Starting phenix.real_space_refine on Wed Jun 25 21:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdp_17617/06_2025/8pdp_17617.cif" } resolution = 2.9 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 130 5.16 5 C 18820 2.51 5 N 5190 2.21 5 O 5950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30160 Number of models: 1 Model: "" Number of chains: 3 Chain: "0" 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} Chain: "1" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Restraints were copied for chains: 3, E, F, I, L, O, R, U, X, B, D, H, K, N, Q, T, W, Z, A, C, G, J, M, P, S, V, Y Time building chain proxies: 10.32, per 1000 atoms: 0.34 Number of scatterers: 30160 At special positions: 0 Unit cell: (192.15, 192.15, 89.25, 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 130 16.00 P 70 15.00 O 5950 8.00 N 5190 7.00 C 18820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.03 Conformation dependent library (CDL) restraints added in 3.9 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6880 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 20 sheets defined 69.2% alpha, 5.1% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 10.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 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: 3.844A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (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 142 removed outlier: 3.629A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.921A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN B 13 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'C' and resid 9 through 20 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: 3.844A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (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 142 removed outlier: 3.628A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.922A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN D 13 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 10 through 14' Processing helix chain 'G' and resid 9 through 20 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: 3.844A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (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 142 removed outlier: 3.629A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 190 removed outlier: 3.921A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN H 13 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 10 through 14' Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 251 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 301 through 306 Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 361 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN K 13 " --> pdb=" O ASP K 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 14' Processing helix chain 'M' and resid 9 through 20 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: 3.844A pdb=" N LEU M 47 " --> pdb=" O GLU M 43 " (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 142 removed outlier: 3.628A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 190 removed outlier: 3.921A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN N 13 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 10 through 14' Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG P 189 " --> pdb=" O ARG P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 198 Processing helix chain 'P' and resid 202 through 217 Processing helix chain 'P' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 251 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 Processing helix chain 'P' and resid 275 through 280 Processing helix chain 'P' and resid 281 through 296 Processing helix chain 'P' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY P 300 " --> pdb=" O PRO P 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 297 through 300' Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 318 through 332 Processing helix chain 'P' and resid 344 through 361 Processing helix chain 'Q' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Q 13 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 10 through 14' Processing helix chain 'S' and resid 9 through 20 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: 3.844A pdb=" N LEU S 47 " --> pdb=" O GLU S 43 " (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 142 removed outlier: 3.629A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 190 removed outlier: 3.922A 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: 3.716A 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 268 removed outlier: 3.658A 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 280 Processing helix chain 'S' and resid 281 through 296 Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'T' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN T 13 " --> pdb=" O ASP T 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 10 through 14' Processing helix chain 'V' and resid 9 through 20 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 75 through 86 Processing helix chain 'V' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG V 189 " --> pdb=" O ARG V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 198 Processing helix chain 'V' and resid 202 through 217 Processing helix chain 'V' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 251 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 Processing helix chain 'V' and resid 275 through 280 Processing helix chain 'V' and resid 281 through 296 Processing helix chain 'V' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY V 300 " --> pdb=" O PRO V 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 297 through 300' Processing helix chain 'V' and resid 301 through 306 Processing helix chain 'V' and resid 318 through 332 Processing helix chain 'V' and resid 344 through 361 Processing helix chain 'W' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN W 13 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 10 through 14' Processing helix chain 'Y' and resid 9 through 20 Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU Y 47 " --> pdb=" O GLU Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 75 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG Y 189 " --> pdb=" O ARG Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 Processing helix chain 'Y' and resid 202 through 217 Processing helix chain 'Y' and resid 218 through 233 removed outlier: 3.715A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 251 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 Processing helix chain 'Y' and resid 275 through 280 Processing helix chain 'Y' and resid 281 through 296 Processing helix chain 'Y' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY Y 300 " --> pdb=" O PRO Y 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 297 through 300' Processing helix chain 'Y' and resid 301 through 306 Processing helix chain 'Y' and resid 318 through 332 Processing helix chain 'Y' and resid 344 through 361 Processing helix chain 'Z' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Z 13 " --> pdb=" O ASP Z 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 10 through 14' Processing helix chain '1' and resid 9 through 20 Processing helix chain '1' and resid 37 through 39 No H-bonds generated for 'chain '1' and resid 37 through 39' Processing helix chain '1' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 75 Processing helix chain '1' and resid 75 through 86 Processing helix chain '1' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG 1 189 " --> pdb=" O ARG 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 198 Processing helix chain '1' and resid 202 through 217 Processing helix chain '1' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 251 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 Processing helix chain '1' and resid 275 through 280 Processing helix chain '1' and resid 281 through 296 Processing helix chain '1' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY 1 300 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 301 through 306 Processing helix chain '1' and resid 318 through 332 Processing helix chain '1' and resid 344 through 361 Processing helix chain '2' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN 2 13 " --> pdb=" O ASP 2 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 10 through 14' Processing sheet with id=1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.189A 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 104 removed outlier: 7.620A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.189A 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 104 removed outlier: 7.620A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'J' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'M' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'M' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU M 111 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR P 33 " --> pdb=" O VAL P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'P' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU P 111 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'S' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU S 111 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'V' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR V 33 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'V' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU V 111 " --> pdb=" O LEU V 100 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR Y 33 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Y' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU Y 111 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain '1' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR 1 33 " --> pdb=" O VAL 1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain '1' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 11.84 Time building geometry restraints manager: 9.63 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: 9700 1.34 - 1.46: 5244 1.46 - 1.57: 15416 1.57 - 1.69: 130 1.69 - 1.81: 230 Bond restraints: 30720 Sorted by residual: bond pdb=" C ALA M 310 " pdb=" N GLY M 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA 1 310 " pdb=" N GLY 1 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA G 310 " pdb=" N GLY G 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA V 310 " pdb=" N GLY V 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA S 310 " pdb=" N GLY S 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.04e+00 ... (remaining 30715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39629 1.20 - 2.39: 1797 2.39 - 3.59: 218 3.59 - 4.79: 36 4.79 - 5.98: 30 Bond angle restraints: 41710 Sorted by residual: angle pdb=" N LYS V 55 " pdb=" CA LYS V 55 " pdb=" CB LYS V 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS G 55 " pdb=" CA LYS G 55 " pdb=" CB LYS G 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS Y 55 " pdb=" CA LYS Y 55 " pdb=" CB LYS Y 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS J 55 " pdb=" CA LYS J 55 " pdb=" CB LYS J 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS S 55 " pdb=" CA LYS S 55 " pdb=" CB LYS S 55 " ideal model delta sigma weight residual 109.87 113.25 -3.38 1.63e+00 3.76e-01 4.30e+00 ... (remaining 41705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 17029 16.59 - 33.19: 1401 33.19 - 49.78: 300 49.78 - 66.37: 110 66.37 - 82.96: 120 Dihedral angle restraints: 18960 sinusoidal: 8250 harmonic: 10710 Sorted by residual: dihedral pdb=" CA ALA J 251 " pdb=" C ALA J 251 " pdb=" N TYR J 252 " pdb=" CA TYR J 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA Y 251 " pdb=" C ALA Y 251 " pdb=" N TYR Y 252 " pdb=" CA TYR Y 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA 1 251 " pdb=" C ALA 1 251 " pdb=" N TYR 1 252 " pdb=" CA TYR 1 252 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2857 0.031 - 0.062: 1457 0.062 - 0.094: 418 0.094 - 0.125: 150 0.125 - 0.156: 38 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CB VAL C 35 " pdb=" CA VAL C 35 " pdb=" CG1 VAL C 35 " pdb=" CG2 VAL C 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB VAL S 35 " pdb=" CA VAL S 35 " pdb=" CG1 VAL S 35 " pdb=" CG2 VAL S 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB VAL M 35 " pdb=" CA VAL M 35 " pdb=" CG1 VAL M 35 " pdb=" CG2 VAL M 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 4917 not shown) Planarity restraints: 5050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C F 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C F 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C F 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C F 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C F 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C U 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C U 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C U 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C I 73 " -0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C I 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C I 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C I 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C I 73 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C I 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C I 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 5047 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 120 1.43 - 2.30: 200 2.30 - 3.17: 26141 3.17 - 4.03: 81053 4.03 - 4.90: 150190 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257704 Sorted by model distance: nonbonded pdb=" CE1 TYR Y 23 " pdb=" CZ ARG 1 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR J 23 " pdb=" CZ ARG M 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR G 23 " pdb=" CZ ARG J 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR A 23 " pdb=" CZ ARG C 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR P 23 " pdb=" CZ ARG S 78 " model vdw 0.568 3.570 ... (remaining 257699 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: 0.29 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 0.050 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 69.770 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 0.004 0.032 30720 Z= 0.183 Angle : 0.583 5.983 41710 Z= 0.329 Chirality : 0.042 0.156 4920 Planarity : 0.003 0.028 5050 Dihedral : 14.904 82.962 12080 Min Nonbonded Distance : 0.568 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.66 (0.14), residues: 3640 helix: 1.16 (0.11), residues: 2270 sheet: -0.79 (0.30), residues: 210 loop : -0.63 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 123 HIS 0.005 0.001 HIS G 15 PHE 0.014 0.002 PHE C 169 TYR 0.018 0.002 TYR V 53 ARG 0.015 0.001 ARG J 78 Details of bonding type rmsd hydrogen bonds : bond 0.13114 ( 1680) hydrogen bonds : angle 5.49334 ( 4920) covalent geometry : bond 0.00419 (30720) covalent geometry : angle 0.58265 (41710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6685 (tp30) cc_final: 0.6247 (mm-30) REVERT: C 55 LYS cc_start: 0.7701 (mppt) cc_final: 0.7427 (mppt) REVERT: C 180 LEU cc_start: 0.8539 (mt) cc_final: 0.8254 (mt) REVERT: J 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8216 (m110) REVERT: J 249 MET cc_start: 0.8336 (mmt) cc_final: 0.8045 (mmp) REVERT: J 281 GLU cc_start: 0.6960 (tp30) cc_final: 0.6746 (tp30) REVERT: K 12 TYR cc_start: 0.7451 (m-80) cc_final: 0.7173 (m-10) REVERT: K 16 MET cc_start: 0.4604 (mmm) cc_final: 0.4281 (mmt) REVERT: M 200 ARG cc_start: 0.7529 (ptp90) cc_final: 0.7326 (ptt-90) REVERT: N 12 TYR cc_start: 0.7298 (m-80) cc_final: 0.7067 (m-10) REVERT: P 281 GLU cc_start: 0.6681 (tp30) cc_final: 0.6243 (mm-30) REVERT: S 55 LYS cc_start: 0.7698 (mppt) cc_final: 0.7427 (mppt) REVERT: S 180 LEU cc_start: 0.8541 (mt) cc_final: 0.8249 (mt) REVERT: Y 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8219 (m110) REVERT: Y 249 MET cc_start: 0.8335 (mmt) cc_final: 0.8044 (mmp) REVERT: Y 281 GLU cc_start: 0.6962 (tp30) cc_final: 0.6750 (tp30) REVERT: Z 12 TYR cc_start: 0.7452 (m-80) cc_final: 0.7174 (m-10) REVERT: Z 16 MET cc_start: 0.4605 (mmm) cc_final: 0.4276 (mmt) REVERT: 2 12 TYR cc_start: 0.7300 (m-80) cc_final: 0.7070 (m-10) outliers start: 0 outliers final: 2 residues processed: 437 average time/residue: 1.5957 time to fit residues: 808.5141 Evaluate side-chains 301 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain S residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 0.0670 chunk 210 optimal weight: 0.5980 chunk 326 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 112 GLN A 306 GLN A 365 ASN C 42 GLN C 112 GLN C 306 GLN C 365 ASN G 42 GLN G 112 GLN G 306 GLN G 365 ASN J 112 GLN J 306 GLN J 365 ASN M 42 GLN M 85 ASN M 112 GLN M 279 GLN M 306 GLN M 365 ASN P 42 GLN P 112 GLN P 306 GLN P 365 ASN S 42 GLN S 112 GLN S 306 GLN S 365 ASN V 42 GLN V 112 GLN V 306 GLN V 365 ASN Y 112 GLN Y 306 GLN Y 365 ASN 1 42 GLN 1 85 ASN 1 112 GLN 1 279 GLN 1 306 GLN 1 365 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135988 restraints weight = 34529.326| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.66 r_work: 0.3323 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30720 Z= 0.137 Angle : 0.566 8.216 41710 Z= 0.297 Chirality : 0.042 0.234 4920 Planarity : 0.004 0.048 5050 Dihedral : 11.508 74.031 5116 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.85 % Allowed : 7.31 % Favored : 91.84 % 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: 1.33 (0.14), residues: 3640 helix: 1.65 (0.11), residues: 2310 sheet: -0.61 (0.32), residues: 210 loop : -0.36 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS V 275 PHE 0.010 0.001 PHE A 169 TYR 0.029 0.002 TYR G 354 ARG 0.004 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1680) hydrogen bonds : angle 4.39374 ( 4920) covalent geometry : bond 0.00297 (30720) covalent geometry : angle 0.56627 (41710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 325 time to evaluate : 3.285 Fit side-chains REVERT: A 281 GLU cc_start: 0.6519 (tp30) cc_final: 0.5987 (mm-30) REVERT: C 135 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6496 (ttp) REVERT: C 180 LEU cc_start: 0.8568 (mt) cc_final: 0.8324 (mt) REVERT: C 200 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7530 (ptp90) REVERT: C 281 GLU cc_start: 0.6495 (tp30) cc_final: 0.5499 (mt-10) REVERT: C 339 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7877 (mtp180) REVERT: G 281 GLU cc_start: 0.6264 (tp30) cc_final: 0.5651 (mm-30) REVERT: J 281 GLU cc_start: 0.6368 (tp30) cc_final: 0.6019 (mm-30) REVERT: K 12 TYR cc_start: 0.7017 (m-80) cc_final: 0.6647 (m-10) REVERT: M 200 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7478 (ptt-90) REVERT: M 281 GLU cc_start: 0.6582 (tp30) cc_final: 0.5965 (mm-30) REVERT: N 12 TYR cc_start: 0.6961 (m-80) cc_final: 0.6725 (m-10) REVERT: P 281 GLU cc_start: 0.6514 (tp30) cc_final: 0.5985 (mm-30) REVERT: S 135 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6498 (ttp) REVERT: S 180 LEU cc_start: 0.8570 (mt) cc_final: 0.8328 (mt) REVERT: S 200 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7536 (ptp90) REVERT: S 281 GLU cc_start: 0.6507 (tp30) cc_final: 0.5496 (mt-10) REVERT: S 339 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7882 (mtp180) REVERT: V 281 GLU cc_start: 0.6283 (tp30) cc_final: 0.5674 (mm-30) REVERT: Y 281 GLU cc_start: 0.6377 (tp30) cc_final: 0.6023 (mm-30) REVERT: Z 12 TYR cc_start: 0.7007 (m-80) cc_final: 0.6639 (m-10) REVERT: 1 281 GLU cc_start: 0.6566 (tp30) cc_final: 0.5945 (mm-30) REVERT: 2 12 TYR cc_start: 0.6964 (m-80) cc_final: 0.6726 (m-10) outliers start: 27 outliers final: 18 residues processed: 335 average time/residue: 1.5916 time to fit residues: 625.0914 Evaluate side-chains 298 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain 1 residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 345 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 312 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 294 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN M 320 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN 1 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.185410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135672 restraints weight = 34564.906| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.61 r_work: 0.3309 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 30720 Z= 0.133 Angle : 0.534 7.145 41710 Z= 0.276 Chirality : 0.040 0.182 4920 Planarity : 0.004 0.054 5050 Dihedral : 11.376 74.060 5110 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.52 % Allowed : 8.35 % Favored : 90.13 % 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: 1.55 (0.14), residues: 3640 helix: 1.88 (0.11), residues: 2300 sheet: -0.72 (0.33), residues: 210 loop : -0.34 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 261 HIS 0.003 0.001 HIS V 275 PHE 0.011 0.001 PHE P 169 TYR 0.036 0.002 TYR S 53 ARG 0.005 0.000 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1680) hydrogen bonds : angle 4.16889 ( 4920) covalent geometry : bond 0.00293 (30720) covalent geometry : angle 0.53376 (41710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 4.950 Fit side-chains REVERT: A 22 GLN cc_start: 0.8039 (mp10) cc_final: 0.7521 (tp40) REVERT: A 281 GLU cc_start: 0.6468 (tp30) cc_final: 0.6023 (mm-30) REVERT: A 339 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7789 (mtp180) REVERT: C 76 SER cc_start: 0.7177 (t) cc_final: 0.6872 (m) REVERT: C 281 GLU cc_start: 0.6520 (tp30) cc_final: 0.5440 (mt-10) REVERT: C 339 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7852 (mtp180) REVERT: G 281 GLU cc_start: 0.6322 (tp30) cc_final: 0.5741 (mm-30) REVERT: J 281 GLU cc_start: 0.6163 (tp30) cc_final: 0.5772 (mm-30) REVERT: K 12 TYR cc_start: 0.7033 (m-80) cc_final: 0.6692 (m-10) REVERT: M 200 ARG cc_start: 0.7819 (ptp90) cc_final: 0.7464 (ptt-90) REVERT: M 337 MET cc_start: 0.7859 (mtm) cc_final: 0.7254 (ppp) REVERT: N 12 TYR cc_start: 0.6949 (m-80) cc_final: 0.6706 (m-10) REVERT: P 22 GLN cc_start: 0.8019 (mp10) cc_final: 0.7522 (tp40) REVERT: P 281 GLU cc_start: 0.6466 (tp30) cc_final: 0.6013 (mm-30) REVERT: P 339 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7821 (mtp180) REVERT: S 76 SER cc_start: 0.7209 (t) cc_final: 0.6912 (m) REVERT: S 281 GLU cc_start: 0.6537 (tp30) cc_final: 0.5451 (mt-10) REVERT: S 339 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7856 (mtp180) REVERT: V 281 GLU cc_start: 0.6321 (tp30) cc_final: 0.5739 (mm-30) REVERT: Y 281 GLU cc_start: 0.6170 (tp30) cc_final: 0.5770 (mm-30) REVERT: Z 12 TYR cc_start: 0.7025 (m-80) cc_final: 0.6686 (m-10) REVERT: 1 337 MET cc_start: 0.7907 (mtm) cc_final: 0.7265 (ppp) REVERT: 2 12 TYR cc_start: 0.6959 (m-80) cc_final: 0.6716 (m-10) outliers start: 48 outliers final: 34 residues processed: 331 average time/residue: 1.4535 time to fit residues: 564.8067 Evaluate side-chains 315 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 53 TYR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 16 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 281 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN G 150 GLN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 GLN P 320 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.184998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135730 restraints weight = 34907.106| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.55 r_work: 0.3324 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30720 Z= 0.136 Angle : 0.535 8.343 41710 Z= 0.275 Chirality : 0.040 0.151 4920 Planarity : 0.004 0.057 5050 Dihedral : 11.299 74.093 5110 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.68 % Allowed : 9.62 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3640 helix: 1.98 (0.11), residues: 2300 sheet: -0.98 (0.31), residues: 210 loop : -0.31 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 261 HIS 0.003 0.001 HIS G 275 PHE 0.011 0.001 PHE P 169 TYR 0.035 0.002 TYR P 53 ARG 0.006 0.000 ARG S 341 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1680) hydrogen bonds : angle 4.11375 ( 4920) covalent geometry : bond 0.00308 (30720) covalent geometry : angle 0.53515 (41710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 3.043 Fit side-chains REVERT: A 22 GLN cc_start: 0.8085 (mp10) cc_final: 0.7781 (tp40) REVERT: A 339 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7815 (mtp180) REVERT: B 12 TYR cc_start: 0.6726 (m-10) cc_final: 0.6520 (m-10) REVERT: C 76 SER cc_start: 0.7314 (t) cc_final: 0.7020 (m) REVERT: C 94 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7213 (mp) REVERT: C 339 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7853 (mtp180) REVERT: G 281 GLU cc_start: 0.6285 (tp30) cc_final: 0.5878 (mm-30) REVERT: K 12 TYR cc_start: 0.7072 (m-80) cc_final: 0.6852 (m-10) REVERT: K 16 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4507 (mmt) REVERT: M 76 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.7059 (t) REVERT: M 200 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7490 (ptt-90) REVERT: N 12 TYR cc_start: 0.7051 (m-80) cc_final: 0.6824 (m-10) REVERT: P 22 GLN cc_start: 0.8069 (mp10) cc_final: 0.7767 (tp40) REVERT: P 339 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7831 (mtp180) REVERT: Q 12 TYR cc_start: 0.6719 (m-10) cc_final: 0.6513 (m-10) REVERT: S 76 SER cc_start: 0.7350 (t) cc_final: 0.7058 (m) REVERT: S 94 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7213 (mp) REVERT: S 339 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7879 (mtp180) REVERT: V 281 GLU cc_start: 0.6268 (tp30) cc_final: 0.5861 (mm-30) REVERT: Z 12 TYR cc_start: 0.7063 (m-80) cc_final: 0.6842 (m-10) REVERT: Z 16 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4507 (mmt) REVERT: 1 76 SER cc_start: 0.7324 (OUTLIER) cc_final: 0.7071 (t) REVERT: 1 317 ASN cc_start: 0.7904 (m-40) cc_final: 0.7674 (t0) REVERT: 2 12 TYR cc_start: 0.7055 (m-80) cc_final: 0.6819 (m-10) outliers start: 53 outliers final: 38 residues processed: 310 average time/residue: 1.4740 time to fit residues: 535.6192 Evaluate side-chains 305 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Z residue 16 MET Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 150 GLN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133870 restraints weight = 34513.296| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.71 r_work: 0.3290 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30720 Z= 0.142 Angle : 0.554 9.012 41710 Z= 0.279 Chirality : 0.040 0.153 4920 Planarity : 0.004 0.056 5050 Dihedral : 11.265 74.171 5110 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.03 % Allowed : 10.22 % Favored : 87.75 % 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: 1.66 (0.14), residues: 3640 helix: 2.01 (0.11), residues: 2300 sheet: -1.14 (0.30), residues: 210 loop : -0.31 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS G 275 PHE 0.012 0.002 PHE P 169 TYR 0.023 0.001 TYR P 53 ARG 0.006 0.000 ARG S 341 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 1680) hydrogen bonds : angle 4.09570 ( 4920) covalent geometry : bond 0.00326 (30720) covalent geometry : angle 0.55376 (41710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 3.482 Fit side-chains REVERT: A 22 GLN cc_start: 0.8101 (mp10) cc_final: 0.7738 (tp40) REVERT: B 12 TYR cc_start: 0.6677 (m-10) cc_final: 0.6436 (m-10) REVERT: C 76 SER cc_start: 0.7334 (t) cc_final: 0.7080 (m) REVERT: C 94 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 339 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7850 (mtp180) REVERT: G 148 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6492 (tm-30) REVERT: J 26 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7821 (mtmt) REVERT: K 12 TYR cc_start: 0.7074 (m-80) cc_final: 0.6862 (m-10) REVERT: M 76 SER cc_start: 0.7301 (OUTLIER) cc_final: 0.7026 (t) REVERT: M 200 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7521 (ptt-90) REVERT: N 12 TYR cc_start: 0.7021 (m-80) cc_final: 0.6814 (m-10) REVERT: P 22 GLN cc_start: 0.8076 (mp10) cc_final: 0.7735 (tp40) REVERT: Q 12 TYR cc_start: 0.6664 (m-10) cc_final: 0.6422 (m-10) REVERT: S 76 SER cc_start: 0.7330 (t) cc_final: 0.7068 (m) REVERT: S 94 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7385 (mp) REVERT: S 339 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7904 (mtp180) REVERT: V 148 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6488 (tm-30) REVERT: Y 26 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7803 (mtmt) REVERT: Z 12 TYR cc_start: 0.7068 (m-80) cc_final: 0.6857 (m-10) REVERT: 1 76 SER cc_start: 0.7305 (OUTLIER) cc_final: 0.7032 (t) REVERT: 1 215 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: 1 317 ASN cc_start: 0.7884 (m-40) cc_final: 0.7609 (t0) REVERT: 2 12 TYR cc_start: 0.7029 (m-80) cc_final: 0.6804 (m-10) outliers start: 64 outliers final: 46 residues processed: 308 average time/residue: 1.4360 time to fit residues: 526.0466 Evaluate side-chains 316 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 48 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 329 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131095 restraints weight = 34655.984| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.60 r_work: 0.3250 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30720 Z= 0.218 Angle : 0.631 9.848 41710 Z= 0.316 Chirality : 0.043 0.165 4920 Planarity : 0.004 0.059 5050 Dihedral : 11.293 74.732 5110 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.50 % Allowed : 10.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.14), residues: 3640 helix: 1.74 (0.11), residues: 2300 sheet: -1.25 (0.31), residues: 210 loop : -0.41 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 261 HIS 0.004 0.001 HIS V 275 PHE 0.017 0.002 PHE P 169 TYR 0.025 0.002 TYR G 53 ARG 0.007 0.001 ARG V 341 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 1680) hydrogen bonds : angle 4.28855 ( 4920) covalent geometry : bond 0.00520 (30720) covalent geometry : angle 0.63136 (41710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 283 time to evaluate : 3.312 Fit side-chains REVERT: A 22 GLN cc_start: 0.8113 (mp10) cc_final: 0.7746 (tp-100) REVERT: B 12 TYR cc_start: 0.6810 (m-10) cc_final: 0.6529 (m-10) REVERT: C 55 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7498 (mppt) REVERT: C 76 SER cc_start: 0.7401 (t) cc_final: 0.7109 (m) REVERT: C 94 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7663 (mp) REVERT: C 339 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7920 (mtp180) REVERT: G 148 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6630 (tm-30) REVERT: J 26 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: J 215 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: K 12 TYR cc_start: 0.7203 (m-80) cc_final: 0.6935 (m-10) REVERT: M 22 GLN cc_start: 0.8078 (mp10) cc_final: 0.7636 (tp40) REVERT: M 76 SER cc_start: 0.7320 (OUTLIER) cc_final: 0.7062 (t) REVERT: M 200 ARG cc_start: 0.7828 (ptp90) cc_final: 0.7484 (ptt-90) REVERT: M 215 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: N 12 TYR cc_start: 0.7188 (m-80) cc_final: 0.6953 (m-10) REVERT: N 16 MET cc_start: 0.4615 (mmm) cc_final: 0.3806 (mmp) REVERT: P 22 GLN cc_start: 0.8100 (mp10) cc_final: 0.7743 (tp-100) REVERT: Q 12 TYR cc_start: 0.6809 (m-10) cc_final: 0.6527 (m-10) REVERT: S 55 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7503 (mppt) REVERT: S 94 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7704 (mp) REVERT: S 339 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7884 (mtp180) REVERT: V 148 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6635 (tm-30) REVERT: Y 26 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: Y 215 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: Z 12 TYR cc_start: 0.7195 (m-80) cc_final: 0.6930 (m-10) REVERT: 1 22 GLN cc_start: 0.8089 (mp10) cc_final: 0.7639 (tp40) REVERT: 1 76 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.7081 (t) REVERT: 1 215 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: 2 12 TYR cc_start: 0.7207 (m-80) cc_final: 0.6942 (m-10) outliers start: 79 outliers final: 55 residues processed: 330 average time/residue: 1.4291 time to fit residues: 555.8767 Evaluate side-chains 334 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 TYR Chi-restraints excluded: chain M residue 76 SER 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 P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 267 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 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 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.183208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131113 restraints weight = 34481.730| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.81 r_work: 0.3263 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30720 Z= 0.143 Angle : 0.583 10.673 41710 Z= 0.290 Chirality : 0.040 0.165 4920 Planarity : 0.004 0.057 5050 Dihedral : 11.243 74.203 5110 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.44 % Allowed : 10.95 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3640 helix: 1.89 (0.11), residues: 2320 sheet: -1.22 (0.31), residues: 210 loop : -0.25 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS G 275 PHE 0.012 0.002 PHE P 224 TYR 0.030 0.002 TYR C 53 ARG 0.007 0.000 ARG G 341 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1680) hydrogen bonds : angle 4.12237 ( 4920) covalent geometry : bond 0.00333 (30720) covalent geometry : angle 0.58330 (41710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 271 time to evaluate : 3.291 Fit side-chains REVERT: A 22 GLN cc_start: 0.8153 (mp10) cc_final: 0.7711 (tp-100) REVERT: B 12 TYR cc_start: 0.6778 (m-10) cc_final: 0.6498 (m-10) REVERT: C 94 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7812 (mp) REVERT: C 339 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7867 (mtp180) REVERT: G 148 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6704 (tm-30) REVERT: H 16 MET cc_start: 0.4356 (mmm) cc_final: 0.3864 (mmp) REVERT: J 26 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7847 (mtmt) REVERT: J 94 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7323 (mp) REVERT: K 12 TYR cc_start: 0.7131 (m-80) cc_final: 0.6881 (m-10) REVERT: M 22 GLN cc_start: 0.8064 (mp10) cc_final: 0.7564 (tp40) REVERT: M 76 SER cc_start: 0.7289 (OUTLIER) cc_final: 0.6998 (t) REVERT: M 200 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7426 (ptt-90) REVERT: N 12 TYR cc_start: 0.7091 (m-80) cc_final: 0.6884 (m-10) REVERT: P 22 GLN cc_start: 0.8119 (mp10) cc_final: 0.7714 (tp-100) REVERT: Q 12 TYR cc_start: 0.6780 (m-10) cc_final: 0.6503 (m-10) REVERT: S 94 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7807 (mp) REVERT: S 339 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7908 (mtp180) REVERT: V 148 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6706 (tm-30) REVERT: W 16 MET cc_start: 0.4368 (mmm) cc_final: 0.3881 (mmp) REVERT: Y 26 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7849 (mtmt) REVERT: Y 94 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7322 (mp) REVERT: Z 12 TYR cc_start: 0.7123 (m-80) cc_final: 0.6877 (m-10) REVERT: 1 22 GLN cc_start: 0.8072 (mp10) cc_final: 0.7561 (tp40) REVERT: 1 76 SER cc_start: 0.7306 (OUTLIER) cc_final: 0.7017 (t) REVERT: 2 12 TYR cc_start: 0.7073 (m-80) cc_final: 0.6817 (m-10) outliers start: 77 outliers final: 52 residues processed: 316 average time/residue: 1.4438 time to fit residues: 540.7506 Evaluate side-chains 324 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 0.0980 chunk 177 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 311 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN C 150 GLN G 270 ASN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 270 ASN V 270 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.183653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131815 restraints weight = 34656.346| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.85 r_work: 0.3268 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30720 Z= 0.136 Angle : 0.597 12.396 41710 Z= 0.293 Chirality : 0.040 0.163 4920 Planarity : 0.004 0.055 5050 Dihedral : 11.231 74.076 5110 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.28 % Allowed : 11.39 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.14), residues: 3640 helix: 1.99 (0.11), residues: 2330 sheet: -1.22 (0.31), residues: 210 loop : -0.20 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS G 275 PHE 0.011 0.001 PHE P 224 TYR 0.027 0.001 TYR S 53 ARG 0.006 0.000 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1680) hydrogen bonds : angle 4.08201 ( 4920) covalent geometry : bond 0.00314 (30720) covalent geometry : angle 0.59720 (41710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 277 time to evaluate : 3.253 Fit side-chains REVERT: A 22 GLN cc_start: 0.8142 (mp10) cc_final: 0.7705 (tp-100) REVERT: A 341 ARG cc_start: 0.7603 (ptm-80) cc_final: 0.7400 (ptm-80) REVERT: B 12 TYR cc_start: 0.6803 (m-10) cc_final: 0.6544 (m-10) REVERT: C 22 GLN cc_start: 0.7974 (mp10) cc_final: 0.7762 (tp-100) REVERT: C 55 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7420 (mppt) REVERT: C 94 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7852 (mp) REVERT: C 339 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7920 (mtp180) REVERT: G 148 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6729 (tm-30) REVERT: J 26 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: J 94 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7347 (mp) REVERT: K 16 MET cc_start: 0.4061 (mmm) cc_final: 0.3411 (mmp) REVERT: M 22 GLN cc_start: 0.8074 (mp10) cc_final: 0.7579 (tp40) REVERT: M 76 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.7004 (t) REVERT: M 200 ARG cc_start: 0.7827 (ptp90) cc_final: 0.7443 (ptt-90) REVERT: N 12 TYR cc_start: 0.7072 (m-80) cc_final: 0.6862 (m-10) REVERT: N 16 MET cc_start: 0.4536 (mmm) cc_final: 0.3901 (mmp) REVERT: P 22 GLN cc_start: 0.8102 (mp10) cc_final: 0.7704 (tp-100) REVERT: P 341 ARG cc_start: 0.7603 (ptm-80) cc_final: 0.7401 (ptm-80) REVERT: Q 12 TYR cc_start: 0.6792 (m-10) cc_final: 0.6534 (m-10) REVERT: S 22 GLN cc_start: 0.7977 (mp10) cc_final: 0.7771 (tp-100) REVERT: S 55 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7410 (mppt) REVERT: S 94 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7846 (mp) REVERT: S 339 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7840 (mtp180) REVERT: V 148 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6722 (tm-30) REVERT: Y 26 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: Y 94 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7333 (mp) REVERT: Z 16 MET cc_start: 0.4045 (mmm) cc_final: 0.3430 (mmp) REVERT: 1 22 GLN cc_start: 0.8080 (mp10) cc_final: 0.7580 (tp40) REVERT: 1 76 SER cc_start: 0.7302 (OUTLIER) cc_final: 0.7011 (t) REVERT: 2 12 TYR cc_start: 0.7069 (m-80) cc_final: 0.6848 (m-10) outliers start: 72 outliers final: 49 residues processed: 316 average time/residue: 1.4200 time to fit residues: 531.5480 Evaluate side-chains 318 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 163 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 320 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 314 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN M 150 GLN M 270 ASN S 270 ASN ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 270 ASN 1 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133966 restraints weight = 34564.856| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.72 r_work: 0.3281 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30720 Z= 0.140 Angle : 0.609 12.083 41710 Z= 0.298 Chirality : 0.040 0.269 4920 Planarity : 0.004 0.054 5050 Dihedral : 11.214 74.106 5110 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.03 % Allowed : 12.25 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.14), residues: 3640 helix: 2.02 (0.11), residues: 2330 sheet: -1.16 (0.31), residues: 210 loop : -0.14 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 1 123 HIS 0.002 0.001 HIS Y 275 PHE 0.012 0.002 PHE A 169 TYR 0.037 0.002 TYR Z 12 ARG 0.007 0.000 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 1680) hydrogen bonds : angle 4.11663 ( 4920) covalent geometry : bond 0.00326 (30720) covalent geometry : angle 0.60895 (41710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 5.916 Fit side-chains REVERT: A 22 GLN cc_start: 0.8127 (mp10) cc_final: 0.7721 (tp-100) REVERT: A 94 LEU cc_start: 0.7994 (tp) cc_final: 0.7725 (mp) REVERT: A 341 ARG cc_start: 0.7564 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: B 16 MET cc_start: 0.4426 (mmm) cc_final: 0.3896 (mmp) REVERT: C 22 GLN cc_start: 0.7946 (mp10) cc_final: 0.7658 (tp-100) REVERT: C 55 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7535 (mppt) REVERT: C 339 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7910 (mtp180) REVERT: G 148 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6763 (tm-30) REVERT: J 26 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7883 (mtmt) REVERT: J 94 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7369 (mp) REVERT: K 16 MET cc_start: 0.4235 (mmm) cc_final: 0.3730 (mmp) REVERT: M 22 GLN cc_start: 0.8060 (mp10) cc_final: 0.7612 (tp40) REVERT: M 76 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.7025 (t) REVERT: M 148 GLN cc_start: 0.7376 (tp40) cc_final: 0.7174 (tm-30) REVERT: M 200 ARG cc_start: 0.7818 (ptp90) cc_final: 0.7419 (ptt-90) REVERT: M 337 MET cc_start: 0.8007 (mtm) cc_final: 0.7171 (ppp) REVERT: N 16 MET cc_start: 0.4796 (mmm) cc_final: 0.4178 (mmp) REVERT: P 22 GLN cc_start: 0.8109 (mp10) cc_final: 0.7721 (tp-100) REVERT: P 94 LEU cc_start: 0.7989 (tp) cc_final: 0.7723 (mp) REVERT: P 341 ARG cc_start: 0.7568 (ptm-80) cc_final: 0.7359 (ptm-80) REVERT: Q 16 MET cc_start: 0.4427 (mmm) cc_final: 0.3892 (mmp) REVERT: S 22 GLN cc_start: 0.7939 (mp10) cc_final: 0.7662 (tp-100) REVERT: S 55 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7534 (mppt) REVERT: S 339 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7848 (mtp180) REVERT: V 148 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6754 (tm-30) REVERT: Y 26 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7869 (mtmt) REVERT: Y 94 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7375 (mp) REVERT: Z 16 MET cc_start: 0.4353 (mmm) cc_final: 0.3884 (mmp) REVERT: 1 22 GLN cc_start: 0.8070 (mp10) cc_final: 0.7610 (tp40) REVERT: 1 76 SER cc_start: 0.7302 (OUTLIER) cc_final: 0.7015 (t) REVERT: 1 148 GLN cc_start: 0.7301 (tp40) cc_final: 0.7079 (tm-30) REVERT: 1 337 MET cc_start: 0.8023 (mtm) cc_final: 0.7171 (ppp) REVERT: 2 12 TYR cc_start: 0.7047 (m-80) cc_final: 0.6842 (m-10) REVERT: 2 16 MET cc_start: 0.4825 (mmm) cc_final: 0.4282 (mmp) outliers start: 64 outliers final: 49 residues processed: 307 average time/residue: 1.6138 time to fit residues: 584.6214 Evaluate side-chains 316 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 6.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 282 optimal weight: 0.0980 chunk 128 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.183652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133209 restraints weight = 34693.714| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.83 r_work: 0.3280 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30720 Z= 0.141 Angle : 0.622 13.038 41710 Z= 0.303 Chirality : 0.040 0.257 4920 Planarity : 0.004 0.054 5050 Dihedral : 11.205 74.114 5110 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 12.97 % Favored : 85.25 % 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: 1.83 (0.14), residues: 3640 helix: 2.07 (0.11), residues: 2330 sheet: -1.05 (0.31), residues: 210 loop : -0.13 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 123 HIS 0.002 0.001 HIS J 275 PHE 0.012 0.002 PHE P 169 TYR 0.036 0.002 TYR C 53 ARG 0.007 0.000 ARG 1 341 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1680) hydrogen bonds : angle 4.11459 ( 4920) covalent geometry : bond 0.00330 (30720) covalent geometry : angle 0.62170 (41710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 3.738 Fit side-chains REVERT: A 22 GLN cc_start: 0.8134 (mp10) cc_final: 0.7719 (tp-100) REVERT: A 94 LEU cc_start: 0.8013 (tp) cc_final: 0.7771 (mp) REVERT: A 341 ARG cc_start: 0.7598 (ptm-80) cc_final: 0.7392 (ptm-80) REVERT: B 16 MET cc_start: 0.4409 (mmm) cc_final: 0.3844 (mmp) REVERT: C 22 GLN cc_start: 0.7972 (mp10) cc_final: 0.7652 (tp-100) REVERT: C 55 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7410 (mppt) REVERT: C 339 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7900 (mtp180) REVERT: G 22 GLN cc_start: 0.8051 (mp10) cc_final: 0.7525 (mm110) REVERT: G 148 GLN cc_start: 0.7086 (tm-30) cc_final: 0.6782 (tm-30) REVERT: G 341 ARG cc_start: 0.7601 (ptm-80) cc_final: 0.6352 (mtm110) REVERT: J 26 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7880 (mtmt) REVERT: J 94 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7391 (mp) REVERT: J 341 ARG cc_start: 0.7703 (ptm-80) cc_final: 0.6479 (mtm-85) REVERT: K 16 MET cc_start: 0.4685 (mmm) cc_final: 0.4131 (mmp) REVERT: M 22 GLN cc_start: 0.8040 (mp10) cc_final: 0.7593 (tp40) REVERT: M 76 SER cc_start: 0.7287 (OUTLIER) cc_final: 0.6988 (t) REVERT: M 148 GLN cc_start: 0.7376 (tp40) cc_final: 0.7175 (tm-30) REVERT: M 200 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7421 (ptt-90) REVERT: P 22 GLN cc_start: 0.8113 (mp10) cc_final: 0.7719 (tp-100) REVERT: P 94 LEU cc_start: 0.8009 (tp) cc_final: 0.7766 (mp) REVERT: P 341 ARG cc_start: 0.7599 (ptm-80) cc_final: 0.7381 (ptm-80) REVERT: Q 16 MET cc_start: 0.4418 (mmm) cc_final: 0.3842 (mmp) REVERT: S 22 GLN cc_start: 0.7964 (mp10) cc_final: 0.7660 (tp-100) REVERT: S 55 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7406 (mppt) REVERT: S 339 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7839 (mtp180) REVERT: S 341 ARG cc_start: 0.7694 (ptm-80) cc_final: 0.6523 (mtm110) REVERT: V 22 GLN cc_start: 0.8051 (mp10) cc_final: 0.7531 (mm110) REVERT: V 148 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6776 (tm-30) REVERT: V 341 ARG cc_start: 0.7581 (ptm-80) cc_final: 0.6312 (mtm110) REVERT: Y 26 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: Y 94 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7393 (mp) REVERT: Y 341 ARG cc_start: 0.7706 (ptm-80) cc_final: 0.6473 (mtm-85) REVERT: Z 16 MET cc_start: 0.4697 (mmm) cc_final: 0.4154 (mmp) REVERT: 1 22 GLN cc_start: 0.8048 (mp10) cc_final: 0.7594 (tp40) REVERT: 1 76 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6996 (t) REVERT: 1 148 GLN cc_start: 0.7314 (tp40) cc_final: 0.7104 (tm-30) REVERT: 2 16 MET cc_start: 0.4664 (mmm) cc_final: 0.4013 (mmp) outliers start: 56 outliers final: 47 residues processed: 307 average time/residue: 1.7144 time to fit residues: 628.2777 Evaluate side-chains 317 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 76 SER Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 341 optimal weight: 0.0670 chunk 118 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129384 restraints weight = 34484.755| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.81 r_work: 0.3249 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30720 Z= 0.193 Angle : 0.656 12.895 41710 Z= 0.321 Chirality : 0.043 0.298 4920 Planarity : 0.004 0.053 5050 Dihedral : 11.228 74.546 5110 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.99 % Allowed : 12.69 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.14), residues: 3640 helix: 1.87 (0.11), residues: 2330 sheet: -1.01 (0.32), residues: 210 loop : -0.22 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 261 HIS 0.003 0.001 HIS A 275 PHE 0.015 0.002 PHE A 169 TYR 0.023 0.002 TYR J 53 ARG 0.009 0.001 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 1680) hydrogen bonds : angle 4.24398 ( 4920) covalent geometry : bond 0.00459 (30720) covalent geometry : angle 0.65565 (41710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24545.22 seconds wall clock time: 430 minutes 43.21 seconds (25843.21 seconds total)