Starting phenix.real_space_refine on Mon Oct 13 02:57:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdp_17617/10_2025/8pdp_17617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdp_17617/10_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_17617/10_2025/8pdp_17617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdp_17617/10_2025/8pdp_17617.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdp_17617/10_2025/8pdp_17617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdp_17617/10_2025/8pdp_17617.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30160 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" 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: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Restraints were copied for chains: C, G, J, M, P, S, V, Y, 1, D, H, K, N, Q, T, W, Z, 2, F, I, L, O, R, U, X, 0, 3 Time building chain proxies: 3.60, per 1000 atoms: 0.12 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: 2.43 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 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: 3.62 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: 5.94 Time building geometry restraints manager: 3.24 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: 0.12 Found NCS groups: ncs_group { reference = 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' selection = chain '1' } ncs_group { reference = 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' selection = chain '2' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain '0' selection = chain '3' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.440 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG J 78 TYR 0.018 0.002 TYR V 53 PHE 0.014 0.002 PHE C 169 TRP 0.006 0.002 TRP C 123 HIS 0.005 0.001 HIS G 15 Details of bonding type rmsd covalent geometry : bond 0.00419 (30720) covalent geometry : angle 0.58265 (41710) hydrogen bonds : bond 0.13114 ( 1680) hydrogen bonds : angle 5.49334 ( 4920) *********************** 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 : 1.180 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: 0.7708 time to fit residues: 388.2349 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 : 1.030 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 112 GLN A 306 GLN A 365 ASN C 42 GLN C 112 GLN C 306 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4043 r_free = 0.4043 target = 0.184905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134503 restraints weight = 34829.599| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.90 r_work: 0.3273 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1344 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= 0.147 Angle : 0.570 8.136 41710 Z= 0.299 Chirality : 0.042 0.223 4920 Planarity : 0.004 0.046 5050 Dihedral : 11.480 74.162 5116 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.89 % Allowed : 7.41 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.14), residues: 3640 helix: 1.61 (0.11), residues: 2310 sheet: -0.62 (0.32), residues: 210 loop : -0.36 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 208 TYR 0.028 0.002 TYR G 354 PHE 0.012 0.002 PHE A 169 TRP 0.003 0.001 TRP P 123 HIS 0.003 0.001 HIS V 275 Details of bonding type rmsd covalent geometry : bond 0.00326 (30720) covalent geometry : angle 0.56993 (41710) hydrogen bonds : bond 0.04574 ( 1680) hydrogen bonds : angle 4.43360 ( 4920) *********************** 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 350 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 322 time to evaluate : 1.101 Fit side-chains REVERT: A 281 GLU cc_start: 0.6431 (tp30) cc_final: 0.5845 (mm-30) REVERT: C 55 LYS cc_start: 0.7660 (mppt) cc_final: 0.7440 (mmmm) REVERT: C 135 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6437 (ttp) REVERT: C 180 LEU cc_start: 0.8533 (mt) cc_final: 0.8283 (mt) REVERT: C 200 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7504 (ptp90) REVERT: C 281 GLU cc_start: 0.6362 (tp30) cc_final: 0.5336 (mt-10) REVERT: G 40 LEU cc_start: 0.8203 (mp) cc_final: 0.7983 (mp) REVERT: G 281 GLU cc_start: 0.6308 (tp30) cc_final: 0.5641 (mm-30) REVERT: J 281 GLU cc_start: 0.6275 (tp30) cc_final: 0.5896 (mm-30) REVERT: K 12 TYR cc_start: 0.7025 (m-80) cc_final: 0.6686 (m-10) REVERT: M 200 ARG cc_start: 0.7774 (ptp90) cc_final: 0.7485 (ptt-90) REVERT: M 281 GLU cc_start: 0.6510 (tp30) cc_final: 0.5834 (mm-30) REVERT: N 12 TYR cc_start: 0.6926 (m-80) cc_final: 0.6703 (m-10) REVERT: P 281 GLU cc_start: 0.6441 (tp30) cc_final: 0.5863 (mm-30) REVERT: S 55 LYS cc_start: 0.7676 (mppt) cc_final: 0.7449 (mmmm) REVERT: S 135 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6452 (ttp) REVERT: S 180 LEU cc_start: 0.8536 (mt) cc_final: 0.8285 (mt) REVERT: S 200 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7512 (ptp90) REVERT: S 281 GLU cc_start: 0.6369 (tp30) cc_final: 0.5332 (mt-10) REVERT: S 339 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7943 (mtp180) REVERT: V 40 LEU cc_start: 0.8199 (mp) cc_final: 0.7978 (mp) REVERT: V 281 GLU cc_start: 0.6312 (tp30) cc_final: 0.5645 (mm-30) REVERT: Y 281 GLU cc_start: 0.6277 (tp30) cc_final: 0.5891 (mm-30) REVERT: Z 12 TYR cc_start: 0.7016 (m-80) cc_final: 0.6681 (m-10) REVERT: 1 281 GLU cc_start: 0.6492 (tp30) cc_final: 0.5807 (mm-30) REVERT: 2 12 TYR cc_start: 0.6926 (m-80) cc_final: 0.6705 (m-10) outliers start: 28 outliers final: 16 residues processed: 330 average time/residue: 0.7644 time to fit residues: 293.0764 Evaluate side-chains 305 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 287 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 82 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 339 optimal weight: 0.0070 chunk 271 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 344 ASN J 320 ASN M 320 ASN P 320 ASN V 344 ASN Y 320 ASN 1 320 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130506 restraints weight = 34697.167| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.74 r_work: 0.3253 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30720 Z= 0.173 Angle : 0.570 7.302 41710 Z= 0.294 Chirality : 0.042 0.181 4920 Planarity : 0.004 0.053 5050 Dihedral : 11.416 74.400 5110 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.49 % Allowed : 8.26 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3640 helix: 1.68 (0.11), residues: 2300 sheet: -0.67 (0.33), residues: 210 loop : -0.39 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 221 TYR 0.034 0.002 TYR S 53 PHE 0.014 0.002 PHE P 169 TRP 0.004 0.001 TRP M 261 HIS 0.004 0.001 HIS V 275 Details of bonding type rmsd covalent geometry : bond 0.00399 (30720) covalent geometry : angle 0.57006 (41710) hydrogen bonds : bond 0.04587 ( 1680) hydrogen bonds : angle 4.31658 ( 4920) *********************** 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 359 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 1.103 Fit side-chains REVERT: A 281 GLU cc_start: 0.6581 (tp30) cc_final: 0.6111 (mm-30) REVERT: C 76 SER cc_start: 0.7384 (t) cc_final: 0.7087 (m) REVERT: C 180 LEU cc_start: 0.8558 (mt) cc_final: 0.8298 (mt) REVERT: C 281 GLU cc_start: 0.6459 (tp30) cc_final: 0.5434 (mt-10) REVERT: C 339 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7932 (mtp180) REVERT: G 148 GLN cc_start: 0.6834 (tm-30) cc_final: 0.6551 (tm-30) REVERT: G 272 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5759 (ttt) REVERT: G 281 GLU cc_start: 0.6399 (tp30) cc_final: 0.5802 (mm-30) REVERT: J 281 GLU cc_start: 0.6263 (tp30) cc_final: 0.6053 (mm-30) REVERT: J 337 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7414 (ppp) REVERT: K 12 TYR cc_start: 0.7102 (m-80) cc_final: 0.6777 (m-10) REVERT: M 200 ARG cc_start: 0.7855 (ptp90) cc_final: 0.7482 (ptt-90) REVERT: M 281 GLU cc_start: 0.6422 (tp30) cc_final: 0.6059 (mm-30) REVERT: N 12 TYR cc_start: 0.7028 (m-80) cc_final: 0.6758 (m-10) REVERT: P 281 GLU cc_start: 0.6586 (tp30) cc_final: 0.6116 (mm-30) REVERT: S 76 SER cc_start: 0.7375 (t) cc_final: 0.7080 (m) REVERT: S 281 GLU cc_start: 0.6476 (tp30) cc_final: 0.5455 (mt-10) REVERT: S 339 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7954 (mtp180) REVERT: V 148 GLN cc_start: 0.6835 (tm-30) cc_final: 0.6550 (tm-30) REVERT: V 272 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5754 (ttt) REVERT: V 281 GLU cc_start: 0.6401 (tp30) cc_final: 0.5802 (mm-30) REVERT: Y 281 GLU cc_start: 0.6260 (tp30) cc_final: 0.6042 (mm-30) REVERT: Y 337 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7410 (ppp) REVERT: Z 12 TYR cc_start: 0.7096 (m-80) cc_final: 0.6773 (m-10) REVERT: 1 281 GLU cc_start: 0.6425 (tp30) cc_final: 0.6059 (mm-30) REVERT: 2 12 TYR cc_start: 0.7031 (m-80) cc_final: 0.6762 (m-10) outliers start: 47 outliers final: 37 residues processed: 331 average time/residue: 0.7555 time to fit residues: 291.6424 Evaluate side-chains 329 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 272 MET Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 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 J residue 337 MET 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 P residue 32 THR 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 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 272 MET Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 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 Y residue 337 MET 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 18 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 296 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 359 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 320 ASN G 150 GLN P 150 GLN V 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134430 restraints weight = 34504.575| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.69 r_work: 0.3263 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30720 Z= 0.157 Angle : 0.557 8.171 41710 Z= 0.288 Chirality : 0.041 0.167 4920 Planarity : 0.004 0.056 5050 Dihedral : 11.350 74.318 5110 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.93 % Allowed : 9.68 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.14), residues: 3640 helix: 1.77 (0.11), residues: 2300 sheet: -0.93 (0.32), residues: 210 loop : -0.40 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 341 TYR 0.036 0.002 TYR A 53 PHE 0.013 0.002 PHE A 169 TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00364 (30720) covalent geometry : angle 0.55731 (41710) hydrogen bonds : bond 0.04351 ( 1680) hydrogen bonds : angle 4.23559 ( 4920) *********************** 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 355 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 1.188 Fit side-chains REVERT: A 22 GLN cc_start: 0.8181 (mp10) cc_final: 0.7587 (tp40) REVERT: A 113 MET cc_start: 0.5567 (mmp) cc_final: 0.5364 (mmp) REVERT: C 76 SER cc_start: 0.7355 (t) cc_final: 0.7080 (m) REVERT: C 94 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7362 (mp) REVERT: C 339 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7898 (mtp180) REVERT: G 148 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6502 (tm-30) REVERT: G 281 GLU cc_start: 0.6226 (tp30) cc_final: 0.5753 (mm-30) REVERT: J 26 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7790 (mtmt) REVERT: K 12 TYR cc_start: 0.7121 (m-80) cc_final: 0.6731 (m-10) REVERT: M 200 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7451 (ptt-90) REVERT: M 215 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: N 12 TYR cc_start: 0.7040 (m-80) cc_final: 0.6784 (m-10) REVERT: P 22 GLN cc_start: 0.8151 (mp10) cc_final: 0.7578 (tp40) REVERT: S 76 SER cc_start: 0.7344 (t) cc_final: 0.7069 (m) REVERT: S 94 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7360 (mp) REVERT: S 180 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8244 (mt) REVERT: S 339 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7917 (mtp180) REVERT: V 148 GLN cc_start: 0.6823 (tm-30) cc_final: 0.6514 (tm-30) REVERT: V 281 GLU cc_start: 0.6224 (tp30) cc_final: 0.5756 (mm-30) REVERT: Y 26 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7776 (mtmt) REVERT: Z 12 TYR cc_start: 0.7112 (m-80) cc_final: 0.6725 (m-10) REVERT: 1 215 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: 2 12 TYR cc_start: 0.7034 (m-80) cc_final: 0.6779 (m-10) outliers start: 61 outliers final: 40 residues processed: 318 average time/residue: 0.7273 time to fit residues: 270.1828 Evaluate side-chains 322 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 95 THR 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 190 VAL Chi-restraints excluded: chain M residue 215 GLU 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 180 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 94 LEU Chi-restraints excluded: chain Y residue 95 THR 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 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 79 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130137 restraints weight = 34606.311| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.86 r_work: 0.3236 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30720 Z= 0.160 Angle : 0.574 9.079 41710 Z= 0.291 Chirality : 0.041 0.160 4920 Planarity : 0.004 0.056 5050 Dihedral : 11.303 74.322 5110 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.41 % Allowed : 9.81 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.14), residues: 3640 helix: 1.82 (0.11), residues: 2300 sheet: -1.10 (0.31), residues: 210 loop : -0.41 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 341 TYR 0.034 0.002 TYR 1 53 PHE 0.013 0.002 PHE A 169 TRP 0.004 0.001 TRP S 261 HIS 0.003 0.001 HIS V 275 Details of bonding type rmsd covalent geometry : bond 0.00373 (30720) covalent geometry : angle 0.57395 (41710) hydrogen bonds : bond 0.04319 ( 1680) hydrogen bonds : angle 4.19603 ( 4920) *********************** 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 356 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 280 time to evaluate : 1.201 Fit side-chains REVERT: A 22 GLN cc_start: 0.8112 (mp10) cc_final: 0.7651 (tp40) REVERT: C 76 SER cc_start: 0.7262 (t) cc_final: 0.6993 (m) REVERT: C 94 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7586 (mp) REVERT: C 180 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8244 (mt) REVERT: C 339 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7834 (mtp180) REVERT: G 148 GLN cc_start: 0.6960 (tm-30) cc_final: 0.6620 (tm-30) REVERT: J 26 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7836 (mtmt) REVERT: K 12 TYR cc_start: 0.7110 (m-80) cc_final: 0.6862 (m-10) REVERT: M 22 GLN cc_start: 0.8075 (mp10) cc_final: 0.7547 (tp40) REVERT: M 200 ARG cc_start: 0.7778 (ptp90) cc_final: 0.7486 (ptt-90) REVERT: M 215 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: N 12 TYR cc_start: 0.7082 (m-80) cc_final: 0.6837 (m-10) REVERT: N 16 MET cc_start: 0.4569 (mmm) cc_final: 0.3722 (mmp) REVERT: P 22 GLN cc_start: 0.8086 (mp10) cc_final: 0.7643 (tp40) REVERT: S 76 SER cc_start: 0.7266 (t) cc_final: 0.6995 (m) REVERT: S 94 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7590 (mp) REVERT: S 180 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8198 (mt) REVERT: S 339 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7847 (mtp180) REVERT: V 148 GLN cc_start: 0.6961 (tm-30) cc_final: 0.6618 (tm-30) REVERT: Y 26 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: Z 12 TYR cc_start: 0.7100 (m-80) cc_final: 0.6857 (m-10) REVERT: 1 22 GLN cc_start: 0.8083 (mp10) cc_final: 0.7550 (tp40) REVERT: 1 215 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: 2 12 TYR cc_start: 0.7079 (m-80) cc_final: 0.6834 (m-10) outliers start: 76 outliers final: 52 residues processed: 322 average time/residue: 0.6949 time to fit residues: 263.9904 Evaluate side-chains 327 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 46 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 180 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 175 THR 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 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 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 33 THR 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 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 180 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 175 THR 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 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 32 THR Chi-restraints excluded: chain 1 residue 33 THR 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 186 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 297 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 306 optimal weight: 0.5980 chunk 118 optimal weight: 0.0170 chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134069 restraints weight = 34564.608| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.75 r_work: 0.3310 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30720 Z= 0.120 Angle : 0.549 10.004 41710 Z= 0.276 Chirality : 0.039 0.160 4920 Planarity : 0.004 0.056 5050 Dihedral : 11.255 73.931 5110 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.87 % Allowed : 10.85 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.14), residues: 3640 helix: 2.01 (0.11), residues: 2320 sheet: -1.18 (0.31), residues: 210 loop : -0.23 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 341 TYR 0.030 0.002 TYR G 53 PHE 0.010 0.001 PHE A 224 TRP 0.003 0.001 TRP A 123 HIS 0.002 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00271 (30720) covalent geometry : angle 0.54880 (41710) hydrogen bonds : bond 0.03843 ( 1680) hydrogen bonds : angle 4.03033 ( 4920) *********************** 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 338 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 1.006 Fit side-chains REVERT: A 22 GLN cc_start: 0.8082 (mp10) cc_final: 0.7714 (tp40) REVERT: A 339 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7719 (mtp180) REVERT: C 76 SER cc_start: 0.7221 (t) cc_final: 0.6879 (m) REVERT: C 94 LEU cc_start: 0.8027 (tp) cc_final: 0.7694 (mp) REVERT: C 135 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6477 (ttp) REVERT: C 339 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7903 (mtp180) REVERT: G 148 GLN cc_start: 0.7055 (tm-30) cc_final: 0.6716 (tm-30) REVERT: J 26 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: J 94 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7249 (mp) REVERT: K 12 TYR cc_start: 0.7125 (m-80) cc_final: 0.6872 (m-10) REVERT: M 200 ARG cc_start: 0.7780 (ptp90) cc_final: 0.7464 (ptt-90) REVERT: N 12 TYR cc_start: 0.7066 (m-80) cc_final: 0.6855 (m-10) REVERT: P 22 GLN cc_start: 0.8063 (mp10) cc_final: 0.7728 (tp40) REVERT: P 339 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7714 (mtp180) REVERT: S 76 SER cc_start: 0.7209 (t) cc_final: 0.6867 (m) REVERT: S 94 LEU cc_start: 0.8031 (tp) cc_final: 0.7693 (mp) REVERT: S 135 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6488 (ttp) REVERT: S 339 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7920 (mtp180) REVERT: V 148 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6693 (tm-30) REVERT: Y 26 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: Y 94 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7258 (mp) REVERT: Z 12 TYR cc_start: 0.7119 (m-80) cc_final: 0.6867 (m-10) REVERT: 2 12 TYR cc_start: 0.7065 (m-80) cc_final: 0.6854 (m-10) REVERT: 2 16 MET cc_start: 0.4563 (mmm) cc_final: 0.3957 (mmp) outliers start: 59 outliers final: 42 residues processed: 313 average time/residue: 0.7453 time to fit residues: 272.1821 Evaluate side-chains 310 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 190 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 175 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 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 337 MET 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 92 VAL 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 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 190 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain S residue 175 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 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET 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 92 VAL 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 Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 256 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 342 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129707 restraints weight = 34291.840| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.79 r_work: 0.3223 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30720 Z= 0.203 Angle : 0.629 10.874 41710 Z= 0.313 Chirality : 0.042 0.165 4920 Planarity : 0.004 0.061 5050 Dihedral : 11.253 74.592 5110 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.63 % Allowed : 11.14 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.14), residues: 3640 helix: 1.76 (0.11), residues: 2320 sheet: -1.14 (0.31), residues: 210 loop : -0.31 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 341 TYR 0.030 0.002 TYR S 53 PHE 0.016 0.002 PHE P 169 TRP 0.006 0.001 TRP S 261 HIS 0.004 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00480 (30720) covalent geometry : angle 0.62943 (41710) hydrogen bonds : bond 0.04561 ( 1680) hydrogen bonds : angle 4.23412 ( 4920) *********************** 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 366 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 283 time to evaluate : 1.077 Fit side-chains REVERT: A 22 GLN cc_start: 0.8126 (mp10) cc_final: 0.7684 (tp-100) REVERT: A 341 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7421 (ptm-80) REVERT: B 16 MET cc_start: 0.4696 (mmm) cc_final: 0.4393 (mmp) REVERT: C 94 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7880 (mp) REVERT: C 339 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7891 (mtp180) REVERT: G 148 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6731 (tm-30) REVERT: H 16 MET cc_start: 0.4127 (mmm) cc_final: 0.3722 (mmp) REVERT: J 26 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7863 (mtmt) REVERT: J 94 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7372 (mp) REVERT: J 215 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: M 22 GLN cc_start: 0.8068 (mp10) cc_final: 0.7590 (tp-100) REVERT: M 76 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6983 (t) REVERT: M 200 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7419 (ptt-90) REVERT: P 22 GLN cc_start: 0.8104 (mp10) cc_final: 0.7685 (tp-100) REVERT: P 341 ARG cc_start: 0.7651 (ptm-80) cc_final: 0.7433 (ptm-80) REVERT: Q 16 MET cc_start: 0.4716 (mmm) cc_final: 0.4408 (mmp) REVERT: S 94 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7879 (mp) REVERT: S 339 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7899 (mtp180) REVERT: V 148 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6719 (tm-30) REVERT: W 16 MET cc_start: 0.4133 (mmm) cc_final: 0.3731 (mmp) REVERT: Y 26 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: Y 94 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7376 (mp) REVERT: Y 215 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: 1 22 GLN cc_start: 0.8073 (mp10) cc_final: 0.7585 (tp-100) REVERT: 1 76 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.7000 (t) outliers start: 83 outliers final: 52 residues processed: 337 average time/residue: 0.6743 time to fit residues: 268.3003 Evaluate side-chains 325 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 33 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 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 135 MET 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 33 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 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL 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 33 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 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 135 MET 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 33 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 321 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 336 optimal weight: 0.4980 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 270 ASN C 150 GLN P 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131285 restraints weight = 34612.700| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.87 r_work: 0.3273 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30720 Z= 0.136 Angle : 0.588 10.853 41710 Z= 0.293 Chirality : 0.040 0.229 4920 Planarity : 0.004 0.056 5050 Dihedral : 11.246 74.075 5110 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.53 % Allowed : 11.49 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.14), residues: 3640 helix: 1.93 (0.11), residues: 2330 sheet: -1.12 (0.32), residues: 210 loop : -0.27 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 341 TYR 0.034 0.002 TYR K 12 PHE 0.011 0.001 PHE 1 169 TRP 0.003 0.001 TRP 1 123 HIS 0.002 0.001 HIS V 275 Details of bonding type rmsd covalent geometry : bond 0.00315 (30720) covalent geometry : angle 0.58839 (41710) hydrogen bonds : bond 0.04002 ( 1680) hydrogen bonds : angle 4.09332 ( 4920) *********************** 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 350 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 0.908 Fit side-chains REVERT: A 22 GLN cc_start: 0.8127 (mp10) cc_final: 0.7707 (tp-100) REVERT: A 94 LEU cc_start: 0.8079 (tp) cc_final: 0.7824 (mp) REVERT: A 341 ARG cc_start: 0.7605 (ptm-80) cc_final: 0.7346 (ptm-80) REVERT: B 16 MET cc_start: 0.5002 (mmm) cc_final: 0.4315 (tpt) REVERT: C 22 GLN cc_start: 0.8001 (mp10) cc_final: 0.7773 (tp-100) REVERT: C 180 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8281 (mt) REVERT: C 332 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7700 (mp) REVERT: C 339 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7828 (mtp180) REVERT: G 148 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6824 (tm-30) REVERT: G 272 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.5220 (tmt) REVERT: G 347 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6695 (mt) REVERT: J 26 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: J 94 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7351 (mp) REVERT: M 22 GLN cc_start: 0.8059 (mp10) cc_final: 0.7586 (tp40) REVERT: M 76 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.6948 (t) REVERT: M 148 GLN cc_start: 0.7388 (tp40) cc_final: 0.7175 (tm-30) REVERT: M 200 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7418 (ptt-90) REVERT: P 22 GLN cc_start: 0.8079 (mp10) cc_final: 0.7720 (tp-100) REVERT: P 94 LEU cc_start: 0.8076 (tp) cc_final: 0.7822 (mp) REVERT: P 341 ARG cc_start: 0.7608 (ptm-80) cc_final: 0.7346 (ptm-80) REVERT: Q 16 MET cc_start: 0.5014 (mmm) cc_final: 0.4323 (tpt) REVERT: S 22 GLN cc_start: 0.8001 (mp10) cc_final: 0.7784 (tp-100) REVERT: S 332 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7699 (mp) REVERT: S 339 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7852 (mtp180) REVERT: V 148 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6829 (tm-30) REVERT: V 272 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5225 (tmt) REVERT: V 347 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6692 (mt) REVERT: Y 26 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: Y 94 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7362 (mp) REVERT: 1 22 GLN cc_start: 0.8074 (mp10) cc_final: 0.7583 (tp40) REVERT: 1 76 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6962 (t) REVERT: 1 148 GLN cc_start: 0.7366 (tp40) cc_final: 0.7161 (tm-30) REVERT: 2 16 MET cc_start: 0.4740 (mmm) cc_final: 0.4009 (mmp) outliers start: 80 outliers final: 51 residues processed: 322 average time/residue: 0.6840 time to fit residues: 259.3181 Evaluate side-chains 324 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 332 LEU 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 272 MET Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 347 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 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 135 MET 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 33 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 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 332 LEU 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 272 MET Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain V residue 347 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 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 135 MET 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 33 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 224 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 354 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 254 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN J 270 ASN M 270 ASN S 270 ASN Y 270 ASN 1 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132887 restraints weight = 34633.932| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.66 r_work: 0.3279 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2438 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 : 0.599 12.222 41710 Z= 0.296 Chirality : 0.040 0.281 4920 Planarity : 0.004 0.055 5050 Dihedral : 11.224 74.072 5110 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.09 % Allowed : 12.12 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.14), residues: 3640 helix: 2.02 (0.11), residues: 2330 sheet: -1.07 (0.31), residues: 210 loop : -0.21 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 341 TYR 0.025 0.002 TYR S 53 PHE 0.011 0.002 PHE A 169 TRP 0.003 0.001 TRP 1 123 HIS 0.002 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00316 (30720) covalent geometry : angle 0.59938 (41710) hydrogen bonds : bond 0.03994 ( 1680) hydrogen bonds : angle 4.11159 ( 4920) *********************** 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 338 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 1.125 Fit side-chains REVERT: A 22 GLN cc_start: 0.8107 (mp10) cc_final: 0.7735 (tp-100) REVERT: A 94 LEU cc_start: 0.8025 (tp) cc_final: 0.7772 (mp) REVERT: A 341 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.7287 (ptm-80) REVERT: C 22 GLN cc_start: 0.7950 (mp10) cc_final: 0.7671 (tp-100) REVERT: C 332 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7710 (mp) REVERT: C 339 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7837 (mtp180) REVERT: G 22 GLN cc_start: 0.8081 (mp10) cc_final: 0.7538 (mm110) REVERT: G 148 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6846 (tm-30) REVERT: J 26 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: J 94 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7370 (mp) REVERT: M 22 GLN cc_start: 0.8046 (mp10) cc_final: 0.7591 (tp40) REVERT: M 76 SER cc_start: 0.7247 (OUTLIER) cc_final: 0.6962 (t) REVERT: M 148 GLN cc_start: 0.7385 (tp40) cc_final: 0.7170 (tm-30) REVERT: M 200 ARG cc_start: 0.7805 (ptp90) cc_final: 0.7421 (ptt-90) REVERT: P 22 GLN cc_start: 0.8063 (mp10) cc_final: 0.7728 (tp-100) REVERT: P 94 LEU cc_start: 0.8021 (tp) cc_final: 0.7767 (mp) REVERT: P 341 ARG cc_start: 0.7553 (ptm-80) cc_final: 0.7287 (ptm-80) REVERT: S 22 GLN cc_start: 0.7940 (mp10) cc_final: 0.7679 (tp-100) REVERT: S 332 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7716 (mp) REVERT: S 339 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7858 (mtp180) REVERT: V 22 GLN cc_start: 0.8083 (mp10) cc_final: 0.7552 (mm110) REVERT: V 148 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6841 (tm-30) REVERT: Y 26 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: Y 94 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7378 (mp) REVERT: 1 22 GLN cc_start: 0.8067 (mp10) cc_final: 0.7597 (tp40) REVERT: 1 76 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.6968 (t) REVERT: 1 148 GLN cc_start: 0.7372 (tp40) cc_final: 0.7124 (tm-30) outliers start: 66 outliers final: 48 residues processed: 309 average time/residue: 0.7153 time to fit residues: 258.8843 Evaluate side-chains 316 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 332 LEU 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 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 33 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 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 332 LEU 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 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 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 135 MET 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 33 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 103 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 353 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 183 optimal weight: 0.0170 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 270 ASN V 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133644 restraints weight = 34296.134| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.75 r_work: 0.3292 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30720 Z= 0.134 Angle : 0.612 13.225 41710 Z= 0.300 Chirality : 0.040 0.276 4920 Planarity : 0.004 0.055 5050 Dihedral : 11.203 74.020 5110 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.14), residues: 3640 helix: 2.10 (0.11), residues: 2330 sheet: -0.95 (0.32), residues: 210 loop : -0.11 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 341 TYR 0.028 0.001 TYR S 53 PHE 0.011 0.001 PHE M 169 TRP 0.003 0.001 TRP Y 123 HIS 0.002 0.001 HIS S 275 Details of bonding type rmsd covalent geometry : bond 0.00312 (30720) covalent geometry : angle 0.61160 (41710) hydrogen bonds : bond 0.03938 ( 1680) hydrogen bonds : angle 4.07431 ( 4920) ********************** 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 326 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 1.188 Fit side-chains REVERT: A 22 GLN cc_start: 0.8078 (mp10) cc_final: 0.7703 (tp-100) REVERT: A 94 LEU cc_start: 0.8026 (tp) cc_final: 0.7813 (mp) REVERT: A 341 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.7214 (ptm-80) REVERT: A 352 GLU cc_start: 0.7545 (tt0) cc_final: 0.7295 (tt0) REVERT: C 22 GLN cc_start: 0.7925 (mp10) cc_final: 0.7625 (tp-100) REVERT: C 339 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7790 (mtp180) REVERT: C 341 ARG cc_start: 0.7714 (ptm-80) cc_final: 0.6555 (mtm110) REVERT: G 22 GLN cc_start: 0.8069 (mp10) cc_final: 0.7541 (mm110) REVERT: G 148 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6842 (tm-30) REVERT: G 341 ARG cc_start: 0.7512 (ptm-80) cc_final: 0.6177 (mtm-85) REVERT: H 16 MET cc_start: 0.4259 (mmm) cc_final: 0.3719 (mmp) REVERT: J 26 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7877 (mtmt) REVERT: J 94 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7409 (mp) REVERT: J 258 MET cc_start: 0.8645 (tpp) cc_final: 0.8402 (mmm) REVERT: J 341 ARG cc_start: 0.7624 (ptm-80) cc_final: 0.6440 (mtm-85) REVERT: M 22 GLN cc_start: 0.8038 (mp10) cc_final: 0.7494 (tp-100) REVERT: M 76 SER cc_start: 0.7235 (OUTLIER) cc_final: 0.6943 (t) REVERT: M 148 GLN cc_start: 0.7366 (tp40) cc_final: 0.7101 (tm-30) REVERT: M 200 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7423 (ptt-90) REVERT: M 337 MET cc_start: 0.7950 (mtm) cc_final: 0.7107 (ppp) REVERT: N 16 MET cc_start: 0.4539 (mmm) cc_final: 0.3712 (mmp) REVERT: P 22 GLN cc_start: 0.8053 (mp10) cc_final: 0.7708 (tp-100) REVERT: P 94 LEU cc_start: 0.8021 (tp) cc_final: 0.7810 (mp) REVERT: P 341 ARG cc_start: 0.7433 (ptm-80) cc_final: 0.7205 (ptm-80) REVERT: P 352 GLU cc_start: 0.7547 (tt0) cc_final: 0.7298 (tt0) REVERT: S 22 GLN cc_start: 0.7901 (mp10) cc_final: 0.7613 (tp-100) REVERT: S 339 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7814 (mtp180) REVERT: S 341 ARG cc_start: 0.7709 (ptm-80) cc_final: 0.6554 (mtm110) REVERT: V 22 GLN cc_start: 0.8074 (mp10) cc_final: 0.7550 (mm110) REVERT: V 148 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6837 (tm-30) REVERT: V 341 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.6111 (mtm-85) REVERT: W 16 MET cc_start: 0.4270 (mmm) cc_final: 0.3728 (mmp) REVERT: Y 26 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: Y 94 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7413 (mp) REVERT: Y 258 MET cc_start: 0.8640 (tpp) cc_final: 0.8394 (mmm) REVERT: Y 341 ARG cc_start: 0.7635 (ptm-80) cc_final: 0.6446 (mtm-85) REVERT: 1 22 GLN cc_start: 0.8047 (mp10) cc_final: 0.7493 (tp-100) REVERT: 1 76 SER cc_start: 0.7244 (OUTLIER) cc_final: 0.6953 (t) REVERT: 1 148 GLN cc_start: 0.7354 (tp40) cc_final: 0.7117 (tm-30) REVERT: 1 337 MET cc_start: 0.7954 (mtm) cc_final: 0.7091 (ppp) outliers start: 56 outliers final: 42 residues processed: 304 average time/residue: 0.7127 time to fit residues: 254.6841 Evaluate side-chains 310 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR 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 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 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 254 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 343 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 349 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 338 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 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** J 365 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.183503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134668 restraints weight = 34636.578| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.64 r_work: 0.3301 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30720 Z= 0.148 Angle : 0.625 13.189 41710 Z= 0.305 Chirality : 0.040 0.233 4920 Planarity : 0.004 0.053 5050 Dihedral : 11.196 74.182 5110 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.84 % Allowed : 12.88 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.14), residues: 3640 helix: 2.07 (0.11), residues: 2330 sheet: -0.88 (0.32), residues: 210 loop : -0.11 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 341 TYR 0.023 0.002 TYR N 12 PHE 0.013 0.002 PHE A 169 TRP 0.003 0.001 TRP A 123 HIS 0.003 0.001 HIS G 275 Details of bonding type rmsd covalent geometry : bond 0.00348 (30720) covalent geometry : angle 0.62461 (41710) hydrogen bonds : bond 0.04071 ( 1680) hydrogen bonds : angle 4.09877 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11339.23 seconds wall clock time: 193 minutes 58.06 seconds (11638.06 seconds total)