Starting phenix.real_space_refine on Wed May 28 20:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdm_17614/05_2025/8pdm_17614.cif" } resolution = 3.3 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= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 121 5.16 5 C 19602 2.51 5 N 5445 2.21 5 O 6226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31471 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'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, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 9.12, per 1000 atoms: 0.29 Number of scatterers: 31471 At special positions: 0 Unit cell: (199.5, 200.55, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 77 15.00 O 6226 8.00 N 5445 7.00 C 19602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.53 Conformation dependent library (CDL) restraints added in 3.6 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 22 sheets defined 68.4% alpha, 2.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.01 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 361 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 361 Processing helix chain 'K' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 361 Processing helix chain 'M' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR M 13 " --> pdb=" O SER M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU M 46 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 141 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 175 through 191 removed outlier: 4.032A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR O 13 " --> pdb=" O SER O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU O 46 " --> pdb=" O GLN O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 141 Processing helix chain 'O' and resid 156 through 170 Processing helix chain 'O' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG O 189 " --> pdb=" O ARG O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 198 Processing helix chain 'O' and resid 202 through 217 Processing helix chain 'O' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER O 222 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 251 Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG O 260 " --> pdb=" O GLN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 274 Processing helix chain 'O' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY O 300 " --> pdb=" O PRO O 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 297 through 300' Processing helix chain 'O' and resid 318 through 332 Processing helix chain 'O' and resid 344 through 361 Processing helix chain 'Q' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR Q 13 " --> pdb=" O SER Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 141 Processing helix chain 'Q' and resid 156 through 170 Processing helix chain 'Q' and resid 175 through 191 removed outlier: 4.034A pdb=" N ARG Q 189 " --> pdb=" O ARG Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 198 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER Q 222 " --> pdb=" O VAL Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 251 Processing helix chain 'Q' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG Q 260 " --> pdb=" O GLN Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 274 Processing helix chain 'Q' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY Q 300 " --> pdb=" O PRO Q 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 297 through 300' Processing helix chain 'Q' and resid 318 through 332 Processing helix chain 'Q' and resid 344 through 361 Processing helix chain 'S' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR S 13 " --> pdb=" O SER S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU S 46 " --> pdb=" O GLN S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 141 Processing helix chain 'S' and resid 156 through 170 Processing helix chain 'S' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'U' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR U 13 " --> pdb=" O SER U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU U 46 " --> pdb=" O GLN U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 75 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'U' and resid 120 through 141 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'U' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG U 189 " --> pdb=" O ARG U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 198 Processing helix chain 'U' and resid 202 through 217 Processing helix chain 'U' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER U 222 " --> pdb=" O VAL U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 251 Processing helix chain 'U' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG U 260 " --> pdb=" O GLN U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 274 Processing helix chain 'U' and resid 275 through 296 removed outlier: 4.527A pdb=" N LYS U 283 " --> pdb=" O GLN U 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY U 300 " --> pdb=" O PRO U 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 297 through 300' Processing helix chain 'U' and resid 318 through 332 Processing helix chain 'U' and resid 344 through 361 Processing sheet with id=1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'M' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG M 96 " --> pdb=" O ASP M 115 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR O 33 " --> pdb=" O VAL O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'O' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG O 96 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Q' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR Q 33 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG Q 96 " --> pdb=" O ASP Q 115 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'S' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'U' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR U 33 " --> pdb=" O VAL U 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'U' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG U 96 " --> pdb=" O ASP U 115 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.54 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10136 1.34 - 1.45: 4378 1.45 - 1.57: 17210 1.57 - 1.69: 154 1.69 - 1.80: 209 Bond restraints: 32087 Sorted by residual: bond pdb=" CB VAL U 325 " pdb=" CG1 VAL U 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CB VAL O 325 " pdb=" CG1 VAL O 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.53e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CB VAL M 325 " pdb=" CG1 VAL M 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 bond pdb=" CB VAL I 325 " pdb=" CG1 VAL I 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 32082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 39930 1.18 - 2.37: 2935 2.37 - 3.55: 587 3.55 - 4.74: 147 4.74 - 5.92: 38 Bond angle restraints: 43637 Sorted by residual: angle pdb=" CA TYR O 61 " pdb=" CB TYR O 61 " pdb=" CG TYR O 61 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR K 61 " pdb=" CB TYR K 61 " pdb=" CG TYR K 61 " ideal model delta sigma weight residual 113.90 118.65 -4.75 1.80e+00 3.09e-01 6.96e+00 angle pdb=" CA TYR S 61 " pdb=" CB TYR S 61 " pdb=" CG TYR S 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.93e+00 angle pdb=" CA TYR I 61 " pdb=" CB TYR I 61 " pdb=" CG TYR I 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.92e+00 angle pdb=" CA TYR E 61 " pdb=" CB TYR E 61 " pdb=" CG TYR E 61 " ideal model delta sigma weight residual 113.90 118.63 -4.73 1.80e+00 3.09e-01 6.92e+00 ... (remaining 43632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17412 16.60 - 33.20: 1806 33.20 - 49.80: 263 49.80 - 66.40: 143 66.40 - 83.00: 132 Dihedral angle restraints: 19756 sinusoidal: 8580 harmonic: 11176 Sorted by residual: dihedral pdb=" CA TYR I 59 " pdb=" C TYR I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR G 59 " pdb=" C TYR G 59 " pdb=" N LYS G 60 " pdb=" CA LYS G 60 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR Q 59 " pdb=" C TYR Q 59 " pdb=" N LYS Q 60 " pdb=" CA LYS Q 60 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2884 0.034 - 0.068: 1519 0.068 - 0.102: 546 0.102 - 0.136: 177 0.136 - 0.171: 22 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C1' C P 75 " pdb=" O4' C P 75 " pdb=" C2' C P 75 " pdb=" N1 C P 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" C1' C N 75 " pdb=" O4' C N 75 " pdb=" C2' C N 75 " pdb=" N1 C N 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C1' C D 75 " pdb=" O4' C D 75 " pdb=" C2' C D 75 " pdb=" N1 C D 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 5145 not shown) Planarity restraints: 5291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY S 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLY S 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY S 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS S 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY G 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY G 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY Q 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY Q 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 229 " 0.018 2.00e-02 2.50e+03 ... (remaining 5288 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.36: 121 1.36 - 2.25: 352 2.25 - 3.13: 26184 3.13 - 4.02: 84872 4.02 - 4.90: 156081 Warning: very small nonbonded interaction distances. Nonbonded interactions: 267610 Sorted by model distance: nonbonded pdb=" C3' C J 77 " pdb=" OP1 C L 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C F 77 " pdb=" OP1 C H 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C T 77 " pdb=" OP1 C V 71 " model vdw 0.481 3.470 nonbonded pdb=" C3' C R 77 " pdb=" OP1 C T 71 " model vdw 0.481 3.470 nonbonded pdb=" OP1 C B 71 " pdb=" C3' C V 77 " model vdw 0.481 3.470 ... (remaining 267605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.28 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 63.990 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.151 32098 Z= 2.146 Angle : 0.733 5.921 43637 Z= 0.417 Chirality : 0.047 0.171 5148 Planarity : 0.006 0.052 5291 Dihedral : 15.484 82.999 12584 Min Nonbonded Distance : 0.481 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.13), residues: 3817 helix: 1.00 (0.10), residues: 2464 sheet: -1.19 (0.33), residues: 165 loop : -0.11 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 261 HIS 0.003 0.001 HIS U 275 PHE 0.013 0.003 PHE U 214 TYR 0.027 0.003 TYR E 61 ARG 0.007 0.001 ARG S 208 Details of bonding type rmsd hydrogen bonds : bond 0.11926 ( 1826) hydrogen bonds : angle 5.93484 ( 5379) covalent geometry : bond 0.00609 (32087) covalent geometry : angle 0.73258 (43637) Misc. bond : bond 1.15083 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7370 (ttp-110) REVERT: A 347 LEU cc_start: 0.8262 (mt) cc_final: 0.7951 (mt) REVERT: G 138 LEU cc_start: 0.8331 (mp) cc_final: 0.8064 (mp) REVERT: I 53 TYR cc_start: 0.6244 (p90) cc_final: 0.6003 (p90) REVERT: I 138 LEU cc_start: 0.8393 (mp) cc_final: 0.8159 (mp) REVERT: I 249 MET cc_start: 0.7609 (mmm) cc_final: 0.7024 (mmm) REVERT: K 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8360 (mp) REVERT: M 39 SER cc_start: 0.8582 (m) cc_final: 0.8338 (p) REVERT: M 84 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: M 249 MET cc_start: 0.7274 (mmm) cc_final: 0.6836 (mmm) REVERT: O 7 HIS cc_start: 0.7683 (t70) cc_final: 0.7452 (t70) REVERT: Q 138 LEU cc_start: 0.8545 (mp) cc_final: 0.8304 (mp) REVERT: S 249 MET cc_start: 0.7544 (mmm) cc_final: 0.7133 (mmm) REVERT: U 39 SER cc_start: 0.8580 (m) cc_final: 0.8320 (p) REVERT: U 138 LEU cc_start: 0.8580 (mp) cc_final: 0.8334 (mp) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.4733 time to fit residues: 393.3892 Evaluate side-chains 391 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 301 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 349 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 148 GLN A 306 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 306 GLN E 80 GLN E 306 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 306 GLN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN I 80 GLN I 306 GLN ** I 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 306 GLN ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN M 148 GLN M 306 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 148 GLN O 306 GLN ** O 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN Q 306 GLN ** Q 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN S 306 GLN ** S 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 306 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.166803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137714 restraints weight = 42841.322| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.39 r_work: 0.3398 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32098 Z= 0.159 Angle : 0.590 12.617 43637 Z= 0.309 Chirality : 0.042 0.223 5148 Planarity : 0.007 0.108 5291 Dihedral : 14.108 167.775 5412 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.28 % Allowed : 6.71 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.14), residues: 3817 helix: 1.34 (0.11), residues: 2519 sheet: -0.69 (0.34), residues: 165 loop : -0.10 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 261 HIS 0.007 0.001 HIS O 117 PHE 0.025 0.002 PHE A 348 TYR 0.017 0.002 TYR K 23 ARG 0.004 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 1826) hydrogen bonds : angle 4.57887 ( 5379) covalent geometry : bond 0.00355 (32087) covalent geometry : angle 0.59019 (43637) Misc. bond : bond 0.00188 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 484 time to evaluate : 4.508 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 80 GLN cc_start: 0.8803 (tp40) cc_final: 0.8004 (tt0) REVERT: A 249 MET cc_start: 0.7790 (mmm) cc_final: 0.7520 (mmm) REVERT: A 347 LEU cc_start: 0.8411 (mt) cc_final: 0.8194 (mt) REVERT: C 80 GLN cc_start: 0.8916 (tp40) cc_final: 0.8220 (tt0) REVERT: C 115 ASP cc_start: 0.6609 (t70) cc_final: 0.6390 (t70) REVERT: C 249 MET cc_start: 0.7690 (mmm) cc_final: 0.7438 (mmm) REVERT: E 53 TYR cc_start: 0.6910 (p90) cc_final: 0.6700 (p90) REVERT: E 80 GLN cc_start: 0.8791 (tp40) cc_final: 0.8043 (tt0) REVERT: E 290 ASP cc_start: 0.8280 (m-30) cc_final: 0.7988 (m-30) REVERT: G 80 GLN cc_start: 0.8790 (tp40) cc_final: 0.8072 (tt0) REVERT: G 138 LEU cc_start: 0.8495 (mp) cc_final: 0.8124 (mp) REVERT: I 53 TYR cc_start: 0.6594 (p90) cc_final: 0.6113 (p90) REVERT: I 80 GLN cc_start: 0.8831 (tp40) cc_final: 0.8156 (tt0) REVERT: I 115 ASP cc_start: 0.6450 (t70) cc_final: 0.6238 (t70) REVERT: I 138 LEU cc_start: 0.8356 (mp) cc_final: 0.8152 (mp) REVERT: I 151 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7281 (ptp-170) REVERT: I 249 MET cc_start: 0.7884 (mmm) cc_final: 0.7543 (mmm) REVERT: K 80 GLN cc_start: 0.8941 (tp40) cc_final: 0.8189 (tt0) REVERT: M 80 GLN cc_start: 0.8854 (tp40) cc_final: 0.8081 (tt0) REVERT: M 115 ASP cc_start: 0.6355 (t70) cc_final: 0.5831 (t70) REVERT: O 80 GLN cc_start: 0.8842 (tp40) cc_final: 0.8067 (tt0) REVERT: O 249 MET cc_start: 0.7755 (mmm) cc_final: 0.7494 (mmm) REVERT: Q 80 GLN cc_start: 0.8865 (tp40) cc_final: 0.8111 (tt0) REVERT: Q 138 LEU cc_start: 0.8442 (mp) cc_final: 0.8199 (mp) REVERT: Q 200 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.7084 (mtm-85) REVERT: S 80 GLN cc_start: 0.8940 (tp40) cc_final: 0.8223 (tt0) REVERT: S 249 MET cc_start: 0.7801 (mmm) cc_final: 0.7522 (mmm) REVERT: U 78 ARG cc_start: 0.7326 (tpt170) cc_final: 0.7120 (tpp80) REVERT: U 80 GLN cc_start: 0.8836 (tp40) cc_final: 0.8084 (tt0) REVERT: U 138 LEU cc_start: 0.8694 (mp) cc_final: 0.8369 (mp) outliers start: 42 outliers final: 10 residues processed: 495 average time/residue: 0.4920 time to fit residues: 370.7119 Evaluate side-chains 425 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 415 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 10 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 378 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 284 GLN K 148 GLN M 148 GLN M 284 GLN Q 148 GLN Q 284 GLN S 284 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135815 restraints weight = 43110.694| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.74 r_work: 0.3312 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32098 Z= 0.146 Angle : 0.532 11.050 43637 Z= 0.276 Chirality : 0.040 0.176 5148 Planarity : 0.005 0.051 5291 Dihedral : 14.174 177.940 5412 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.49 % Allowed : 10.71 % Favored : 87.80 % 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: 1.34 (0.14), residues: 3817 helix: 1.48 (0.11), residues: 2530 sheet: -0.51 (0.35), residues: 165 loop : -0.11 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP M 261 HIS 0.007 0.001 HIS O 275 PHE 0.032 0.002 PHE K 348 TYR 0.013 0.002 TYR M 53 ARG 0.008 0.001 ARG M 151 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1826) hydrogen bonds : angle 4.35831 ( 5379) covalent geometry : bond 0.00333 (32087) covalent geometry : angle 0.53202 (43637) Misc. bond : bond 0.00037 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 483 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7774 (tp30) cc_final: 0.7538 (tp30) REVERT: A 80 GLN cc_start: 0.8685 (tp40) cc_final: 0.7981 (tt0) REVERT: A 115 ASP cc_start: 0.6085 (t70) cc_final: 0.5656 (t70) REVERT: A 346 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 347 LEU cc_start: 0.8496 (mt) cc_final: 0.8075 (mt) REVERT: C 80 GLN cc_start: 0.8835 (tp40) cc_final: 0.8145 (tt0) REVERT: C 249 MET cc_start: 0.7675 (mmm) cc_final: 0.7393 (mmm) REVERT: C 338 TYR cc_start: 0.7174 (t80) cc_final: 0.6827 (t80) REVERT: C 346 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7847 (tt0) REVERT: E 23 TYR cc_start: 0.5434 (m-80) cc_final: 0.5035 (m-80) REVERT: E 53 TYR cc_start: 0.6739 (p90) cc_final: 0.6326 (p90) REVERT: E 80 GLN cc_start: 0.8773 (tp40) cc_final: 0.8059 (tt0) REVERT: E 290 ASP cc_start: 0.8195 (m-30) cc_final: 0.7690 (m-30) REVERT: G 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8095 (tt0) REVERT: G 138 LEU cc_start: 0.8311 (mp) cc_final: 0.7922 (mp) REVERT: I 53 TYR cc_start: 0.6730 (p90) cc_final: 0.6413 (p90) REVERT: I 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8116 (tt0) REVERT: I 128 ASP cc_start: 0.7491 (t70) cc_final: 0.7235 (t0) REVERT: I 138 LEU cc_start: 0.8337 (mp) cc_final: 0.8066 (mp) REVERT: I 249 MET cc_start: 0.7839 (mmm) cc_final: 0.7172 (mmm) REVERT: K 80 GLN cc_start: 0.8857 (tp40) cc_final: 0.8164 (tt0) REVERT: K 347 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7803 (mt) REVERT: M 80 GLN cc_start: 0.8700 (tp40) cc_final: 0.8044 (tt0) REVERT: M 113 MET cc_start: 0.4416 (mtp) cc_final: 0.4167 (mtm) REVERT: O 80 GLN cc_start: 0.8761 (tp40) cc_final: 0.7978 (tt0) REVERT: O 249 MET cc_start: 0.7667 (mmm) cc_final: 0.7360 (mmm) REVERT: O 344 ASN cc_start: 0.6809 (t0) cc_final: 0.6496 (t0) REVERT: O 347 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7250 (mm) REVERT: Q 80 GLN cc_start: 0.8770 (tp40) cc_final: 0.8054 (tt0) REVERT: Q 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8263 (mp) REVERT: Q 200 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.7250 (mtm110) REVERT: S 78 ARG cc_start: 0.7090 (tpt170) cc_final: 0.6861 (tpp-160) REVERT: S 80 GLN cc_start: 0.8799 (tp40) cc_final: 0.8167 (tt0) REVERT: S 249 MET cc_start: 0.7583 (mmm) cc_final: 0.7234 (mmm) REVERT: U 80 GLN cc_start: 0.8679 (tp40) cc_final: 0.7997 (tt0) REVERT: U 113 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3971 (mtm) REVERT: U 138 LEU cc_start: 0.8677 (mp) cc_final: 0.8346 (mp) REVERT: U 151 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7143 (ptp-170) outliers start: 49 outliers final: 22 residues processed: 496 average time/residue: 0.4910 time to fit residues: 365.6192 Evaluate side-chains 445 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 419 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 290 ASP Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 337 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 202 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS C 344 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 ASN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN M 344 ASN ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135723 restraints weight = 43208.240| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.49 r_work: 0.3310 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 32098 Z= 0.207 Angle : 0.583 12.048 43637 Z= 0.299 Chirality : 0.042 0.148 5148 Planarity : 0.006 0.192 5291 Dihedral : 14.113 178.908 5412 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.62 % Allowed : 12.08 % Favored : 85.30 % 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: 1.20 (0.14), residues: 3817 helix: 1.37 (0.11), residues: 2530 sheet: -0.28 (0.37), residues: 165 loop : -0.22 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 261 HIS 0.008 0.001 HIS Q 117 PHE 0.028 0.003 PHE C 348 TYR 0.039 0.002 TYR G 23 ARG 0.005 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1826) hydrogen bonds : angle 4.42709 ( 5379) covalent geometry : bond 0.00486 (32087) covalent geometry : angle 0.58257 (43637) Misc. bond : bond 0.00246 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 429 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8580 (tp40) cc_final: 0.7862 (tt0) REVERT: A 249 MET cc_start: 0.7536 (mmm) cc_final: 0.7254 (mmm) REVERT: A 346 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 80 GLN cc_start: 0.8679 (tp40) cc_final: 0.8015 (tt0) REVERT: C 249 MET cc_start: 0.7588 (mmm) cc_final: 0.7357 (mmm) REVERT: C 338 TYR cc_start: 0.7225 (t80) cc_final: 0.6995 (t80) REVERT: C 346 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7788 (tt0) REVERT: E 53 TYR cc_start: 0.6666 (p90) cc_final: 0.6324 (p90) REVERT: E 80 GLN cc_start: 0.8573 (tp40) cc_final: 0.7905 (tt0) REVERT: G 80 GLN cc_start: 0.8674 (tp40) cc_final: 0.8050 (tt0) REVERT: G 138 LEU cc_start: 0.8414 (mp) cc_final: 0.8049 (mp) REVERT: G 200 ARG cc_start: 0.7305 (ptp90) cc_final: 0.7058 (mtm-85) REVERT: I 80 GLN cc_start: 0.8648 (tp40) cc_final: 0.8030 (tt0) REVERT: I 128 ASP cc_start: 0.7622 (t70) cc_final: 0.7339 (t0) REVERT: I 249 MET cc_start: 0.7719 (mmm) cc_final: 0.7172 (mmm) REVERT: K 80 GLN cc_start: 0.8717 (tp40) cc_final: 0.8045 (tt0) REVERT: K 344 ASN cc_start: 0.6906 (t0) cc_final: 0.6568 (t0) REVERT: K 347 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7437 (mm) REVERT: M 80 GLN cc_start: 0.8613 (tp40) cc_final: 0.7965 (tt0) REVERT: O 80 GLN cc_start: 0.8712 (tp40) cc_final: 0.8015 (tt0) REVERT: O 249 MET cc_start: 0.7610 (mmm) cc_final: 0.7316 (mmm) REVERT: Q 80 GLN cc_start: 0.8641 (tp40) cc_final: 0.7963 (tt0) REVERT: Q 138 LEU cc_start: 0.8661 (mp) cc_final: 0.8446 (mp) REVERT: Q 200 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7222 (mtm110) REVERT: S 80 GLN cc_start: 0.8688 (tp40) cc_final: 0.8087 (tt0) REVERT: S 249 MET cc_start: 0.7507 (mmm) cc_final: 0.7216 (mmm) REVERT: U 80 GLN cc_start: 0.8581 (tp40) cc_final: 0.7941 (tt0) REVERT: U 113 MET cc_start: 0.4602 (mtp) cc_final: 0.4215 (mtm) REVERT: U 138 LEU cc_start: 0.8658 (mp) cc_final: 0.8297 (mp) REVERT: U 151 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7278 (ptp-170) outliers start: 86 outliers final: 54 residues processed: 469 average time/residue: 0.4983 time to fit residues: 353.3737 Evaluate side-chains 460 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 404 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 337 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 290 ASP Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 358 LEU Chi-restraints excluded: chain S residue 23 TYR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 86 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 343 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 365 optimal weight: 0.8980 chunk 242 optimal weight: 0.0970 chunk 16 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN C 148 GLN E 148 GLN G 344 ASN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135721 restraints weight = 42949.046| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.75 r_work: 0.3301 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32098 Z= 0.127 Angle : 0.508 11.987 43637 Z= 0.263 Chirality : 0.039 0.150 5148 Planarity : 0.005 0.107 5291 Dihedral : 14.081 178.814 5412 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 14.37 % Favored : 83.77 % 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: 1.43 (0.14), residues: 3817 helix: 1.59 (0.11), residues: 2541 sheet: -0.34 (0.37), residues: 165 loop : -0.23 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP Q 261 HIS 0.031 0.001 HIS C 275 PHE 0.032 0.002 PHE I 348 TYR 0.018 0.001 TYR G 23 ARG 0.007 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1826) hydrogen bonds : angle 4.23699 ( 5379) covalent geometry : bond 0.00289 (32087) covalent geometry : angle 0.50757 (43637) Misc. bond : bond 0.00118 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 415 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8658 (tp40) cc_final: 0.7948 (tt0) REVERT: C 80 GLN cc_start: 0.8832 (tp40) cc_final: 0.8138 (tt0) REVERT: C 113 MET cc_start: 0.4682 (mtp) cc_final: 0.4462 (mtm) REVERT: C 249 MET cc_start: 0.7693 (mmm) cc_final: 0.7445 (mmm) REVERT: E 53 TYR cc_start: 0.6814 (p90) cc_final: 0.6246 (p90) REVERT: E 80 GLN cc_start: 0.8707 (tp40) cc_final: 0.8077 (tt0) REVERT: E 249 MET cc_start: 0.7945 (mmm) cc_final: 0.7635 (mmm) REVERT: G 80 GLN cc_start: 0.8789 (tp40) cc_final: 0.8110 (tt0) REVERT: G 138 LEU cc_start: 0.8397 (mp) cc_final: 0.8027 (mp) REVERT: I 80 GLN cc_start: 0.8710 (tp40) cc_final: 0.8070 (tt0) REVERT: I 128 ASP cc_start: 0.7525 (t70) cc_final: 0.7272 (t0) REVERT: I 249 MET cc_start: 0.7803 (mmm) cc_final: 0.7276 (mmm) REVERT: K 80 GLN cc_start: 0.8783 (tp40) cc_final: 0.8118 (tt0) REVERT: K 344 ASN cc_start: 0.6697 (t0) cc_final: 0.6460 (t0) REVERT: M 80 GLN cc_start: 0.8616 (tp40) cc_final: 0.7968 (tt0) REVERT: M 338 TYR cc_start: 0.7095 (t80) cc_final: 0.6782 (t80) REVERT: O 50 GLU cc_start: 0.7678 (tp30) cc_final: 0.7474 (mm-30) REVERT: O 80 GLN cc_start: 0.8801 (tp40) cc_final: 0.8095 (tt0) REVERT: O 249 MET cc_start: 0.7681 (mmm) cc_final: 0.7391 (mmm) REVERT: O 347 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7591 (mt) REVERT: Q 80 GLN cc_start: 0.8698 (tp40) cc_final: 0.7996 (tt0) REVERT: Q 138 LEU cc_start: 0.8628 (mp) cc_final: 0.8216 (mp) REVERT: S 80 GLN cc_start: 0.8791 (tp40) cc_final: 0.8135 (tt0) REVERT: S 249 MET cc_start: 0.7570 (mmm) cc_final: 0.7287 (mmm) REVERT: U 80 GLN cc_start: 0.8692 (tp40) cc_final: 0.8024 (tt0) REVERT: U 113 MET cc_start: 0.4883 (mtp) cc_final: 0.4474 (mtm) REVERT: U 138 LEU cc_start: 0.8384 (mp) cc_final: 0.7955 (mp) REVERT: U 151 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7326 (ptp-170) outliers start: 61 outliers final: 40 residues processed: 443 average time/residue: 0.4982 time to fit residues: 333.9730 Evaluate side-chains 431 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 389 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain Q residue 358 LEU Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 383 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 chunk 340 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN C 250 GLN E 344 ASN G 148 GLN G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 GLN U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135905 restraints weight = 43199.679| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.68 r_work: 0.3313 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32098 Z= 0.133 Angle : 0.517 12.493 43637 Z= 0.265 Chirality : 0.038 0.143 5148 Planarity : 0.005 0.107 5291 Dihedral : 14.089 179.465 5412 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.95 % Allowed : 15.50 % Favored : 82.55 % 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: 1.51 (0.14), residues: 3817 helix: 1.67 (0.11), residues: 2541 sheet: -0.31 (0.36), residues: 165 loop : -0.26 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 261 HIS 0.007 0.001 HIS O 117 PHE 0.031 0.003 PHE I 348 TYR 0.012 0.001 TYR G 23 ARG 0.006 0.000 ARG K 78 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1826) hydrogen bonds : angle 4.20324 ( 5379) covalent geometry : bond 0.00304 (32087) covalent geometry : angle 0.51707 (43637) Misc. bond : bond 0.00152 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 397 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8619 (tp40) cc_final: 0.7912 (tt0) REVERT: A 249 MET cc_start: 0.7559 (mmm) cc_final: 0.7296 (mmm) REVERT: C 80 GLN cc_start: 0.8809 (tp40) cc_final: 0.8175 (tt0) REVERT: C 113 MET cc_start: 0.4573 (mtp) cc_final: 0.4218 (mtm) REVERT: C 249 MET cc_start: 0.7672 (mmm) cc_final: 0.7434 (mmm) REVERT: E 53 TYR cc_start: 0.6746 (p90) cc_final: 0.6433 (p90) REVERT: E 80 GLN cc_start: 0.8674 (tp40) cc_final: 0.8049 (tt0) REVERT: E 128 ASP cc_start: 0.7653 (t70) cc_final: 0.7415 (t0) REVERT: G 80 GLN cc_start: 0.8742 (tp40) cc_final: 0.8082 (tt0) REVERT: G 138 LEU cc_start: 0.8354 (mp) cc_final: 0.8003 (mp) REVERT: I 80 GLN cc_start: 0.8674 (tp40) cc_final: 0.8018 (tt0) REVERT: I 128 ASP cc_start: 0.7522 (t70) cc_final: 0.7287 (t0) REVERT: I 249 MET cc_start: 0.7785 (mmm) cc_final: 0.7238 (mmm) REVERT: K 80 GLN cc_start: 0.8759 (tp40) cc_final: 0.8113 (tt0) REVERT: K 344 ASN cc_start: 0.6724 (t0) cc_final: 0.6445 (t0) REVERT: M 80 GLN cc_start: 0.8593 (tp40) cc_final: 0.7946 (tt0) REVERT: M 338 TYR cc_start: 0.7032 (t80) cc_final: 0.6728 (t80) REVERT: O 80 GLN cc_start: 0.8785 (tp40) cc_final: 0.8099 (tt0) REVERT: O 249 MET cc_start: 0.7635 (mmm) cc_final: 0.7377 (mmm) REVERT: O 347 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7762 (mm) REVERT: Q 80 GLN cc_start: 0.8697 (tp40) cc_final: 0.8058 (tt0) REVERT: Q 138 LEU cc_start: 0.8561 (mp) cc_final: 0.8212 (mp) REVERT: Q 250 GLN cc_start: 0.8124 (mt0) cc_final: 0.7854 (mt0) REVERT: S 80 GLN cc_start: 0.8786 (tp40) cc_final: 0.8132 (tt0) REVERT: S 249 MET cc_start: 0.7556 (mmm) cc_final: 0.7256 (mmm) REVERT: U 80 GLN cc_start: 0.8619 (tp40) cc_final: 0.7962 (tt0) REVERT: U 113 MET cc_start: 0.4787 (mtp) cc_final: 0.4393 (mtm) REVERT: U 138 LEU cc_start: 0.8299 (mp) cc_final: 0.7868 (mp) REVERT: U 151 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7330 (ptp-170) outliers start: 64 outliers final: 47 residues processed: 425 average time/residue: 0.5099 time to fit residues: 326.0267 Evaluate side-chains 432 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 290 ASP Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 347 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 281 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 301 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 230 optimal weight: 0.2980 chunk 305 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 117 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135976 restraints weight = 43014.213| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.76 r_work: 0.3313 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32098 Z= 0.127 Angle : 0.524 13.202 43637 Z= 0.266 Chirality : 0.038 0.164 5148 Planarity : 0.005 0.107 5291 Dihedral : 14.101 179.525 5412 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.74 % Allowed : 16.05 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.14), residues: 3817 helix: 1.78 (0.11), residues: 2541 sheet: -0.36 (0.35), residues: 165 loop : -0.26 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 261 HIS 0.011 0.001 HIS U 275 PHE 0.032 0.002 PHE U 348 TYR 0.019 0.001 TYR E 23 ARG 0.011 0.000 ARG C 78 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1826) hydrogen bonds : angle 4.17783 ( 5379) covalent geometry : bond 0.00288 (32087) covalent geometry : angle 0.52424 (43637) Misc. bond : bond 0.00175 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8666 (tp40) cc_final: 0.7988 (tt0) REVERT: A 84 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7649 (ttp-110) REVERT: A 249 MET cc_start: 0.7563 (mmm) cc_final: 0.7316 (mmm) REVERT: C 80 GLN cc_start: 0.8839 (tp40) cc_final: 0.8122 (tt0) REVERT: C 113 MET cc_start: 0.4579 (mtp) cc_final: 0.4197 (mtm) REVERT: C 249 MET cc_start: 0.7696 (mmm) cc_final: 0.7479 (mmm) REVERT: E 80 GLN cc_start: 0.8715 (tp40) cc_final: 0.8065 (tt0) REVERT: E 249 MET cc_start: 0.7974 (mmm) cc_final: 0.7736 (mmm) REVERT: G 80 GLN cc_start: 0.8799 (tp40) cc_final: 0.8121 (tt0) REVERT: G 138 LEU cc_start: 0.8358 (mp) cc_final: 0.8003 (mp) REVERT: I 80 GLN cc_start: 0.8714 (tp40) cc_final: 0.8046 (tt0) REVERT: I 128 ASP cc_start: 0.7497 (t70) cc_final: 0.7285 (t0) REVERT: I 249 MET cc_start: 0.7826 (mmm) cc_final: 0.7289 (mmm) REVERT: K 80 GLN cc_start: 0.8792 (tp40) cc_final: 0.8132 (tt0) REVERT: K 344 ASN cc_start: 0.6688 (t0) cc_final: 0.6393 (t0) REVERT: M 80 GLN cc_start: 0.8649 (tp40) cc_final: 0.7970 (tt0) REVERT: M 151 ARG cc_start: 0.7183 (mtt90) cc_final: 0.6835 (mtm-85) REVERT: O 80 GLN cc_start: 0.8840 (tp40) cc_final: 0.8131 (tt0) REVERT: O 151 ARG cc_start: 0.7018 (mtt90) cc_final: 0.6711 (mtm-85) REVERT: O 249 MET cc_start: 0.7686 (mmm) cc_final: 0.7404 (mmm) REVERT: Q 80 GLN cc_start: 0.8722 (tp40) cc_final: 0.8069 (tt0) REVERT: Q 138 LEU cc_start: 0.8551 (mp) cc_final: 0.8330 (mp) REVERT: Q 250 GLN cc_start: 0.8099 (mt0) cc_final: 0.7887 (mt0) REVERT: S 80 GLN cc_start: 0.8806 (tp40) cc_final: 0.8138 (tt0) REVERT: S 249 MET cc_start: 0.7564 (mmm) cc_final: 0.7272 (mmm) REVERT: U 80 GLN cc_start: 0.8661 (tp40) cc_final: 0.7959 (tt0) REVERT: U 113 MET cc_start: 0.4845 (mtp) cc_final: 0.4498 (mtm) REVERT: U 138 LEU cc_start: 0.8304 (mp) cc_final: 0.7872 (mp) REVERT: U 151 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7392 (ptp-170) outliers start: 57 outliers final: 45 residues processed: 418 average time/residue: 0.5061 time to fit residues: 317.1744 Evaluate side-chains 421 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 375 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 140 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 chunk 347 optimal weight: 0.0470 chunk 174 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 346 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 HIS G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS U 275 HIS U 344 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136952 restraints weight = 43274.986| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.68 r_work: 0.3328 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32098 Z= 0.126 Angle : 0.531 13.493 43637 Z= 0.267 Chirality : 0.038 0.153 5148 Planarity : 0.005 0.123 5291 Dihedral : 14.087 179.631 5412 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.62 % Allowed : 16.69 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.14), residues: 3817 helix: 1.84 (0.11), residues: 2541 sheet: -0.28 (0.35), residues: 165 loop : -0.25 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 261 HIS 0.012 0.001 HIS U 275 PHE 0.033 0.002 PHE M 348 TYR 0.013 0.001 TYR G 23 ARG 0.018 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1826) hydrogen bonds : angle 4.16139 ( 5379) covalent geometry : bond 0.00285 (32087) covalent geometry : angle 0.53099 (43637) Misc. bond : bond 0.00142 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 397 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8626 (tp40) cc_final: 0.7966 (tt0) REVERT: A 84 ARG cc_start: 0.7937 (ttp-110) cc_final: 0.7641 (ttp-110) REVERT: C 80 GLN cc_start: 0.8743 (tp40) cc_final: 0.8089 (tt0) REVERT: C 113 MET cc_start: 0.4572 (mtp) cc_final: 0.4191 (mtm) REVERT: C 249 MET cc_start: 0.7618 (mmm) cc_final: 0.7391 (mmm) REVERT: E 80 GLN cc_start: 0.8695 (tp40) cc_final: 0.8048 (tt0) REVERT: E 249 MET cc_start: 0.7932 (mmm) cc_final: 0.7672 (mmm) REVERT: G 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8091 (tt0) REVERT: G 138 LEU cc_start: 0.8348 (mp) cc_final: 0.8000 (mp) REVERT: I 80 GLN cc_start: 0.8670 (tp40) cc_final: 0.8015 (tt0) REVERT: I 128 ASP cc_start: 0.7530 (t70) cc_final: 0.7275 (t0) REVERT: I 249 MET cc_start: 0.7795 (mmm) cc_final: 0.7268 (mmm) REVERT: K 80 GLN cc_start: 0.8722 (tp40) cc_final: 0.8077 (tt0) REVERT: K 347 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7831 (mt) REVERT: M 80 GLN cc_start: 0.8607 (tp40) cc_final: 0.7945 (tt0) REVERT: O 80 GLN cc_start: 0.8778 (tp40) cc_final: 0.8113 (tt0) REVERT: O 249 MET cc_start: 0.7620 (mmm) cc_final: 0.7355 (mmm) REVERT: Q 80 GLN cc_start: 0.8668 (tp40) cc_final: 0.8041 (tt0) REVERT: Q 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8357 (mp) REVERT: S 67 ILE cc_start: 0.8730 (mm) cc_final: 0.8506 (mm) REVERT: S 80 GLN cc_start: 0.8756 (tp40) cc_final: 0.8095 (tt0) REVERT: S 249 MET cc_start: 0.7525 (mmm) cc_final: 0.7245 (mmm) REVERT: U 80 GLN cc_start: 0.8614 (tp40) cc_final: 0.7919 (tt0) REVERT: U 113 MET cc_start: 0.4752 (mtp) cc_final: 0.4405 (mtm) REVERT: U 138 LEU cc_start: 0.8274 (mp) cc_final: 0.7843 (mp) REVERT: U 151 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7304 (ptp-170) outliers start: 53 outliers final: 43 residues processed: 423 average time/residue: 0.5021 time to fit residues: 318.9769 Evaluate side-chains 425 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 380 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 HIS G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136278 restraints weight = 43151.178| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.70 r_work: 0.3311 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32098 Z= 0.139 Angle : 0.558 15.410 43637 Z= 0.277 Chirality : 0.038 0.132 5148 Planarity : 0.006 0.191 5291 Dihedral : 14.065 179.629 5412 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.59 % Allowed : 17.27 % Favored : 81.15 % 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: 1.72 (0.14), residues: 3817 helix: 1.85 (0.11), residues: 2541 sheet: -0.26 (0.35), residues: 165 loop : -0.23 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 261 HIS 0.008 0.001 HIS U 275 PHE 0.033 0.003 PHE I 348 TYR 0.012 0.001 TYR G 23 ARG 0.028 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1826) hydrogen bonds : angle 4.18786 ( 5379) covalent geometry : bond 0.00323 (32087) covalent geometry : angle 0.55823 (43637) Misc. bond : bond 0.00206 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8642 (tp40) cc_final: 0.7961 (tt0) REVERT: A 84 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7631 (ttp-110) REVERT: C 80 GLN cc_start: 0.8762 (tp40) cc_final: 0.8151 (tt0) REVERT: C 113 MET cc_start: 0.4365 (mtp) cc_final: 0.4019 (mtm) REVERT: C 249 MET cc_start: 0.7702 (mmm) cc_final: 0.7481 (mmm) REVERT: E 80 GLN cc_start: 0.8724 (tp40) cc_final: 0.8054 (tt0) REVERT: E 249 MET cc_start: 0.7920 (mmm) cc_final: 0.7651 (mmm) REVERT: G 80 GLN cc_start: 0.8769 (tp40) cc_final: 0.8093 (tt0) REVERT: G 138 LEU cc_start: 0.8338 (mp) cc_final: 0.7992 (mp) REVERT: I 80 GLN cc_start: 0.8685 (tp40) cc_final: 0.8010 (tt0) REVERT: I 249 MET cc_start: 0.7826 (mmm) cc_final: 0.7290 (mmm) REVERT: K 80 GLN cc_start: 0.8753 (tp40) cc_final: 0.8189 (tt0) REVERT: M 80 GLN cc_start: 0.8626 (tp40) cc_final: 0.7993 (tt0) REVERT: O 80 GLN cc_start: 0.8810 (tp40) cc_final: 0.8119 (tt0) REVERT: O 249 MET cc_start: 0.7650 (mmm) cc_final: 0.7373 (mmm) REVERT: Q 80 GLN cc_start: 0.8705 (tp40) cc_final: 0.8090 (tt0) REVERT: Q 138 LEU cc_start: 0.8573 (mp) cc_final: 0.8304 (mp) REVERT: Q 249 MET cc_start: 0.7785 (tpt) cc_final: 0.7508 (mmm) REVERT: S 80 GLN cc_start: 0.8769 (tp40) cc_final: 0.8100 (tt0) REVERT: S 249 MET cc_start: 0.7544 (mmm) cc_final: 0.7271 (mmm) REVERT: U 80 GLN cc_start: 0.8621 (tp40) cc_final: 0.7916 (tt0) REVERT: U 138 LEU cc_start: 0.8254 (mp) cc_final: 0.7888 (mp) outliers start: 52 outliers final: 44 residues processed: 410 average time/residue: 0.5075 time to fit residues: 311.7607 Evaluate side-chains 417 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 373 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 290 ASP Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 343 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 171 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 340 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 HIS G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.169049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137420 restraints weight = 43158.648| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.82 r_work: 0.3316 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32098 Z= 0.118 Angle : 0.553 16.259 43637 Z= 0.271 Chirality : 0.038 0.158 5148 Planarity : 0.005 0.192 5291 Dihedral : 14.064 179.374 5412 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.31 % Allowed : 17.57 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.14), residues: 3817 helix: 1.95 (0.11), residues: 2541 sheet: -0.28 (0.35), residues: 165 loop : -0.19 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP S 261 HIS 0.012 0.001 HIS U 275 PHE 0.033 0.002 PHE I 348 TYR 0.015 0.001 TYR S 23 ARG 0.023 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 1826) hydrogen bonds : angle 4.11897 ( 5379) covalent geometry : bond 0.00271 (32087) covalent geometry : angle 0.55309 (43637) Misc. bond : bond 0.00205 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 395 time to evaluate : 3.441 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 50 GLU cc_start: 0.7739 (tp30) cc_final: 0.7495 (tp30) REVERT: A 80 GLN cc_start: 0.8664 (tp40) cc_final: 0.7942 (tt0) REVERT: A 339 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6910 (mmt-90) REVERT: C 80 GLN cc_start: 0.8808 (tp40) cc_final: 0.8194 (tt0) REVERT: C 249 MET cc_start: 0.7712 (mmm) cc_final: 0.7483 (mmm) REVERT: C 295 MET cc_start: 0.8685 (mtm) cc_final: 0.8404 (mtp) REVERT: E 80 GLN cc_start: 0.8747 (tp40) cc_final: 0.8069 (tt0) REVERT: E 249 MET cc_start: 0.7919 (mmm) cc_final: 0.7675 (mmm) REVERT: E 339 ARG cc_start: 0.7208 (tpp-160) cc_final: 0.6947 (mmt-90) REVERT: G 80 GLN cc_start: 0.8799 (tp40) cc_final: 0.8114 (tt0) REVERT: G 138 LEU cc_start: 0.8327 (mp) cc_final: 0.7978 (mp) REVERT: I 80 GLN cc_start: 0.8716 (tp40) cc_final: 0.8046 (tt0) REVERT: K 78 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.6909 (tpp-160) REVERT: K 80 GLN cc_start: 0.8787 (tp40) cc_final: 0.8218 (tt0) REVERT: K 339 ARG cc_start: 0.7365 (tpp-160) cc_final: 0.7065 (mmt-90) REVERT: M 80 GLN cc_start: 0.8569 (tp40) cc_final: 0.7995 (tt0) REVERT: M 117 HIS cc_start: 0.7505 (t-90) cc_final: 0.6835 (t-170) REVERT: O 80 GLN cc_start: 0.8842 (tp40) cc_final: 0.8144 (tt0) REVERT: O 249 MET cc_start: 0.7620 (mmm) cc_final: 0.7337 (mmm) REVERT: Q 80 GLN cc_start: 0.8694 (tp40) cc_final: 0.7999 (tt0) REVERT: Q 138 LEU cc_start: 0.8533 (mp) cc_final: 0.8250 (mp) REVERT: Q 249 MET cc_start: 0.7733 (tpt) cc_final: 0.7467 (mmm) REVERT: S 67 ILE cc_start: 0.8717 (mm) cc_final: 0.8508 (mm) REVERT: S 80 GLN cc_start: 0.8794 (tp40) cc_final: 0.8113 (tt0) REVERT: S 249 MET cc_start: 0.7520 (mmm) cc_final: 0.7237 (mmm) REVERT: S 344 ASN cc_start: 0.6670 (t0) cc_final: 0.6408 (t0) REVERT: U 80 GLN cc_start: 0.8642 (tp40) cc_final: 0.7945 (tt0) REVERT: U 138 LEU cc_start: 0.8257 (mp) cc_final: 0.7899 (mp) outliers start: 43 outliers final: 40 residues processed: 421 average time/residue: 0.4992 time to fit residues: 317.2673 Evaluate side-chains 419 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 379 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 17 ILE Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 19 optimal weight: 0.7980 chunk 355 optimal weight: 7.9990 chunk 227 optimal weight: 0.4980 chunk 332 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 354 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 262 optimal weight: 0.8980 chunk 293 optimal weight: 0.0670 chunk 214 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 275 HIS E 117 HIS G 275 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 ASN O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140561 restraints weight = 42813.428| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.38 r_work: 0.3410 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32098 Z= 0.121 Angle : 0.556 17.107 43637 Z= 0.272 Chirality : 0.038 0.172 5148 Planarity : 0.007 0.271 5291 Dihedral : 13.971 179.634 5412 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.37 % Allowed : 17.63 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.14), residues: 3817 helix: 1.97 (0.11), residues: 2541 sheet: -0.30 (0.34), residues: 165 loop : -0.19 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 261 HIS 0.014 0.001 HIS O 275 PHE 0.033 0.002 PHE M 348 TYR 0.017 0.001 TYR S 23 ARG 0.021 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1826) hydrogen bonds : angle 4.11156 ( 5379) covalent geometry : bond 0.00279 (32087) covalent geometry : angle 0.55565 (43637) Misc. bond : bond 0.00195 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14383.26 seconds wall clock time: 250 minutes 59.40 seconds (15059.40 seconds total)