Starting phenix.real_space_refine on Tue Jun 24 08:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdl_17613/06_2025/8pdl_17613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdl_17613/06_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_17613/06_2025/8pdl_17613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdl_17613/06_2025/8pdl_17613.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdl_17613/06_2025/8pdl_17613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdl_17613/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.76, per 1000 atoms: 0.34 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: 7.06 Conformation dependent library (CDL) restraints added in 3.7 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: 9.89 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: 9.90 Time building geometry restraints manager: 8.26 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: 0.27 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: 5.320 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: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 61.940 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.550 ------------------------------------------------------------------------------- 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 : 3.026 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: 0.4209 time to fit residues: 215.8687 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 : 2.934 ------------------------------------------------------------------------------- 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 = 0.200067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170202 restraints weight = 33287.016| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.53 r_work: 0.3535 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- 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 9.347 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 4.50499 ( 4950) covalent geometry : bond 0.00303 (29170) covalent geometry : angle 0.54230 (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 : 3.150 Fit side-chains REVERT: A 337 MET cc_start: 0.7354 (tpp) cc_final: 0.7095 (tmm) REVERT: C 85 ASN cc_start: 0.7683 (m110) cc_final: 0.7374 (m-40) REVERT: C 338 TYR cc_start: 0.7515 (t80) cc_final: 0.7312 (t80) REVERT: E 338 TYR cc_start: 0.7566 (t80) cc_final: 0.7283 (t80) REVERT: G 338 TYR cc_start: 0.7461 (t80) cc_final: 0.7193 (t80) REVERT: I 26 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8351 (mtmm) REVERT: I 46 LEU cc_start: 0.8081 (tp) cc_final: 0.7861 (tp) REVERT: I 337 MET cc_start: 0.7545 (tpp) cc_final: 0.7125 (tmm) REVERT: I 338 TYR cc_start: 0.7521 (t80) cc_final: 0.7288 (t80) REVERT: K 190 VAL cc_start: 0.8426 (t) cc_final: 0.8059 (t) REVERT: K 337 MET cc_start: 0.7378 (tpp) cc_final: 0.7118 (tmm) REVERT: M 85 ASN cc_start: 0.7687 (m110) cc_final: 0.7375 (m-40) REVERT: M 338 TYR cc_start: 0.7527 (t80) cc_final: 0.7326 (t80) REVERT: O 338 TYR cc_start: 0.7589 (t80) cc_final: 0.7302 (t80) REVERT: Q 338 TYR cc_start: 0.7432 (t80) cc_final: 0.7183 (t80) REVERT: S 26 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8365 (mtmm) REVERT: S 46 LEU cc_start: 0.8068 (tp) cc_final: 0.7845 (tp) REVERT: S 216 GLN cc_start: 0.7988 (mt0) cc_final: 0.7785 (mt0) REVERT: S 337 MET cc_start: 0.7558 (tpp) cc_final: 0.7136 (tmm) REVERT: S 338 TYR cc_start: 0.7550 (t80) cc_final: 0.7296 (t80) outliers start: 32 outliers final: 20 residues processed: 326 average time/residue: 0.3816 time to fit residues: 205.6190 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 : 3.150 ------------------------------------------------------------------------------- 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: 0.5980 chunk 306 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 315 optimal weight: 4.9990 chunk 140 optimal weight: 0.0170 chunk 247 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.198157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169269 restraints weight = 33429.895| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.59 r_work: 0.3594 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29170 Z= 0.126 Angle : 0.495 7.236 39670 Z= 0.261 Chirality : 0.039 0.123 4680 Planarity : 0.005 0.054 4810 Dihedral : 11.905 73.925 4920 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.85 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: 0.98 (0.15), residues: 3470 helix: 1.32 (0.11), residues: 2400 sheet: -1.46 (0.28), residues: 190 loop : -0.55 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 123 HIS 0.003 0.001 HIS O 7 PHE 0.008 0.001 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 0.04125 ( 1680) hydrogen bonds : angle 4.26651 ( 4950) covalent geometry : bond 0.00284 (29170) covalent geometry : angle 0.49540 (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 321 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8154 (m110) cc_final: 0.7952 (m110) REVERT: A 113 MET cc_start: 0.4576 (mmm) cc_final: 0.4369 (mmt) REVERT: C 85 ASN cc_start: 0.7760 (m110) cc_final: 0.7386 (m-40) REVERT: C 272 MET cc_start: 0.6706 (mmm) cc_final: 0.6454 (mmp) REVERT: C 341 ARG cc_start: 0.5890 (mpt-90) cc_final: 0.5686 (mpt90) REVERT: E 23 TYR cc_start: 0.8244 (m-80) cc_final: 0.7982 (m-80) REVERT: E 337 MET cc_start: 0.7463 (tpp) cc_final: 0.7233 (tmm) REVERT: G 338 TYR cc_start: 0.7547 (t80) cc_final: 0.7055 (t80) REVERT: I 26 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8430 (mtmm) REVERT: I 337 MET cc_start: 0.7554 (tpp) cc_final: 0.7146 (tmm) REVERT: K 85 ASN cc_start: 0.8155 (m110) cc_final: 0.7954 (m110) REVERT: K 113 MET cc_start: 0.4563 (mmm) cc_final: 0.4357 (mmt) REVERT: K 341 ARG cc_start: 0.5794 (mpt-90) cc_final: 0.5512 (mpt90) REVERT: M 85 ASN cc_start: 0.7776 (m110) cc_final: 0.7403 (m-40) REVERT: M 272 MET cc_start: 0.6729 (mmm) cc_final: 0.6476 (mmp) REVERT: M 337 MET cc_start: 0.7328 (tpp) cc_final: 0.7091 (tmm) REVERT: M 341 ARG cc_start: 0.5892 (mpt-90) cc_final: 0.5689 (mpt90) REVERT: O 23 TYR cc_start: 0.8227 (m-80) cc_final: 0.7963 (m-80) REVERT: Q 338 TYR cc_start: 0.7544 (t80) cc_final: 0.6967 (t80) REVERT: S 26 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8448 (mtmm) REVERT: S 337 MET cc_start: 0.7492 (tpp) cc_final: 0.7132 (tmm) outliers start: 56 outliers final: 24 residues processed: 313 average time/residue: 0.3625 time to fit residues: 189.2849 Evaluate side-chains 268 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 3.090 ------------------------------------------------------------------------------- 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: 0.8980 chunk 269 optimal weight: 0.7980 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: 0.8980 chunk 264 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 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 = 0.4146 r_free = 0.4146 target = 0.197354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167611 restraints weight = 33600.066| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.61 r_work: 0.3579 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29170 Z= 0.138 Angle : 0.502 10.811 39670 Z= 0.261 Chirality : 0.039 0.120 4680 Planarity : 0.004 0.048 4810 Dihedral : 11.648 74.075 4920 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.34 % Allowed : 8.93 % Favored : 89.73 % 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: 1.02 (0.15), residues: 3470 helix: 1.35 (0.11), residues: 2400 sheet: -1.50 (0.29), residues: 190 loop : -0.53 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 261 HIS 0.003 0.001 HIS E 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 0.04035 ( 1680) hydrogen bonds : angle 4.22256 ( 4950) covalent geometry : bond 0.00317 (29170) covalent geometry : angle 0.50245 (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 302 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 3.282 Fit side-chains REVERT: C 85 ASN cc_start: 0.7813 (m110) cc_final: 0.7402 (m110) REVERT: C 338 TYR cc_start: 0.7391 (t80) cc_final: 0.7157 (t80) REVERT: E 23 TYR cc_start: 0.8221 (m-80) cc_final: 0.7952 (m-80) REVERT: E 337 MET cc_start: 0.7392 (tpp) cc_final: 0.7190 (tmm) REVERT: G 272 MET cc_start: 0.7187 (mmm) cc_final: 0.6816 (mmp) REVERT: G 338 TYR cc_start: 0.7560 (t80) cc_final: 0.7053 (t80) REVERT: I 26 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8461 (mtmm) REVERT: I 337 MET cc_start: 0.7529 (tpp) cc_final: 0.7144 (tmm) REVERT: M 85 ASN cc_start: 0.7828 (m110) cc_final: 0.7424 (m110) REVERT: M 337 MET cc_start: 0.7352 (tpp) cc_final: 0.7134 (tmm) REVERT: O 23 TYR cc_start: 0.8223 (m-80) cc_final: 0.7953 (m-80) REVERT: Q 272 MET cc_start: 0.7167 (mmm) cc_final: 0.6799 (mmp) REVERT: Q 338 TYR cc_start: 0.7590 (t80) cc_final: 0.7061 (t80) REVERT: S 26 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8468 (mtmm) REVERT: S 337 MET cc_start: 0.7549 (tpp) cc_final: 0.7158 (tmm) outliers start: 40 outliers final: 24 residues processed: 296 average time/residue: 0.3706 time to fit residues: 184.0237 Evaluate side-chains 274 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 238 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 275 HIS K 85 ASN M 275 HIS O 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.196618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.167060 restraints weight = 33283.182| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.58 r_work: 0.3582 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29170 Z= 0.140 Angle : 0.494 7.065 39670 Z= 0.257 Chirality : 0.039 0.235 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.717 74.088 4920 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.74 % Allowed : 9.77 % Favored : 88.49 % 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: 1.42 (0.11), residues: 2380 sheet: -1.56 (0.30), residues: 190 loop : -0.41 (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 E 7 PHE 0.010 0.002 PHE M 169 TYR 0.017 0.002 TYR Q 354 ARG 0.003 0.000 ARG A 189 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1680) hydrogen bonds : angle 4.19204 ( 4950) covalent geometry : bond 0.00327 (29170) covalent geometry : angle 0.49428 (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 335 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7456 (tpp) cc_final: 0.7033 (tmm) REVERT: C 85 ASN cc_start: 0.7964 (m110) cc_final: 0.7609 (m110) REVERT: E 23 TYR cc_start: 0.8261 (m-80) cc_final: 0.8039 (m-80) REVERT: E 55 LYS cc_start: 0.7911 (tttm) cc_final: 0.7701 (tppt) REVERT: E 94 LEU cc_start: 0.7856 (tp) cc_final: 0.7440 (tt) REVERT: E 337 MET cc_start: 0.7430 (tpp) cc_final: 0.7122 (tmm) REVERT: G 337 MET cc_start: 0.7524 (tpp) cc_final: 0.7013 (tmm) REVERT: G 338 TYR cc_start: 0.7652 (t80) cc_final: 0.7146 (t80) REVERT: G 344 ASN cc_start: 0.5376 (OUTLIER) cc_final: 0.5172 (t0) REVERT: I 46 LEU cc_start: 0.8054 (tp) cc_final: 0.7830 (tp) REVERT: I 258 MET cc_start: 0.8410 (mmm) cc_final: 0.7915 (mmm) REVERT: I 337 MET cc_start: 0.7553 (tpp) cc_final: 0.7173 (tmm) REVERT: K 337 MET cc_start: 0.7528 (tpp) cc_final: 0.7075 (tmm) REVERT: M 85 ASN cc_start: 0.7978 (m110) cc_final: 0.7627 (m110) REVERT: M 337 MET cc_start: 0.7409 (tpp) cc_final: 0.7131 (tmm) REVERT: O 23 TYR cc_start: 0.8242 (m-80) cc_final: 0.8023 (m-80) REVERT: O 55 LYS cc_start: 0.7938 (tttm) cc_final: 0.7716 (tppt) REVERT: O 94 LEU cc_start: 0.7855 (tp) cc_final: 0.7435 (tt) REVERT: O 337 MET cc_start: 0.7498 (tpp) cc_final: 0.7038 (tmm) REVERT: Q 337 MET cc_start: 0.7462 (tpp) cc_final: 0.6992 (tmm) REVERT: Q 338 TYR cc_start: 0.7648 (t80) cc_final: 0.7091 (t80) REVERT: Q 344 ASN cc_start: 0.5354 (OUTLIER) cc_final: 0.4972 (t0) REVERT: S 258 MET cc_start: 0.8412 (mmm) cc_final: 0.7937 (mmm) REVERT: S 337 MET cc_start: 0.7574 (tpp) cc_final: 0.7183 (tmm) outliers start: 52 outliers final: 22 residues processed: 327 average time/residue: 0.3806 time to fit residues: 204.4053 Evaluate side-chains 286 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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 47 LEU 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: 0.6980 chunk 298 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 ASN E 275 HIS ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 275 HIS K 306 GLN O 85 ASN O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Q 275 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.192474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.164026 restraints weight = 33222.274| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.64 r_work: 0.3505 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29170 Z= 0.216 Angle : 0.567 8.178 39670 Z= 0.292 Chirality : 0.042 0.198 4680 Planarity : 0.005 0.049 4810 Dihedral : 11.738 74.592 4920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 11.07 % Favored : 87.65 % 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: 1.03 (0.15), residues: 3470 helix: 1.32 (0.11), residues: 2320 sheet: -1.61 (0.31), residues: 190 loop : -0.22 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 261 HIS 0.005 0.001 HIS E 7 PHE 0.013 0.002 PHE E 169 TYR 0.014 0.002 TYR C 354 ARG 0.005 0.000 ARG O 27 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1680) hydrogen bonds : angle 4.44068 ( 4950) covalent geometry : bond 0.00517 (29170) covalent geometry : angle 0.56703 (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 311 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 3.430 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: A 337 MET cc_start: 0.7599 (tpp) cc_final: 0.7259 (tmm) REVERT: E 94 LEU cc_start: 0.8065 (tp) cc_final: 0.7601 (tt) REVERT: E 337 MET cc_start: 0.7613 (tpp) cc_final: 0.7206 (tmm) REVERT: G 337 MET cc_start: 0.7723 (tpp) cc_final: 0.7119 (tmm) REVERT: G 338 TYR cc_start: 0.7806 (t80) cc_final: 0.7547 (t80) REVERT: I 94 LEU cc_start: 0.8000 (tp) cc_final: 0.7435 (tt) REVERT: I 279 GLN cc_start: 0.7557 (mm110) cc_final: 0.7245 (mm-40) REVERT: I 337 MET cc_start: 0.7731 (tpp) cc_final: 0.7322 (tmm) REVERT: K 337 MET cc_start: 0.7610 (tpp) cc_final: 0.7248 (tmm) REVERT: K 338 TYR cc_start: 0.7971 (t80) cc_final: 0.7434 (t80) REVERT: M 337 MET cc_start: 0.7608 (tpp) cc_final: 0.7105 (tmm) REVERT: O 94 LEU cc_start: 0.8073 (tp) cc_final: 0.7603 (tt) REVERT: Q 337 MET cc_start: 0.7704 (tpp) cc_final: 0.7136 (tmm) REVERT: S 94 LEU cc_start: 0.8018 (tp) cc_final: 0.7461 (tt) REVERT: S 337 MET cc_start: 0.7783 (tpp) cc_final: 0.7327 (tmm) outliers start: 38 outliers final: 30 residues processed: 303 average time/residue: 0.4730 time to fit residues: 237.1669 Evaluate side-chains 290 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 4.703 ------------------------------------------------------------------------------- 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 286 THR 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 88 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 286 THR Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 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 286 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 240 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 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 80 GLN E 279 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN G 279 GLN M 80 GLN O 279 GLN ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.195556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.168933 restraints weight = 33275.368| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.60 r_work: 0.3568 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29170 Z= 0.141 Angle : 0.503 8.632 39670 Z= 0.261 Chirality : 0.039 0.150 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.709 74.152 4920 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.38 % Allowed : 12.01 % Favored : 86.61 % 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: 1.01 (0.15), residues: 3470 helix: 1.36 (0.11), residues: 2380 sheet: -1.48 (0.32), residues: 190 loop : -0.56 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 123 HIS 0.004 0.001 HIS E 7 PHE 0.011 0.002 PHE M 169 TYR 0.017 0.002 TYR C 354 ARG 0.003 0.000 ARG O 27 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 1680) hydrogen bonds : angle 4.24003 ( 4950) covalent geometry : bond 0.00328 (29170) covalent geometry : angle 0.50344 (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 342 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7571 (tpp) cc_final: 0.7207 (tmm) REVERT: C 258 MET cc_start: 0.8657 (mmm) cc_final: 0.7900 (mmm) REVERT: E 94 LEU cc_start: 0.7964 (tp) cc_final: 0.7563 (tt) REVERT: E 337 MET cc_start: 0.7551 (tpp) cc_final: 0.7153 (tmm) REVERT: G 337 MET cc_start: 0.7647 (tpp) cc_final: 0.7083 (tmm) REVERT: G 338 TYR cc_start: 0.7703 (t80) cc_final: 0.7455 (t80) REVERT: I 94 LEU cc_start: 0.7971 (tp) cc_final: 0.7399 (tt) REVERT: I 279 GLN cc_start: 0.7461 (mm110) cc_final: 0.7169 (mm-40) REVERT: I 337 MET cc_start: 0.7672 (tpp) cc_final: 0.7314 (tmm) REVERT: K 337 MET cc_start: 0.7548 (tpp) cc_final: 0.7190 (tmm) REVERT: K 338 TYR cc_start: 0.7907 (t80) cc_final: 0.7380 (t80) REVERT: M 85 ASN cc_start: 0.8002 (m110) cc_final: 0.7622 (m110) REVERT: M 258 MET cc_start: 0.8644 (mmm) cc_final: 0.7862 (mmm) REVERT: M 337 MET cc_start: 0.7636 (tpp) cc_final: 0.7147 (tmm) REVERT: Q 337 MET cc_start: 0.7668 (tpp) cc_final: 0.7097 (tmm) REVERT: Q 338 TYR cc_start: 0.7703 (t80) cc_final: 0.7456 (t80) REVERT: S 94 LEU cc_start: 0.7990 (tp) cc_final: 0.7425 (tt) REVERT: S 279 GLN cc_start: 0.7492 (mm110) cc_final: 0.7185 (mm-40) REVERT: S 337 MET cc_start: 0.7741 (tpp) cc_final: 0.7307 (tmm) outliers start: 41 outliers final: 22 residues processed: 332 average time/residue: 0.3740 time to fit residues: 206.3047 Evaluate side-chains 297 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 3.004 ------------------------------------------------------------------------------- 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 88 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 120 optimal weight: 0.9990 chunk 272 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 242 optimal weight: 0.5980 chunk 270 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 344 ASN G 306 GLN I 41 GLN I 150 GLN K 85 ASN O 85 ASN O 344 ASN Q 306 GLN S 150 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.195810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167862 restraints weight = 33320.453| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.71 r_work: 0.3558 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29170 Z= 0.134 Angle : 0.504 7.461 39670 Z= 0.260 Chirality : 0.039 0.131 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.707 74.067 4920 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.91 % Allowed : 12.95 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.15), residues: 3470 helix: 1.43 (0.11), residues: 2390 sheet: -1.40 (0.32), residues: 190 loop : -0.71 (0.21), residues: 890 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 0.010 0.002 PHE C 169 TYR 0.018 0.002 TYR C 354 ARG 0.003 0.000 ARG S 27 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1680) hydrogen bonds : angle 4.17044 ( 4950) covalent geometry : bond 0.00312 (29170) covalent geometry : angle 0.50407 (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 327 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8509 (tp40) cc_final: 0.8261 (tp40) REVERT: A 85 ASN cc_start: 0.8231 (m-40) cc_final: 0.7744 (t0) REVERT: A 337 MET cc_start: 0.7580 (tpp) cc_final: 0.7195 (tmm) REVERT: C 55 LYS cc_start: 0.8218 (tttm) cc_final: 0.7889 (tppt) REVERT: C 258 MET cc_start: 0.8687 (mmm) cc_final: 0.8021 (mmm) REVERT: E 55 LYS cc_start: 0.7839 (tttm) cc_final: 0.7630 (tppt) REVERT: E 337 MET cc_start: 0.7547 (tpp) cc_final: 0.7049 (tmm) REVERT: G 337 MET cc_start: 0.7692 (tpp) cc_final: 0.7072 (tmm) REVERT: G 338 TYR cc_start: 0.7731 (t80) cc_final: 0.7079 (t80) REVERT: I 337 MET cc_start: 0.7706 (tpp) cc_final: 0.7297 (tmm) REVERT: K 80 GLN cc_start: 0.8505 (tp40) cc_final: 0.8267 (tp40) REVERT: K 85 ASN cc_start: 0.8259 (m-40) cc_final: 0.7767 (t0) REVERT: K 337 MET cc_start: 0.7581 (tpp) cc_final: 0.7204 (tmm) REVERT: M 55 LYS cc_start: 0.8236 (tttm) cc_final: 0.7911 (tppt) REVERT: M 85 ASN cc_start: 0.7951 (m110) cc_final: 0.7585 (m110) REVERT: M 258 MET cc_start: 0.8675 (mmm) cc_final: 0.7979 (mmm) REVERT: M 337 MET cc_start: 0.7593 (tpp) cc_final: 0.7107 (tmm) REVERT: O 55 LYS cc_start: 0.7837 (tttm) cc_final: 0.7615 (tppt) REVERT: Q 337 MET cc_start: 0.7721 (tpp) cc_final: 0.7105 (tmm) REVERT: Q 338 TYR cc_start: 0.7733 (t80) cc_final: 0.7076 (t80) REVERT: S 337 MET cc_start: 0.7743 (tpp) cc_final: 0.7302 (tmm) outliers start: 27 outliers final: 21 residues processed: 323 average time/residue: 0.3695 time to fit residues: 197.6547 Evaluate side-chains 305 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 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 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 68 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 344 ASN S 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.167517 restraints weight = 33081.813| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.54 r_work: 0.3576 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2526 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= 0.140 Angle : 0.513 6.992 39670 Z= 0.263 Chirality : 0.039 0.193 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.703 74.091 4920 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.74 % Allowed : 13.29 % Favored : 85.97 % 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: 1.10 (0.15), residues: 3470 helix: 1.45 (0.11), residues: 2380 sheet: -1.46 (0.32), residues: 190 loop : -0.60 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 123 HIS 0.003 0.001 HIS E 7 PHE 0.011 0.002 PHE M 169 TYR 0.019 0.002 TYR C 354 ARG 0.003 0.000 ARG I 27 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1680) hydrogen bonds : angle 4.17225 ( 4950) covalent geometry : bond 0.00326 (29170) covalent geometry : angle 0.51251 (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 326 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8212 (m-40) cc_final: 0.7773 (t0) REVERT: A 337 MET cc_start: 0.7569 (tpp) cc_final: 0.7219 (tmm) REVERT: C 55 LYS cc_start: 0.8212 (tttm) cc_final: 0.7908 (tppt) REVERT: C 354 TYR cc_start: 0.6918 (t80) cc_final: 0.6662 (t80) REVERT: G 337 MET cc_start: 0.7655 (tpp) cc_final: 0.7083 (tmm) REVERT: G 338 TYR cc_start: 0.7663 (t80) cc_final: 0.7038 (t80) REVERT: I 55 LYS cc_start: 0.8060 (tttm) cc_final: 0.7749 (tppt) REVERT: I 337 MET cc_start: 0.7665 (tpp) cc_final: 0.7307 (tmm) REVERT: K 81 GLN cc_start: 0.8416 (tt0) cc_final: 0.8212 (tt0) REVERT: K 85 ASN cc_start: 0.8223 (m-40) cc_final: 0.7793 (t0) REVERT: K 337 MET cc_start: 0.7560 (tpp) cc_final: 0.7210 (tmm) REVERT: M 55 LYS cc_start: 0.8260 (tttm) cc_final: 0.7941 (tppt) REVERT: M 81 GLN cc_start: 0.8394 (tt0) cc_final: 0.8173 (tt0) REVERT: M 337 MET cc_start: 0.7457 (tpp) cc_final: 0.7106 (tmm) REVERT: Q 337 MET cc_start: 0.7677 (tpp) cc_final: 0.7120 (tmm) REVERT: Q 338 TYR cc_start: 0.7595 (t80) cc_final: 0.7034 (t80) REVERT: S 337 MET cc_start: 0.7706 (tpp) cc_final: 0.7317 (tmm) outliers start: 22 outliers final: 22 residues processed: 321 average time/residue: 0.3901 time to fit residues: 207.4100 Evaluate side-chains 313 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 291 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 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 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 83 optimal weight: 0.4980 chunk 216 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 M 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168338 restraints weight = 33006.208| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.71 r_work: 0.3561 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29170 Z= 0.132 Angle : 0.509 6.797 39670 Z= 0.261 Chirality : 0.039 0.171 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.700 74.032 4920 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.94 % Allowed : 13.52 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.33), residues: 190 loop : -0.59 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 123 HIS 0.006 0.001 HIS C 117 PHE 0.010 0.002 PHE K 169 TYR 0.018 0.002 TYR C 354 ARG 0.003 0.000 ARG S 27 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 1680) hydrogen bonds : angle 4.13500 ( 4950) covalent geometry : bond 0.00307 (29170) covalent geometry : angle 0.50851 (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 327 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.7660 (tpp) cc_final: 0.7247 (tmm) REVERT: C 55 LYS cc_start: 0.8197 (tttm) cc_final: 0.7865 (tppt) REVERT: C 85 ASN cc_start: 0.8097 (m110) cc_final: 0.7711 (m110) REVERT: C 354 TYR cc_start: 0.6930 (t80) cc_final: 0.6719 (t80) REVERT: G 55 LYS cc_start: 0.8164 (tttm) cc_final: 0.7869 (tppt) REVERT: G 337 MET cc_start: 0.7701 (tpp) cc_final: 0.7070 (tmm) REVERT: G 338 TYR cc_start: 0.7579 (t80) cc_final: 0.6941 (t80) REVERT: I 55 LYS cc_start: 0.8045 (tttm) cc_final: 0.7721 (tppt) REVERT: I 337 MET cc_start: 0.7652 (tpp) cc_final: 0.7304 (tmm) REVERT: K 85 ASN cc_start: 0.8144 (m-40) cc_final: 0.7770 (t0) REVERT: K 337 MET cc_start: 0.7613 (tpp) cc_final: 0.7240 (tmm) REVERT: M 55 LYS cc_start: 0.8222 (tttm) cc_final: 0.7889 (tppt) REVERT: M 81 GLN cc_start: 0.8343 (tt0) cc_final: 0.7895 (tt0) REVERT: M 85 ASN cc_start: 0.8090 (m110) cc_final: 0.7715 (m110) REVERT: M 337 MET cc_start: 0.7516 (tpp) cc_final: 0.7102 (tmm) REVERT: Q 55 LYS cc_start: 0.8193 (tttm) cc_final: 0.7888 (tppt) REVERT: Q 337 MET cc_start: 0.7686 (tpp) cc_final: 0.7091 (tmm) REVERT: Q 338 TYR cc_start: 0.7604 (t80) cc_final: 0.6971 (t80) REVERT: S 337 MET cc_start: 0.7703 (tpp) cc_final: 0.7316 (tmm) outliers start: 28 outliers final: 22 residues processed: 320 average time/residue: 0.4340 time to fit residues: 230.6430 Evaluate side-chains 304 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 282 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU 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 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 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 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 42 GLN 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 164 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 254 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 273 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN I 344 ASN M 80 GLN S 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.195827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166929 restraints weight = 32973.039| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.59 r_work: 0.3575 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29170 Z= 0.139 Angle : 0.516 9.814 39670 Z= 0.264 Chirality : 0.039 0.154 4680 Planarity : 0.004 0.044 4810 Dihedral : 11.701 74.077 4920 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.87 % Allowed : 14.30 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.11), residues: 2380 sheet: -1.36 (0.32), residues: 190 loop : -0.61 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 123 HIS 0.003 0.001 HIS G 117 PHE 0.011 0.002 PHE M 169 TYR 0.017 0.002 TYR C 354 ARG 0.003 0.000 ARG I 27 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 1680) hydrogen bonds : angle 4.15241 ( 4950) covalent geometry : bond 0.00325 (29170) covalent geometry : angle 0.51604 (39670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16054.44 seconds wall clock time: 282 minutes 47.40 seconds (16967.40 seconds total)