REVERT: K 85 ASN cc_start: 0.8161 (m-40) cc_final: 0.7710 (t0) REVERT: K 337 MET cc_start: 0.7585 (tpp) cc_final: 0.7206 (tmm) REVERT: M 55 LYS cc_start: 0.8303 (tttm) cc_final: 0.7942 (tppt) REVERT: M 337 MET cc_start: 0.7587 (tpp) cc_final: 0.7151 (tmm) REVERT: O 177 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: Q 337 MET cc_start: 0.7726 (tpp) cc_final: 0.7116 (tmm) REVERT: Q 338 TYR cc_start: 0.7705 (t80) cc_final: 0.7069 (t80) REVERT: S 85 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7737 (t0) REVERT: S 279 GLN cc_start: 0.7456 (mm110) cc_final: 0.7127 (mm-40) REVERT: S 337 MET cc_start: 0.7768 (tpp) cc_final: 0.7350 (tmm) outliers start: 26 outliers final: 17 residues processed: 308 average time/residue: 0.3729 time to fit residues: 188.6510 Evaluate side-chains 295 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 177 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 295 MET 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 177 GLU Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain S residue 85 ASN 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 164 optimal weight: 0.9990 chunk 299 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.168715 restraints weight = 32997.937| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.57 r_work: 0.3553 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 29170 Z= 0.173 Angle : 0.663 59.184 39670 Z= 0.366 Chirality : 0.041 0.532 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.689 74.153 4920 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 0.74 % Allowed : 14.16 % Favored : 85.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3470 helix: 1.44 (0.11), residues: 2380 sheet: -1.54 (0.32), residues: 190 loop : -0.53 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 123 HIS 0.013 0.001 HIS Q 117 PHE 0.011 0.002 PHE M 169 TYR 0.017 0.002 TYR C 354 ARG 0.003 0.000 ARG S 27 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1680) hydrogen bonds : angle 4.23711 ( 4950) covalent geometry : bond 0.00398 (29170) covalent geometry : angle 0.66282 (39670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13965.10 seconds wall clock time: 243 minutes 24.62 seconds (14604.62 seconds total)