Starting phenix.real_space_refine on Fri Jun 27 00:39:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdm_17614/06_2025/8pdm_17614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdm_17614/06_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_17614/06_2025/8pdm_17614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdm_17614/06_2025/8pdm_17614.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdm_17614/06_2025/8pdm_17614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdm_17614/06_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-5710/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: 9.23, 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: 7.80 Conformation dependent library (CDL) restraints added in 3.5 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: 9.46 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: 9.97 Time building geometry restraints manager: 9.09 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: 0.27 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.240 Set scattering table: 0.270 Process input model: 61.750 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.710 ------------------------------------------------------------------------------- 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 : 3.545 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: 0.4821 time to fit residues: 400.5725 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 : 3.171 ------------------------------------------------------------------------------- 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 = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137974 restraints weight = 42842.129| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.37 r_work: 0.3402 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 3.320 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: 0.8795 (tp40) cc_final: 0.7999 (tt0) REVERT: A 249 MET cc_start: 0.7781 (mmm) cc_final: 0.7511 (mmm) REVERT: A 347 LEU cc_start: 0.8399 (mt) cc_final: 0.8194 (mt) REVERT: C 80 GLN cc_start: 0.8898 (tp40) cc_final: 0.8207 (tt0) REVERT: C 115 ASP cc_start: 0.6641 (t70) cc_final: 0.6421 (t70) REVERT: C 249 MET cc_start: 0.7678 (mmm) cc_final: 0.7426 (mmm) REVERT: E 53 TYR cc_start: 0.6909 (p90) cc_final: 0.6706 (p90) REVERT: E 80 GLN cc_start: 0.8782 (tp40) cc_final: 0.8036 (tt0) REVERT: E 290 ASP cc_start: 0.8254 (m-30) cc_final: 0.7961 (m-30) REVERT: G 80 GLN cc_start: 0.8781 (tp40) cc_final: 0.8066 (tt0) REVERT: G 138 LEU cc_start: 0.8529 (mp) cc_final: 0.8169 (mp) REVERT: I 53 TYR cc_start: 0.6608 (p90) cc_final: 0.6128 (p90) REVERT: I 80 GLN cc_start: 0.8821 (tp40) cc_final: 0.8151 (tt0) REVERT: I 115 ASP cc_start: 0.6464 (t70) cc_final: 0.6256 (t70) REVERT: I 151 ARG cc_start: 0.7682 (ptp-170) cc_final: 0.7265 (ptp-170) REVERT: I 249 MET cc_start: 0.7880 (mmm) cc_final: 0.7541 (mmm) REVERT: K 80 GLN cc_start: 0.8934 (tp40) cc_final: 0.8178 (tt0) REVERT: M 80 GLN cc_start: 0.8849 (tp40) cc_final: 0.8078 (tt0) REVERT: M 115 ASP cc_start: 0.6364 (t70) cc_final: 0.5852 (t70) REVERT: O 80 GLN cc_start: 0.8824 (tp40) cc_final: 0.8052 (tt0) REVERT: O 249 MET cc_start: 0.7739 (mmm) cc_final: 0.7479 (mmm) REVERT: Q 80 GLN cc_start: 0.8854 (tp40) cc_final: 0.8103 (tt0) REVERT: Q 138 LEU cc_start: 0.8484 (mp) cc_final: 0.8256 (mp) REVERT: Q 200 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7082 (mtm-85) REVERT: S 80 GLN cc_start: 0.8929 (tp40) cc_final: 0.8214 (tt0) REVERT: S 249 MET cc_start: 0.7790 (mmm) cc_final: 0.7508 (mmm) REVERT: U 78 ARG cc_start: 0.7335 (tpt170) cc_final: 0.7127 (tpp80) REVERT: U 80 GLN cc_start: 0.8815 (tp40) cc_final: 0.8068 (tt0) REVERT: U 138 LEU cc_start: 0.8732 (mp) cc_final: 0.8420 (mp) outliers start: 42 outliers final: 10 residues processed: 495 average time/residue: 0.5179 time to fit residues: 394.1342 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 : 3.516 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 0.8980 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: 0.9990 chunk 104 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3934 r_free = 0.3934 target = 0.167952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136090 restraints weight = 43085.118| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.74 r_work: 0.3314 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32098 Z= 0.144 Angle : 0.530 10.553 43637 Z= 0.275 Chirality : 0.040 0.151 5148 Planarity : 0.005 0.048 5291 Dihedral : 14.159 177.574 5412 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 10.92 % Favored : 87.58 % 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: -0.52 (0.35), residues: 165 loop : -0.10 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP M 261 HIS 0.008 0.001 HIS O 275 PHE 0.031 0.002 PHE O 348 TYR 0.014 0.002 TYR U 53 ARG 0.009 0.001 ARG M 151 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1826) hydrogen bonds : angle 4.34585 ( 5379) covalent geometry : bond 0.00328 (32087) covalent geometry : angle 0.53025 (43637) Misc. bond : bond 0.00048 ( 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 531 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 482 time to evaluate : 3.801 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7781 (tp30) cc_final: 0.7538 (tp30) REVERT: A 80 GLN cc_start: 0.8689 (tp40) cc_final: 0.7993 (tt0) REVERT: A 346 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 80 GLN cc_start: 0.8829 (tp40) cc_final: 0.8132 (tt0) REVERT: C 249 MET cc_start: 0.7673 (mmm) cc_final: 0.7400 (mmm) REVERT: C 346 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7833 (tt0) REVERT: E 23 TYR cc_start: 0.5453 (m-80) cc_final: 0.4983 (m-80) REVERT: E 53 TYR cc_start: 0.6533 (p90) cc_final: 0.6169 (p90) REVERT: E 80 GLN cc_start: 0.8753 (tp40) cc_final: 0.8022 (tt0) REVERT: E 290 ASP cc_start: 0.8195 (m-30) cc_final: 0.7694 (m-30) REVERT: G 80 GLN cc_start: 0.8758 (tp40) cc_final: 0.8101 (tt0) REVERT: G 138 LEU cc_start: 0.8305 (mp) cc_final: 0.7915 (mp) REVERT: I 53 TYR cc_start: 0.6712 (p90) cc_final: 0.6409 (p90) REVERT: I 80 GLN cc_start: 0.8759 (tp40) cc_final: 0.8116 (tt0) REVERT: I 128 ASP cc_start: 0.7489 (t70) cc_final: 0.7241 (t0) REVERT: I 249 MET cc_start: 0.7820 (mmm) cc_final: 0.7135 (mmm) REVERT: K 80 GLN cc_start: 0.8857 (tp40) cc_final: 0.8160 (tt0) REVERT: M 80 GLN cc_start: 0.8702 (tp40) cc_final: 0.8033 (tt0) REVERT: O 80 GLN cc_start: 0.8788 (tp40) cc_final: 0.8001 (tt0) REVERT: O 249 MET cc_start: 0.7661 (mmm) cc_final: 0.7328 (mmm) REVERT: Q 80 GLN cc_start: 0.8809 (tp40) cc_final: 0.8065 (tt0) REVERT: Q 113 MET cc_start: 0.4313 (mtp) cc_final: 0.4089 (mtm) REVERT: Q 138 LEU cc_start: 0.8602 (mp) cc_final: 0.8258 (mp) REVERT: Q 200 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7255 (mtm110) REVERT: S 23 TYR cc_start: 0.5295 (m-80) cc_final: 0.5094 (m-80) REVERT: S 78 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6834 (tpp-160) REVERT: S 80 GLN cc_start: 0.8806 (tp40) cc_final: 0.8167 (tt0) REVERT: S 249 MET cc_start: 0.7580 (mmm) cc_final: 0.7231 (mmm) REVERT: U 80 GLN cc_start: 0.8658 (tp40) cc_final: 0.8016 (tt0) REVERT: U 113 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.4087 (mtm) REVERT: U 138 LEU cc_start: 0.8672 (mp) cc_final: 0.8344 (mp) REVERT: U 151 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7145 (ptp-170) outliers start: 49 outliers final: 22 residues processed: 496 average time/residue: 0.5149 time to fit residues: 386.4669 Evaluate side-chains 437 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 413 time to evaluate : 3.169 ------------------------------------------------------------------------------- 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 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 17 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 51 ILE 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: 0.7980 chunk 10 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 359 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 153 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137855 restraints weight = 43050.014| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.72 r_work: 0.3345 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32098 Z= 0.119 Angle : 0.508 11.976 43637 Z= 0.263 Chirality : 0.038 0.171 5148 Planarity : 0.006 0.243 5291 Dihedral : 14.107 178.576 5412 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 12.23 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.14), residues: 3817 helix: 1.61 (0.11), residues: 2530 sheet: -0.41 (0.37), residues: 165 loop : -0.09 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 261 HIS 0.008 0.001 HIS S 117 PHE 0.028 0.002 PHE K 348 TYR 0.023 0.001 TYR Q 61 ARG 0.005 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 1826) hydrogen bonds : angle 4.20146 ( 5379) covalent geometry : bond 0.00262 (32087) covalent geometry : angle 0.50756 (43637) Misc. bond : bond 0.00183 ( 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 494 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 3.152 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: 0.8668 (tp40) cc_final: 0.8006 (tt0) REVERT: A 249 MET cc_start: 0.7530 (mmm) cc_final: 0.7247 (mmm) REVERT: A 344 ASN cc_start: 0.6983 (t0) cc_final: 0.6683 (t0) REVERT: C 80 GLN cc_start: 0.8787 (tp40) cc_final: 0.8075 (tt0) REVERT: C 249 MET cc_start: 0.7607 (mmm) cc_final: 0.7339 (mmm) REVERT: C 346 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7740 (tt0) REVERT: E 53 TYR cc_start: 0.6547 (p90) cc_final: 0.6160 (p90) REVERT: E 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8041 (tt0) REVERT: E 128 ASP cc_start: 0.7597 (t70) cc_final: 0.7351 (t0) REVERT: E 290 ASP cc_start: 0.8243 (m-30) cc_final: 0.7679 (m-30) REVERT: G 80 GLN cc_start: 0.8716 (tp40) cc_final: 0.8094 (tt0) REVERT: G 138 LEU cc_start: 0.8359 (mp) cc_final: 0.7870 (mp) REVERT: G 200 ARG cc_start: 0.7453 (ptp90) cc_final: 0.7250 (mtm-85) REVERT: I 50 GLU cc_start: 0.7707 (tp30) cc_final: 0.7479 (tp30) REVERT: I 53 TYR cc_start: 0.6663 (p90) cc_final: 0.6450 (p90) REVERT: I 80 GLN cc_start: 0.8718 (tp40) cc_final: 0.8105 (tt0) REVERT: I 128 ASP cc_start: 0.7527 (t70) cc_final: 0.7273 (t0) REVERT: I 249 MET cc_start: 0.7774 (mmm) cc_final: 0.7232 (mmm) REVERT: K 80 GLN cc_start: 0.8765 (tp40) cc_final: 0.8070 (tt0) REVERT: K 347 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7777 (mt) REVERT: M 80 GLN cc_start: 0.8547 (tp40) cc_final: 0.7926 (tt0) REVERT: M 347 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8124 (mp) REVERT: O 50 GLU cc_start: 0.7586 (tp30) cc_final: 0.7358 (mm-30) REVERT: O 80 GLN cc_start: 0.8747 (tp40) cc_final: 0.7980 (tt0) REVERT: O 249 MET cc_start: 0.7617 (mmm) cc_final: 0.7325 (mmm) REVERT: O 347 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7618 (mm) REVERT: Q 80 GLN cc_start: 0.8751 (tp40) cc_final: 0.7978 (tt0) REVERT: Q 113 MET cc_start: 0.4764 (mtp) cc_final: 0.4331 (mtm) REVERT: Q 138 LEU cc_start: 0.8585 (mp) cc_final: 0.8190 (mp) REVERT: S 78 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6801 (tpp-160) REVERT: S 80 GLN cc_start: 0.8797 (tp40) cc_final: 0.8135 (tt0) REVERT: S 249 MET cc_start: 0.7521 (mmm) cc_final: 0.7198 (mmm) REVERT: S 344 ASN cc_start: 0.6385 (t0) cc_final: 0.5025 (t0) REVERT: U 80 GLN cc_start: 0.8652 (tp40) cc_final: 0.7987 (tt0) REVERT: U 113 MET cc_start: 0.4413 (mtp) cc_final: 0.4044 (mtm) REVERT: U 138 LEU cc_start: 0.8615 (mp) cc_final: 0.8228 (mp) REVERT: U 151 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7224 (ptp-170) outliers start: 59 outliers final: 28 residues processed: 462 average time/residue: 0.5151 time to fit residues: 360.8565 Evaluate side-chains 435 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 403 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 358 LEU 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 K residue 17 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 347 LEU 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 347 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 358 LEU 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 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: 3.9990 chunk 296 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 chunk 343 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 GLN E 148 GLN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN S 148 GLN S 275 HIS U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135354 restraints weight = 42961.530| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.81 r_work: 0.3281 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32098 Z= 0.157 Angle : 0.531 12.071 43637 Z= 0.272 Chirality : 0.039 0.145 5148 Planarity : 0.005 0.089 5291 Dihedral : 14.154 179.516 5412 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.47 % Allowed : 12.78 % Favored : 84.75 % 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: 1.41 (0.14), residues: 3817 helix: 1.62 (0.11), residues: 2541 sheet: -1.23 (0.32), residues: 209 loop : -0.14 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 261 HIS 0.021 0.001 HIS C 275 PHE 0.032 0.003 PHE M 348 TYR 0.018 0.002 TYR O 23 ARG 0.007 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 1826) hydrogen bonds : angle 4.26384 ( 5379) covalent geometry : bond 0.00365 (32087) covalent geometry : angle 0.53078 (43637) Misc. bond : bond 0.00126 ( 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 493 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 412 time to evaluate : 3.304 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: A 80 GLN cc_start: 0.8749 (tp40) cc_final: 0.7984 (tt0) REVERT: A 249 MET cc_start: 0.7677 (mmm) cc_final: 0.7454 (mmm) REVERT: A 344 ASN cc_start: 0.7084 (t0) cc_final: 0.6647 (t0) REVERT: C 80 GLN cc_start: 0.8855 (tp40) cc_final: 0.8157 (tt0) REVERT: C 249 MET cc_start: 0.7750 (mmm) cc_final: 0.7508 (mmm) REVERT: E 53 TYR cc_start: 0.6778 (p90) cc_final: 0.6398 (p90) REVERT: E 80 GLN cc_start: 0.8791 (tp40) cc_final: 0.8040 (tt0) REVERT: E 128 ASP cc_start: 0.7650 (t70) cc_final: 0.7426 (t0) REVERT: G 80 GLN cc_start: 0.8788 (tp40) cc_final: 0.8132 (tt0) REVERT: G 138 LEU cc_start: 0.8377 (mp) cc_final: 0.7980 (mp) REVERT: I 53 TYR cc_start: 0.6957 (p90) cc_final: 0.6737 (p90) REVERT: I 80 GLN cc_start: 0.8774 (tp40) cc_final: 0.8124 (tt0) REVERT: I 128 ASP cc_start: 0.7554 (t70) cc_final: 0.7313 (t0) REVERT: I 249 MET cc_start: 0.7871 (mmm) cc_final: 0.7292 (mmm) REVERT: K 80 GLN cc_start: 0.8820 (tp40) cc_final: 0.8151 (tt0) REVERT: K 347 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7697 (mt) REVERT: M 80 GLN cc_start: 0.8658 (tp40) cc_final: 0.8008 (tt0) REVERT: O 50 GLU cc_start: 0.7712 (tp30) cc_final: 0.7504 (mm-30) REVERT: O 80 GLN cc_start: 0.8855 (tp40) cc_final: 0.8080 (tt0) REVERT: O 249 MET cc_start: 0.7732 (mmm) cc_final: 0.7442 (mmm) REVERT: O 347 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7636 (mm) REVERT: Q 80 GLN cc_start: 0.8809 (tp40) cc_final: 0.8090 (tt0) REVERT: Q 113 MET cc_start: 0.4961 (mtp) cc_final: 0.4715 (mtm) REVERT: Q 138 LEU cc_start: 0.8540 (mp) cc_final: 0.8178 (mp) REVERT: S 80 GLN cc_start: 0.8827 (tp40) cc_final: 0.8127 (tt0) REVERT: S 249 MET cc_start: 0.7648 (mmm) cc_final: 0.7326 (mmm) REVERT: U 80 GLN cc_start: 0.8701 (tp40) cc_final: 0.7996 (tt0) REVERT: U 113 MET cc_start: 0.4749 (mtp) cc_final: 0.4330 (mtm) REVERT: U 138 LEU cc_start: 0.8375 (mp) cc_final: 0.7916 (mp) REVERT: U 151 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7338 (ptp-170) outliers start: 81 outliers final: 53 residues processed: 446 average time/residue: 0.5129 time to fit residues: 345.9239 Evaluate side-chains 446 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 190 VAL 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 36 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 24 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 358 LEU 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 190 VAL 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 36 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 175 THR 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 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 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 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: 3.9990 chunk 166 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 340 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 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 344 ASN G 148 GLN G 275 HIS ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3925 r_free = 0.3925 target = 0.167148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136194 restraints weight = 43211.678| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.69 r_work: 0.3320 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32098 Z= 0.139 Angle : 0.518 12.660 43637 Z= 0.266 Chirality : 0.039 0.141 5148 Planarity : 0.005 0.097 5291 Dihedral : 14.102 179.282 5412 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.92 % Allowed : 14.58 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.14), residues: 3817 helix: 1.73 (0.11), residues: 2541 sheet: -0.29 (0.36), residues: 165 loop : -0.25 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 261 HIS 0.008 0.001 HIS O 117 PHE 0.031 0.003 PHE M 348 TYR 0.017 0.001 TYR G 338 ARG 0.005 0.000 ARG K 78 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1826) hydrogen bonds : angle 4.19364 ( 5379) covalent geometry : bond 0.00318 (32087) covalent geometry : angle 0.51792 (43637) Misc. bond : bond 0.00091 ( 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 463 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 400 time to evaluate : 5.747 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: A 80 GLN cc_start: 0.8662 (tp40) cc_final: 0.7930 (tt0) REVERT: A 344 ASN cc_start: 0.6934 (t0) cc_final: 0.6539 (t0) REVERT: C 80 GLN cc_start: 0.8801 (tp40) cc_final: 0.8177 (tt0) REVERT: C 249 MET cc_start: 0.7687 (mmm) cc_final: 0.7440 (mmm) REVERT: E 53 TYR cc_start: 0.6717 (p90) cc_final: 0.6398 (p90) REVERT: E 80 GLN cc_start: 0.8737 (tp40) cc_final: 0.7996 (tt0) REVERT: E 249 MET cc_start: 0.7950 (mmm) cc_final: 0.7691 (mmm) REVERT: G 80 GLN cc_start: 0.8779 (tp40) cc_final: 0.8106 (tt0) REVERT: G 138 LEU cc_start: 0.8352 (mp) cc_final: 0.7985 (mp) REVERT: I 80 GLN cc_start: 0.8678 (tp40) cc_final: 0.8039 (tt0) REVERT: I 128 ASP cc_start: 0.7542 (t70) cc_final: 0.7292 (t0) REVERT: I 249 MET cc_start: 0.7802 (mmm) cc_final: 0.7250 (mmm) REVERT: K 80 GLN cc_start: 0.8755 (tp40) cc_final: 0.8097 (tt0) REVERT: K 344 ASN cc_start: 0.6694 (t0) cc_final: 0.6061 (t0) REVERT: M 80 GLN cc_start: 0.8619 (tp40) cc_final: 0.7950 (tt0) REVERT: O 80 GLN cc_start: 0.8803 (tp40) cc_final: 0.8106 (tt0) REVERT: O 249 MET cc_start: 0.7695 (mmm) cc_final: 0.7440 (mmm) REVERT: Q 80 GLN cc_start: 0.8720 (tp40) cc_final: 0.8048 (tt0) REVERT: Q 113 MET cc_start: 0.4961 (mtp) cc_final: 0.4737 (mtm) REVERT: Q 138 LEU cc_start: 0.8594 (mp) cc_final: 0.8360 (mp) REVERT: S 80 GLN cc_start: 0.8769 (tp40) cc_final: 0.8093 (tt0) REVERT: S 249 MET cc_start: 0.7564 (mmm) cc_final: 0.7257 (mmm) REVERT: U 80 GLN cc_start: 0.8649 (tp40) cc_final: 0.7958 (tt0) REVERT: U 113 MET cc_start: 0.4783 (mtp) cc_final: 0.4352 (mtm) REVERT: U 138 LEU cc_start: 0.8287 (mp) cc_final: 0.7950 (mp) REVERT: U 151 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7328 (ptp-170) outliers start: 63 outliers final: 50 residues processed: 433 average time/residue: 0.7047 time to fit residues: 465.0243 Evaluate side-chains 437 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 386 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL 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 C residue 290 ASP 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 332 LEU 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 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 19 LYS Chi-restraints excluded: chain M residue 175 THR 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 175 THR Chi-restraints excluded: chain Q residue 176 ILE 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 275 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 281 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 184 optimal weight: 0.0010 chunk 301 optimal weight: 0.7980 chunk 353 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 GLN E 117 HIS I 117 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 GLN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136931 restraints weight = 43010.584| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.76 r_work: 0.3317 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32098 Z= 0.123 Angle : 0.519 12.988 43637 Z= 0.264 Chirality : 0.038 0.150 5148 Planarity : 0.005 0.107 5291 Dihedral : 14.106 179.425 5412 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.83 % Allowed : 15.38 % Favored : 82.79 % 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: 1.64 (0.14), residues: 3817 helix: 1.84 (0.11), residues: 2541 sheet: -1.24 (0.31), residues: 209 loop : -0.16 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 261 HIS 0.008 0.001 HIS O 117 PHE 0.032 0.002 PHE M 348 TYR 0.015 0.001 TYR G 338 ARG 0.005 0.000 ARG K 78 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1826) hydrogen bonds : angle 4.13414 ( 5379) covalent geometry : bond 0.00277 (32087) covalent geometry : angle 0.51926 (43637) Misc. bond : bond 0.00159 ( 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 456 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 396 time to evaluate : 3.443 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: 0.8699 (tp40) cc_final: 0.7967 (tt0) REVERT: A 344 ASN cc_start: 0.6859 (t0) cc_final: 0.6480 (t0) REVERT: C 80 GLN cc_start: 0.8844 (tp40) cc_final: 0.8123 (tt0) REVERT: C 249 MET cc_start: 0.7679 (mmm) cc_final: 0.7425 (mmm) REVERT: E 53 TYR cc_start: 0.6687 (p90) cc_final: 0.6319 (p90) REVERT: E 80 GLN cc_start: 0.8765 (tp40) cc_final: 0.8021 (tt0) REVERT: G 80 GLN cc_start: 0.8800 (tp40) cc_final: 0.8124 (tt0) REVERT: G 138 LEU cc_start: 0.8334 (mp) cc_final: 0.7986 (mp) REVERT: I 80 GLN cc_start: 0.8715 (tp40) cc_final: 0.8042 (tt0) REVERT: I 128 ASP cc_start: 0.7511 (t70) cc_final: 0.7302 (t0) REVERT: K 80 GLN cc_start: 0.8796 (tp40) cc_final: 0.8133 (tt0) REVERT: K 347 LEU cc_start: 0.8401 (mm) cc_final: 0.8076 (mt) REVERT: M 80 GLN cc_start: 0.8671 (tp40) cc_final: 0.8020 (tt0) REVERT: M 84 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7768 (ttp-110) REVERT: M 250 GLN cc_start: 0.7889 (mt0) cc_final: 0.7687 (mt0) REVERT: O 80 GLN cc_start: 0.8838 (tp40) cc_final: 0.8050 (tt0) REVERT: O 249 MET cc_start: 0.7701 (mmm) cc_final: 0.7405 (mmm) REVERT: O 347 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7746 (mt) REVERT: Q 80 GLN cc_start: 0.8740 (tp40) cc_final: 0.8031 (tt0) REVERT: Q 113 MET cc_start: 0.4986 (mtp) cc_final: 0.4779 (mtm) REVERT: Q 138 LEU cc_start: 0.8620 (mp) cc_final: 0.8365 (mp) REVERT: Q 250 GLN cc_start: 0.8098 (mt0) cc_final: 0.7882 (mt0) REVERT: S 80 GLN cc_start: 0.8816 (tp40) cc_final: 0.8147 (tt0) REVERT: S 249 MET cc_start: 0.7539 (mmm) cc_final: 0.7279 (mmm) REVERT: U 80 GLN cc_start: 0.8648 (tp40) cc_final: 0.7952 (tt0) REVERT: U 138 LEU cc_start: 0.8315 (mp) cc_final: 0.7967 (mp) REVERT: U 151 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7353 (ptp-170) outliers start: 60 outliers final: 46 residues processed: 427 average time/residue: 0.5062 time to fit residues: 326.2533 Evaluate side-chains 430 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 382 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU 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 K residue 290 ASP Chi-restraints excluded: chain M residue 19 LYS 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 176 ILE 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 275 HIS Chi-restraints excluded: chain S residue 290 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 140 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 322 optimal weight: 0.5980 chunk 347 optimal weight: 0.0030 chunk 174 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 346 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 HIS E 117 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS U 117 HIS U 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137494 restraints weight = 43205.320| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.78 r_work: 0.3327 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32098 Z= 0.120 Angle : 0.533 15.738 43637 Z= 0.265 Chirality : 0.037 0.132 5148 Planarity : 0.005 0.095 5291 Dihedral : 14.120 179.710 5412 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.71 % Allowed : 15.71 % Favored : 82.58 % 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: 1.80 (0.14), residues: 3817 helix: 1.94 (0.11), residues: 2541 sheet: -0.27 (0.35), residues: 165 loop : -0.26 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 261 HIS 0.008 0.001 HIS O 117 PHE 0.032 0.002 PHE M 348 TYR 0.012 0.001 TYR G 338 ARG 0.008 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1826) hydrogen bonds : angle 4.10193 ( 5379) covalent geometry : bond 0.00272 (32087) covalent geometry : angle 0.53314 (43637) Misc. bond : bond 0.00109 ( 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 459 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 3.215 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: 0.8704 (tp40) cc_final: 0.8005 (tt0) REVERT: A 84 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7651 (ttp-110) REVERT: A 344 ASN cc_start: 0.6745 (t0) cc_final: 0.6402 (t0) REVERT: C 80 GLN cc_start: 0.8760 (tp40) cc_final: 0.8080 (tt0) REVERT: C 249 MET cc_start: 0.7676 (mmm) cc_final: 0.7445 (mmm) REVERT: E 53 TYR cc_start: 0.6695 (p90) cc_final: 0.6408 (p90) REVERT: E 80 GLN cc_start: 0.8750 (tp40) cc_final: 0.8026 (tt0) REVERT: G 50 GLU cc_start: 0.7938 (tp30) cc_final: 0.7686 (tp30) REVERT: G 80 GLN cc_start: 0.8780 (tp40) cc_final: 0.8110 (tt0) REVERT: G 138 LEU cc_start: 0.8310 (mp) cc_final: 0.7967 (mp) REVERT: G 249 MET cc_start: 0.7753 (tpt) cc_final: 0.7329 (mmm) REVERT: G 339 ARG cc_start: 0.7162 (tpp-160) cc_final: 0.6802 (mmt-90) REVERT: I 80 GLN cc_start: 0.8691 (tp40) cc_final: 0.8035 (tt0) REVERT: K 80 GLN cc_start: 0.8766 (tp40) cc_final: 0.8102 (tt0) REVERT: M 80 GLN cc_start: 0.8650 (tp40) cc_final: 0.8011 (tt0) REVERT: M 84 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7764 (ttp-110) REVERT: O 80 GLN cc_start: 0.8841 (tp40) cc_final: 0.8067 (tt0) REVERT: O 249 MET cc_start: 0.7660 (mmm) cc_final: 0.7367 (mmm) REVERT: O 347 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7722 (mm) REVERT: Q 80 GLN cc_start: 0.8723 (tp40) cc_final: 0.8123 (tt0) REVERT: Q 138 LEU cc_start: 0.8594 (mp) cc_final: 0.8322 (mp) REVERT: S 80 GLN cc_start: 0.8800 (tp40) cc_final: 0.8119 (tt0) REVERT: S 249 MET cc_start: 0.7524 (mmm) cc_final: 0.7269 (mmm) REVERT: S 344 ASN cc_start: 0.6666 (t0) cc_final: 0.6419 (t0) REVERT: U 80 GLN cc_start: 0.8631 (tp40) cc_final: 0.7928 (tt0) REVERT: U 138 LEU cc_start: 0.8272 (mp) cc_final: 0.7918 (mp) REVERT: U 151 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7381 (ptp-170) outliers start: 56 outliers final: 48 residues processed: 432 average time/residue: 0.5110 time to fit residues: 333.2662 Evaluate side-chains 426 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 376 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 290 ASP 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 TYR 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 36 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 175 THR 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 175 THR Chi-restraints excluded: chain Q residue 176 ILE 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 275 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 161 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 HIS E 117 HIS G 275 HIS ** I 275 HIS ** 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 117 HIS U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136728 restraints weight = 43201.417| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.82 r_work: 0.3306 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32098 Z= 0.129 Angle : 0.555 16.274 43637 Z= 0.273 Chirality : 0.038 0.138 5148 Planarity : 0.005 0.196 5291 Dihedral : 14.089 179.876 5412 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.86 % Allowed : 15.92 % 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: 1.82 (0.14), residues: 3817 helix: 1.95 (0.11), residues: 2541 sheet: -0.28 (0.35), residues: 165 loop : -0.23 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 123 HIS 0.008 0.001 HIS U 117 PHE 0.033 0.002 PHE M 348 TYR 0.015 0.001 TYR G 338 ARG 0.025 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1826) hydrogen bonds : angle 4.10569 ( 5379) covalent geometry : bond 0.00299 (32087) covalent geometry : angle 0.55528 (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 451 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 390 time to evaluate : 3.296 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 50 GLU cc_start: 0.7767 (tp30) cc_final: 0.7508 (tp30) REVERT: A 80 GLN cc_start: 0.8668 (tp40) cc_final: 0.7963 (tt0) REVERT: A 84 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: A 344 ASN cc_start: 0.6695 (t0) cc_final: 0.6394 (t0) REVERT: C 80 GLN cc_start: 0.8805 (tp40) cc_final: 0.8182 (tt0) REVERT: C 249 MET cc_start: 0.7740 (mmm) cc_final: 0.7507 (mmm) REVERT: E 80 GLN cc_start: 0.8787 (tp40) cc_final: 0.8041 (tt0) REVERT: E 339 ARG cc_start: 0.7213 (tpp-160) cc_final: 0.6907 (mmt-90) REVERT: G 50 GLU cc_start: 0.7947 (tp30) cc_final: 0.7735 (tp30) REVERT: G 80 GLN cc_start: 0.8813 (tp40) cc_final: 0.8123 (tt0) REVERT: G 138 LEU cc_start: 0.8347 (mp) cc_final: 0.8005 (mp) REVERT: G 249 MET cc_start: 0.7788 (tpt) cc_final: 0.7384 (mmm) REVERT: I 80 GLN cc_start: 0.8722 (tp40) cc_final: 0.8054 (tt0) REVERT: I 151 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7166 (ptp-170) REVERT: I 249 MET cc_start: 0.7679 (mmm) cc_final: 0.7368 (mmm) REVERT: K 78 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6984 (tpp-160) REVERT: K 80 GLN cc_start: 0.8785 (tp40) cc_final: 0.8225 (tt0) REVERT: M 80 GLN cc_start: 0.8656 (tp40) cc_final: 0.7999 (tt0) REVERT: O 80 GLN cc_start: 0.8858 (tp40) cc_final: 0.8148 (tt0) REVERT: O 249 MET cc_start: 0.7658 (mmm) cc_final: 0.7361 (mmm) REVERT: O 347 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7716 (mm) REVERT: Q 80 GLN cc_start: 0.8706 (tp40) cc_final: 0.8094 (tt0) REVERT: Q 138 LEU cc_start: 0.8599 (mp) cc_final: 0.8326 (mp) REVERT: Q 249 MET cc_start: 0.7771 (tpt) cc_final: 0.7506 (mmm) REVERT: S 80 GLN cc_start: 0.8816 (tp40) cc_final: 0.8131 (tt0) REVERT: S 249 MET cc_start: 0.7526 (mmm) cc_final: 0.7279 (mmm) REVERT: U 80 GLN cc_start: 0.8656 (tp40) cc_final: 0.7955 (tt0) REVERT: U 138 LEU cc_start: 0.8297 (mp) cc_final: 0.7950 (mp) REVERT: U 151 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7338 (ptp-170) outliers start: 61 outliers final: 51 residues processed: 421 average time/residue: 0.5016 time to fit residues: 319.0566 Evaluate side-chains 435 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 381 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 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 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 290 ASP 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU 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 K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain M residue 175 THR 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 175 THR Chi-restraints excluded: chain Q residue 176 ILE 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 215 GLU Chi-restraints excluded: chain S residue 275 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 343 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 340 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 HIS E 117 HIS G 275 HIS ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 344 ASN ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136973 restraints weight = 43118.611| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.64 r_work: 0.3335 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32098 Z= 0.128 Angle : 0.561 16.963 43637 Z= 0.274 Chirality : 0.038 0.128 5148 Planarity : 0.005 0.189 5291 Dihedral : 14.083 179.708 5412 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.83 % Allowed : 16.32 % Favored : 81.85 % 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: 1.98 (0.11), residues: 2541 sheet: -0.27 (0.35), residues: 165 loop : -0.20 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 261 HIS 0.008 0.001 HIS O 117 PHE 0.033 0.002 PHE M 348 TYR 0.014 0.001 TYR S 23 ARG 0.024 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1826) hydrogen bonds : angle 4.10743 ( 5379) covalent geometry : bond 0.00298 (32087) covalent geometry : angle 0.56074 (43637) Misc. bond : bond 0.00172 ( 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 453 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 393 time to evaluate : 3.433 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: 0.8619 (tp40) cc_final: 0.7894 (tt0) REVERT: A 339 ARG cc_start: 0.7113 (tpp-160) cc_final: 0.6902 (mmt-90) REVERT: A 344 ASN cc_start: 0.6639 (t0) cc_final: 0.6392 (t0) REVERT: C 80 GLN cc_start: 0.8741 (tp40) cc_final: 0.8108 (tt0) REVERT: C 117 HIS cc_start: 0.7789 (t-90) cc_final: 0.7462 (t70) REVERT: C 249 MET cc_start: 0.7672 (mmm) cc_final: 0.7443 (mmm) REVERT: E 80 GLN cc_start: 0.8701 (tp40) cc_final: 0.7979 (tt0) REVERT: G 50 GLU cc_start: 0.7929 (tp30) cc_final: 0.7720 (tp30) REVERT: G 80 GLN cc_start: 0.8738 (tp40) cc_final: 0.8068 (tt0) REVERT: G 138 LEU cc_start: 0.8294 (mp) cc_final: 0.7935 (mp) REVERT: G 249 MET cc_start: 0.7758 (tpt) cc_final: 0.7490 (mmm) REVERT: I 80 GLN cc_start: 0.8653 (tp40) cc_final: 0.8003 (tt0) REVERT: I 151 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7202 (ptp-170) REVERT: I 249 MET cc_start: 0.7485 (mmm) cc_final: 0.7197 (mmm) REVERT: K 80 GLN cc_start: 0.8711 (tp40) cc_final: 0.8177 (tt0) REVERT: M 80 GLN cc_start: 0.8520 (tp40) cc_final: 0.7942 (tt0) REVERT: O 80 GLN cc_start: 0.8788 (tp40) cc_final: 0.8113 (tt0) REVERT: O 249 MET cc_start: 0.7546 (mmm) cc_final: 0.7244 (mmm) REVERT: Q 80 GLN cc_start: 0.8617 (tp40) cc_final: 0.8042 (tt0) REVERT: Q 138 LEU cc_start: 0.8535 (mp) cc_final: 0.8258 (mp) REVERT: S 80 GLN cc_start: 0.8742 (tp40) cc_final: 0.8060 (tt0) REVERT: S 249 MET cc_start: 0.7476 (mmm) cc_final: 0.7240 (mmm) REVERT: U 80 GLN cc_start: 0.8586 (tp40) cc_final: 0.7909 (tt0) REVERT: U 138 LEU cc_start: 0.8271 (mp) cc_final: 0.7919 (mp) outliers start: 60 outliers final: 51 residues processed: 426 average time/residue: 0.5243 time to fit residues: 341.3032 Evaluate side-chains 430 residues out of total 3278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 378 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 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 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 TYR 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 K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain M residue 175 THR 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 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 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 215 GLU Chi-restraints excluded: chain S residue 275 HIS Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL 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: 8.9990 chunk 227 optimal weight: 0.9990 chunk 332 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS E 117 HIS G 275 HIS ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139340 restraints weight = 42923.434| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.38 r_work: 0.3371 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 0.070 32098 Z= 0.142 Angle : 0.573 16.077 43637 Z= 0.282 Chirality : 0.039 0.190 5148 Planarity : 0.005 0.177 5291 Dihedral : 14.090 179.703 5412 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 16.23 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3817 helix: 1.93 (0.11), residues: 2541 sheet: -0.25 (0.35), residues: 165 loop : -0.19 (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 O 117 PHE 0.034 0.002 PHE M 348 TYR 0.020 0.001 TYR M 23 ARG 0.022 0.000 ARG M 78 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 1826) hydrogen bonds : angle 4.17284 ( 5379) covalent geometry : bond 0.00332 (32087) covalent geometry : angle 0.57315 (43637) Misc. bond : bond 0.00204 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14745.22 seconds wall clock time: 256 minutes 50.57 seconds (15410.57 seconds total)