Starting phenix.real_space_refine on Tue Aug 26 03:10:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2025/8pdq_17618.map" } resolution = 3.1 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 143 5.16 5 C 20702 2.51 5 N 5709 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33176 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, 4, D, H, K, N, Q, T, W, Z, 2, 5, F, I, L, O, R, U, X, 0, 3, 6 Time building chain proxies: 3.46, per 1000 atoms: 0.10 Number of scatterers: 33176 At special positions: 0 Unit cell: (197.4, 199.5, 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 143 16.00 P 77 15.00 O 6545 8.00 N 5709 7.00 C 20702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 22 sheets defined 68.4% alpha, 5.1% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 4.33 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: 4.009A 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: 3.726A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 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: 3.949A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) 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: 3.644A 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: 3.577A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) 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: 4.009A 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: 3.725A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 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: 3.949A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU C 273 " --> pdb=" O ASN C 270 " (cutoff:3.500A) 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: 3.644A 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: 3.577A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) 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: 4.009A 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: 3.725A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 188 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: 3.949A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 250 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU G 273 " --> pdb=" O ASN G 270 " (cutoff:3.500A) 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: 3.643A 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: 3.577A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) 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: 4.009A 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: 3.726A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.547A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 188 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: 3.949A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 250 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU J 273 " --> pdb=" O ASN J 270 " (cutoff:3.500A) 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: 3.644A 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: 3.578A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) 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: 4.009A 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: 3.725A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 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: 3.949A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 250 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU M 273 " --> pdb=" O ASN M 270 " (cutoff:3.500A) 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: 3.643A 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: 3.577A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) 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: 4.009A 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: 3.726A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 188 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: 3.949A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 250 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU P 273 " --> pdb=" O ASN P 270 " (cutoff:3.500A) 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: 3.644A 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: 3.577A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) 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: 4.010A 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: 3.725A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 188 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: 3.949A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 250 Processing helix chain 'S' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU S 273 " --> pdb=" O ASN S 270 " (cutoff:3.500A) 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: 3.644A 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: 3.576A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) 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: 4.009A 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: 3.725A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 188 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: 3.950A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 250 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU V 273 " --> pdb=" O ASN V 270 " (cutoff:3.500A) 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: 3.643A 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: 3.578A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) 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: 4.009A 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: 3.726A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 188 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: 3.949A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 250 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.756A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU Y 273 " --> pdb=" O ASN Y 270 " (cutoff:3.500A) 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: 3.644A 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: 3.577A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) 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: 4.009A 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: 3.726A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.978A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 188 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: 3.949A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 250 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU 1 273 " --> pdb=" O ASN 1 270 " (cutoff:3.500A) 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: 3.644A 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: 3.577A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 20 Processing helix chain '4' and resid 37 through 39 No H-bonds generated for 'chain '4' and resid 37 through 39' Processing helix chain '4' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU 4 47 " --> pdb=" O GLU 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 75 Processing helix chain '4' and resid 75 through 86 Processing helix chain '4' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL 4 124 " --> pdb=" O GLU 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN 4 150 " --> pdb=" O PRO 4 147 " (cutoff:3.500A) Processing helix chain '4' and resid 156 through 171 removed outlier: 3.980A pdb=" N LYS 4 171 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 175 through 188 Processing helix chain '4' and resid 191 through 198 Processing helix chain '4' and resid 202 through 217 Processing helix chain '4' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER 4 222 " --> pdb=" O VAL 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 250 Processing helix chain '4' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 4 260 " --> pdb=" O GLN 4 256 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU 4 273 " --> pdb=" O ASN 4 270 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 280 Processing helix chain '4' and resid 281 through 296 Processing helix chain '4' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY 4 300 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 297 through 300' Processing helix chain '4' and resid 301 through 306 Processing helix chain '4' and resid 318 through 332 Processing helix chain '4' and resid 344 through 361 Processing helix chain '5' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU 5 14 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.467A 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: 7.738A 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: 6.466A 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: 7.738A 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: 6.467A 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: 7.738A 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: 6.468A 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: 7.738A 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: 6.466A 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: 7.738A 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: 6.466A 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: 7.738A 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: 6.467A 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: 7.737A 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: 6.466A 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: 7.737A 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: 6.466A 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: 7.738A 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: 6.467A 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: 7.737A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain '4' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR 4 33 " --> pdb=" O VAL 4 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain '4' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU 4 111 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10681 1.34 - 1.46: 6694 1.46 - 1.58: 16021 1.58 - 1.69: 143 1.69 - 1.81: 253 Bond restraints: 33792 Sorted by residual: bond pdb=" CA ILE J 203 " pdb=" CB ILE J 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.33e-01 bond pdb=" CA ILE Y 203 " pdb=" CB ILE Y 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.09e-01 bond pdb=" CA ILE M 203 " pdb=" CB ILE M 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.78e-01 bond pdb=" CA ILE S 203 " pdb=" CB ILE S 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.55e-01 bond pdb=" CA ILE 4 203 " pdb=" CB ILE 4 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.45e-01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 43908 1.20 - 2.39: 1549 2.39 - 3.59: 359 3.59 - 4.78: 41 4.78 - 5.98: 24 Bond angle restraints: 45881 Sorted by residual: angle pdb=" N GLU Y 125 " pdb=" CA GLU Y 125 " pdb=" CB GLU Y 125 " ideal model delta sigma weight residual 110.28 113.47 -3.19 1.55e+00 4.16e-01 4.24e+00 angle pdb=" N GLU J 125 " pdb=" CA GLU J 125 " pdb=" CB GLU J 125 " ideal model delta sigma weight residual 110.28 113.46 -3.18 1.55e+00 4.16e-01 4.21e+00 angle pdb=" N GLU P 125 " pdb=" CA GLU P 125 " pdb=" CB GLU P 125 " ideal model delta sigma weight residual 110.28 113.45 -3.17 1.55e+00 4.16e-01 4.19e+00 angle pdb=" N GLU C 125 " pdb=" CA GLU C 125 " pdb=" CB GLU C 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.17e+00 angle pdb=" N GLU A 125 " pdb=" CA GLU A 125 " pdb=" CB GLU A 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.16e+00 ... (remaining 45876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 18198 15.55 - 31.10: 1877 31.10 - 46.65: 550 46.65 - 62.20: 99 62.20 - 77.75: 132 Dihedral angle restraints: 20856 sinusoidal: 9075 harmonic: 11781 Sorted by residual: dihedral pdb=" CA LEU G 52 " pdb=" C LEU G 52 " pdb=" N TYR G 53 " pdb=" CA TYR G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU 4 52 " pdb=" C LEU 4 52 " pdb=" N TYR 4 53 " pdb=" CA TYR 4 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU Y 52 " pdb=" C LEU Y 52 " pdb=" N TYR Y 53 " pdb=" CA TYR Y 53 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3117 0.027 - 0.055: 1345 0.055 - 0.082: 714 0.082 - 0.110: 153 0.110 - 0.137: 83 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CA THR C 157 " pdb=" N THR C 157 " pdb=" C THR C 157 " pdb=" CB THR C 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA THR S 157 " pdb=" N THR S 157 " pdb=" C THR S 157 " pdb=" CB THR S 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA THR V 157 " pdb=" N THR V 157 " pdb=" C THR V 157 " pdb=" CB THR V 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 5409 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " 0.027 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 C U 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C U 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C U 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.05e+00 pdb=" N1 C X 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C X 73 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C X 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C X 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C X 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C X 73 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C O 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C O 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C O 73 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C O 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C O 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C O 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 73 " -0.006 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 0.37 - 1.28: 88 1.28 - 2.18: 231 2.18 - 3.09: 24036 3.09 - 3.99: 90489 3.99 - 4.90: 167287 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282131 Sorted by model distance: nonbonded pdb=" NE ARG J 78 " pdb=" CD2 TYR M 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG P 78 " pdb=" CD2 TYR S 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG G 78 " pdb=" CD2 TYR J 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG A 78 " pdb=" CD2 TYR C 23 " model vdw 0.371 3.420 nonbonded pdb=" CD2 TYR A 23 " pdb=" NE ARG 4 78 " model vdw 0.371 3.420 ... (remaining 282126 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: 0.09 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' selection = chain '4' } 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' selection = chain '5' } 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' selection = chain '6' } 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.195 33803 Z= 2.161 Angle : 0.566 5.976 45881 Z= 0.324 Chirality : 0.040 0.137 5412 Planarity : 0.004 0.040 5555 Dihedral : 15.289 77.749 13288 Min Nonbonded Distance : 0.371 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.16 (0.13), residues: 4004 helix: 0.83 (0.10), residues: 2486 sheet: -1.25 (0.27), residues: 231 loop : -0.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 78 TYR 0.013 0.001 TYR C 69 PHE 0.014 0.002 PHE M 169 TRP 0.002 0.001 TRP J 123 HIS 0.003 0.001 HIS S 15 Details of bonding type rmsd covalent geometry : bond 0.00381 (33792) covalent geometry : angle 0.56575 (45881) hydrogen bonds : bond 0.12847 ( 1826) hydrogen bonds : angle 5.23660 ( 5346) Misc. bond : bond 1.19416 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7017 (ttpp) REVERT: G 129 LYS cc_start: 0.7603 (ttmt) cc_final: 0.7105 (mttp) REVERT: M 113 MET cc_start: 0.7771 (mmt) cc_final: 0.7546 (mmt) REVERT: M 249 MET cc_start: 0.8216 (mmm) cc_final: 0.7451 (mmm) REVERT: P 129 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7158 (ttpp) REVERT: P 249 MET cc_start: 0.8193 (mmm) cc_final: 0.7702 (mmm) REVERT: P 258 MET cc_start: 0.8107 (tpp) cc_final: 0.7799 (tpp) REVERT: P 339 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7502 (mtp180) REVERT: S 339 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7285 (mtp180) REVERT: V 339 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7565 (mtp180) REVERT: 1 201 MET cc_start: 0.7967 (ptt) cc_final: 0.7508 (ptt) REVERT: 4 249 MET cc_start: 0.8255 (mmm) cc_final: 0.7994 (mmm) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.1820 time to fit residues: 138.1689 Evaluate side-chains 415 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN P 15 HIS ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 306 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 306 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140857 restraints weight = 40826.000| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.47 r_work: 0.3181 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33803 Z= 0.183 Angle : 0.566 8.838 45881 Z= 0.304 Chirality : 0.042 0.163 5412 Planarity : 0.006 0.108 5555 Dihedral : 11.675 74.412 5621 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.75 % Allowed : 8.08 % Favored : 91.17 % 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: 0.70 (0.13), residues: 4004 helix: 1.25 (0.10), residues: 2519 sheet: -1.40 (0.29), residues: 231 loop : -0.66 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 78 TYR 0.022 0.002 TYR G 23 PHE 0.015 0.002 PHE 1 169 TRP 0.005 0.001 TRP 4 123 HIS 0.005 0.001 HIS V 56 Details of bonding type rmsd covalent geometry : bond 0.00427 (33792) covalent geometry : angle 0.56633 (45881) hydrogen bonds : bond 0.04712 ( 1826) hydrogen bonds : angle 4.25054 ( 5346) Misc. bond : bond 0.00333 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 419 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7682 (mmm) cc_final: 0.7316 (mmm) REVERT: A 279 GLN cc_start: 0.7272 (mm110) cc_final: 0.6798 (mm-40) REVERT: C 129 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7022 (ttpp) REVERT: C 272 MET cc_start: 0.7850 (mmm) cc_final: 0.7302 (mmm) REVERT: G 129 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7196 (mttp) REVERT: J 23 TYR cc_start: 0.7657 (m-80) cc_final: 0.7421 (m-80) REVERT: J 272 MET cc_start: 0.7799 (mmm) cc_final: 0.7498 (mmm) REVERT: M 249 MET cc_start: 0.8359 (mmm) cc_final: 0.8045 (mmm) REVERT: M 279 GLN cc_start: 0.7227 (mm110) cc_final: 0.6973 (mm-40) REVERT: P 129 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7115 (ttpp) REVERT: P 135 MET cc_start: 0.7538 (ttm) cc_final: 0.7269 (tpp) REVERT: P 272 MET cc_start: 0.7920 (mmm) cc_final: 0.7464 (mmm) REVERT: P 339 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7976 (mtp180) REVERT: S 125 GLU cc_start: 0.7599 (mp0) cc_final: 0.6513 (mp0) REVERT: S 135 MET cc_start: 0.7427 (ttm) cc_final: 0.6907 (tpp) REVERT: S 138 LEU cc_start: 0.8257 (mm) cc_final: 0.8055 (mm) REVERT: S 339 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7805 (mtp180) REVERT: V 135 MET cc_start: 0.7479 (ttm) cc_final: 0.7242 (tpp) REVERT: Y 272 MET cc_start: 0.7768 (mmm) cc_final: 0.7100 (mmm) REVERT: 1 135 MET cc_start: 0.7699 (ttm) cc_final: 0.7492 (tpp) REVERT: 1 272 MET cc_start: 0.7857 (mmm) cc_final: 0.7414 (mmm) REVERT: 4 337 MET cc_start: 0.8318 (mmm) cc_final: 0.8105 (tmm) outliers start: 26 outliers final: 19 residues processed: 433 average time/residue: 0.1793 time to fit residues: 128.4774 Evaluate side-chains 407 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 388 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 134 THR Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 376 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 390 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 375 optimal weight: 0.7980 chunk 335 optimal weight: 1.9990 chunk 300 optimal weight: 0.0270 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN P 279 GLN 1 279 GLN ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144599 restraints weight = 40727.632| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.32 r_work: 0.3312 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33803 Z= 0.118 Angle : 0.481 5.796 45881 Z= 0.262 Chirality : 0.039 0.143 5412 Planarity : 0.004 0.063 5555 Dihedral : 11.256 74.004 5621 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.35 % Allowed : 8.52 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.14), residues: 4004 helix: 1.61 (0.10), residues: 2530 sheet: -1.32 (0.31), residues: 231 loop : -0.55 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 78 TYR 0.013 0.001 TYR M 23 PHE 0.011 0.001 PHE C 224 TRP 0.004 0.001 TRP 4 123 HIS 0.006 0.001 HIS V 7 Details of bonding type rmsd covalent geometry : bond 0.00262 (33792) covalent geometry : angle 0.48149 (45881) hydrogen bonds : bond 0.03890 ( 1826) hydrogen bonds : angle 3.95076 ( 5346) Misc. bond : bond 0.00314 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 422 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7008 (ttpp) REVERT: A 272 MET cc_start: 0.7682 (mmm) cc_final: 0.7405 (mmm) REVERT: C 129 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7075 (ttpp) REVERT: C 272 MET cc_start: 0.7929 (mmm) cc_final: 0.7237 (mmm) REVERT: G 129 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7171 (mttp) REVERT: G 272 MET cc_start: 0.7663 (mmm) cc_final: 0.7324 (mmm) REVERT: G 283 LYS cc_start: 0.8157 (tppt) cc_final: 0.7786 (ttpt) REVERT: J 129 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7151 (mttp) REVERT: J 135 MET cc_start: 0.7378 (ttm) cc_final: 0.6853 (tpp) REVERT: J 272 MET cc_start: 0.7919 (mmm) cc_final: 0.7658 (mmm) REVERT: J 283 LYS cc_start: 0.8067 (tppt) cc_final: 0.7806 (ttpt) REVERT: M 272 MET cc_start: 0.7835 (mmm) cc_final: 0.7396 (mmm) REVERT: M 345 THR cc_start: 0.8104 (m) cc_final: 0.7689 (m) REVERT: P 135 MET cc_start: 0.7486 (ttm) cc_final: 0.7263 (tpp) REVERT: P 339 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7811 (mtp180) REVERT: S 112 GLN cc_start: 0.7731 (mm110) cc_final: 0.7465 (mm-40) REVERT: S 272 MET cc_start: 0.7760 (mmm) cc_final: 0.7372 (mmm) REVERT: S 339 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7753 (mtp180) REVERT: V 135 MET cc_start: 0.7500 (ttm) cc_final: 0.7132 (tpp) REVERT: V 272 MET cc_start: 0.7850 (mmm) cc_final: 0.7483 (mmm) REVERT: V 339 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7878 (mtp180) REVERT: Y 283 LYS cc_start: 0.8081 (tppt) cc_final: 0.7772 (ttpt) REVERT: Y 339 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7898 (mtp180) REVERT: 1 125 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: 1 272 MET cc_start: 0.7711 (mmm) cc_final: 0.7222 (mmm) REVERT: 4 10 ASP cc_start: 0.8080 (m-30) cc_final: 0.7537 (m-30) REVERT: 4 272 MET cc_start: 0.7607 (mmm) cc_final: 0.7162 (mmm) REVERT: 4 283 LYS cc_start: 0.8382 (tppt) cc_final: 0.7925 (ttpt) outliers start: 47 outliers final: 24 residues processed: 458 average time/residue: 0.2166 time to fit residues: 163.1522 Evaluate side-chains 417 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 392 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 207 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 336 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 344 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141498 restraints weight = 40693.088| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.54 r_work: 0.3185 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33803 Z= 0.168 Angle : 0.522 9.630 45881 Z= 0.275 Chirality : 0.041 0.148 5412 Planarity : 0.004 0.049 5555 Dihedral : 11.078 74.387 5621 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 9.29 % Favored : 89.10 % 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: 1.15 (0.13), residues: 4004 helix: 1.60 (0.10), residues: 2530 sheet: -1.32 (0.31), residues: 231 loop : -0.48 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 78 TYR 0.020 0.002 TYR J 23 PHE 0.017 0.002 PHE 1 169 TRP 0.005 0.001 TRP 4 123 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00393 (33792) covalent geometry : angle 0.52245 (45881) hydrogen bonds : bond 0.04185 ( 1826) hydrogen bonds : angle 3.94188 ( 5346) Misc. bond : bond 0.00239 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 398 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7737 (mmm) cc_final: 0.7470 (mmm) REVERT: C 129 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7109 (ttpp) REVERT: C 272 MET cc_start: 0.7981 (mmm) cc_final: 0.7364 (mmm) REVERT: G 129 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7254 (mttp) REVERT: G 272 MET cc_start: 0.7751 (mmm) cc_final: 0.7466 (mmm) REVERT: G 283 LYS cc_start: 0.8265 (tppt) cc_final: 0.7866 (ttpt) REVERT: J 129 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7237 (mttp) REVERT: J 135 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7277 (tpp) REVERT: J 272 MET cc_start: 0.7964 (mmm) cc_final: 0.7358 (mmm) REVERT: J 283 LYS cc_start: 0.8130 (tppt) cc_final: 0.7830 (ttpt) REVERT: M 23 TYR cc_start: 0.7685 (m-80) cc_final: 0.7477 (m-80) REVERT: M 249 MET cc_start: 0.8367 (mmm) cc_final: 0.8007 (mmm) REVERT: M 272 MET cc_start: 0.7871 (mmm) cc_final: 0.7445 (mmm) REVERT: M 279 GLN cc_start: 0.7558 (mm-40) cc_final: 0.6710 (mm-40) REVERT: M 345 THR cc_start: 0.8158 (m) cc_final: 0.7738 (m) REVERT: P 339 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7888 (mtm-85) REVERT: S 135 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7202 (tpp) REVERT: S 272 MET cc_start: 0.7816 (mmm) cc_final: 0.7455 (mmm) REVERT: S 339 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7811 (mtp180) REVERT: V 272 MET cc_start: 0.7961 (mmm) cc_final: 0.7580 (mmm) REVERT: V 339 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7905 (mtp180) REVERT: Y 125 GLU cc_start: 0.7837 (mp0) cc_final: 0.6847 (mp0) REVERT: 1 125 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: 1 272 MET cc_start: 0.7767 (mmm) cc_final: 0.7293 (mmm) REVERT: 4 10 ASP cc_start: 0.8158 (m-30) cc_final: 0.7615 (m-30) REVERT: 4 272 MET cc_start: 0.7798 (mmm) cc_final: 0.7225 (mmm) REVERT: 4 283 LYS cc_start: 0.8424 (tppt) cc_final: 0.7934 (ttpt) outliers start: 56 outliers final: 33 residues processed: 435 average time/residue: 0.2227 time to fit residues: 159.4676 Evaluate side-chains 423 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 387 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 305 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 306 optimal weight: 0.0050 chunk 390 optimal weight: 0.8980 chunk 301 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143375 restraints weight = 40532.817| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.45 r_work: 0.3206 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33803 Z= 0.123 Angle : 0.477 7.278 45881 Z= 0.255 Chirality : 0.039 0.144 5412 Planarity : 0.003 0.035 5555 Dihedral : 11.077 74.092 5621 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.01 % Allowed : 10.18 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.14), residues: 4004 helix: 1.78 (0.10), residues: 2530 sheet: -1.22 (0.32), residues: 231 loop : -0.45 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 185 TYR 0.012 0.001 TYR S 69 PHE 0.012 0.002 PHE 1 169 TRP 0.004 0.001 TRP A 123 HIS 0.004 0.001 HIS S 15 Details of bonding type rmsd covalent geometry : bond 0.00280 (33792) covalent geometry : angle 0.47697 (45881) hydrogen bonds : bond 0.03772 ( 1826) hydrogen bonds : angle 3.81088 ( 5346) Misc. bond : bond 0.00209 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 408 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8254 (tt0) cc_final: 0.7957 (pt0) REVERT: A 272 MET cc_start: 0.7866 (mmm) cc_final: 0.7589 (mmm) REVERT: C 129 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7075 (ttpp) REVERT: C 272 MET cc_start: 0.8025 (mmm) cc_final: 0.7733 (mmt) REVERT: G 129 LYS cc_start: 0.7695 (ttmt) cc_final: 0.7220 (mttp) REVERT: G 272 MET cc_start: 0.7841 (mmm) cc_final: 0.7532 (mmm) REVERT: G 338 TYR cc_start: 0.8176 (t80) cc_final: 0.7774 (t80) REVERT: J 129 LYS cc_start: 0.7694 (ttpt) cc_final: 0.7228 (mttp) REVERT: J 135 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7324 (tpp) REVERT: J 272 MET cc_start: 0.7994 (mmm) cc_final: 0.7579 (mmm) REVERT: J 283 LYS cc_start: 0.8137 (tppt) cc_final: 0.7818 (ttpt) REVERT: M 135 MET cc_start: 0.7797 (tpp) cc_final: 0.7147 (tpp) REVERT: M 249 MET cc_start: 0.8294 (mmm) cc_final: 0.7818 (mmm) REVERT: M 272 MET cc_start: 0.7958 (mmm) cc_final: 0.7434 (mmm) REVERT: M 345 THR cc_start: 0.8127 (m) cc_final: 0.7712 (m) REVERT: P 135 MET cc_start: 0.7606 (tpp) cc_final: 0.7083 (tpp) REVERT: P 339 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7906 (mtm-85) REVERT: S 112 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7698 (mm-40) REVERT: S 135 MET cc_start: 0.7540 (ttm) cc_final: 0.6947 (tpp) REVERT: S 272 MET cc_start: 0.7868 (mmm) cc_final: 0.7531 (mmm) REVERT: S 339 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7834 (mtp180) REVERT: V 125 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: V 272 MET cc_start: 0.7985 (mmm) cc_final: 0.7626 (mmm) REVERT: Y 10 ASP cc_start: 0.7943 (m-30) cc_final: 0.7561 (m-30) REVERT: 1 272 MET cc_start: 0.7843 (mmm) cc_final: 0.7436 (mmm) REVERT: 4 272 MET cc_start: 0.7848 (mmm) cc_final: 0.7328 (mmm) REVERT: 4 283 LYS cc_start: 0.8348 (tppt) cc_final: 0.7885 (ttpt) outliers start: 70 outliers final: 44 residues processed: 460 average time/residue: 0.1808 time to fit residues: 137.6550 Evaluate side-chains 434 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 388 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 282 LEU Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 37 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 339 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 216 GLN ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141764 restraints weight = 40567.851| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.45 r_work: 0.3278 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33803 Z= 0.160 Angle : 0.511 5.685 45881 Z= 0.269 Chirality : 0.040 0.145 5412 Planarity : 0.004 0.035 5555 Dihedral : 11.049 74.328 5621 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.81 % Allowed : 11.51 % Favored : 86.68 % 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: 4004 helix: 1.78 (0.10), residues: 2519 sheet: -1.29 (0.33), residues: 231 loop : -0.49 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 78 TYR 0.015 0.001 TYR M 23 PHE 0.016 0.002 PHE 1 169 TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 56 Details of bonding type rmsd covalent geometry : bond 0.00374 (33792) covalent geometry : angle 0.51057 (45881) hydrogen bonds : bond 0.04047 ( 1826) hydrogen bonds : angle 3.85301 ( 5346) Misc. bond : bond 0.00207 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 398 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8095 (tt0) cc_final: 0.7800 (pt0) REVERT: A 272 MET cc_start: 0.7756 (mmm) cc_final: 0.7519 (mmm) REVERT: C 129 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7093 (ttpp) REVERT: C 272 MET cc_start: 0.7985 (mmm) cc_final: 0.7703 (mmt) REVERT: G 129 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7267 (mttp) REVERT: G 272 MET cc_start: 0.7811 (mmm) cc_final: 0.7511 (mmm) REVERT: G 283 LYS cc_start: 0.8234 (tppt) cc_final: 0.7814 (ttpt) REVERT: J 129 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7238 (mttp) REVERT: J 135 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7235 (tpp) REVERT: J 272 MET cc_start: 0.7887 (mmm) cc_final: 0.7410 (mmm) REVERT: J 283 LYS cc_start: 0.8101 (tppt) cc_final: 0.7792 (ttpt) REVERT: M 135 MET cc_start: 0.7868 (tpp) cc_final: 0.7272 (tpp) REVERT: M 249 MET cc_start: 0.8256 (mmm) cc_final: 0.7709 (mmm) REVERT: M 272 MET cc_start: 0.7940 (mmm) cc_final: 0.7417 (mmm) REVERT: M 345 THR cc_start: 0.8155 (m) cc_final: 0.7740 (m) REVERT: P 135 MET cc_start: 0.7561 (tpp) cc_final: 0.7142 (tpp) REVERT: P 339 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7836 (mtm-85) REVERT: S 112 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7608 (mm-40) REVERT: S 272 MET cc_start: 0.7763 (mmm) cc_final: 0.7361 (mmm) REVERT: S 339 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7719 (mtp180) REVERT: V 135 MET cc_start: 0.7651 (ttm) cc_final: 0.7167 (tpp) REVERT: V 272 MET cc_start: 0.7959 (mmm) cc_final: 0.7600 (mmm) REVERT: Y 10 ASP cc_start: 0.7945 (m-30) cc_final: 0.7646 (m-30) REVERT: Y 272 MET cc_start: 0.7821 (mmm) cc_final: 0.7488 (mmm) REVERT: Y 283 LYS cc_start: 0.8071 (tppt) cc_final: 0.7840 (ttpt) REVERT: 1 272 MET cc_start: 0.7789 (mmm) cc_final: 0.7381 (mmm) REVERT: 1 279 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7535 (mm-40) REVERT: 4 272 MET cc_start: 0.7783 (mmm) cc_final: 0.7268 (mmm) REVERT: 4 283 LYS cc_start: 0.8303 (tppt) cc_final: 0.7880 (ttpt) outliers start: 63 outliers final: 50 residues processed: 441 average time/residue: 0.1792 time to fit residues: 130.5872 Evaluate side-chains 443 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 392 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 263 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 330 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 333 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143477 restraints weight = 40633.810| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.40 r_work: 0.3238 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33803 Z= 0.136 Angle : 0.492 5.638 45881 Z= 0.262 Chirality : 0.040 0.145 5412 Planarity : 0.003 0.030 5555 Dihedral : 11.050 74.161 5621 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 12.20 % Favored : 86.05 % 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: 1.43 (0.14), residues: 4004 helix: 1.79 (0.10), residues: 2552 sheet: -1.28 (0.33), residues: 231 loop : -0.31 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.012 0.001 TYR Y 69 PHE 0.013 0.002 PHE 1 169 TRP 0.004 0.001 TRP A 123 HIS 0.003 0.001 HIS V 56 Details of bonding type rmsd covalent geometry : bond 0.00313 (33792) covalent geometry : angle 0.49238 (45881) hydrogen bonds : bond 0.03817 ( 1826) hydrogen bonds : angle 3.79420 ( 5346) Misc. bond : bond 0.00208 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 413 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8177 (tt0) cc_final: 0.7895 (pt0) REVERT: A 272 MET cc_start: 0.7808 (mmm) cc_final: 0.7561 (mmm) REVERT: C 249 MET cc_start: 0.8292 (mmm) cc_final: 0.8004 (mmm) REVERT: C 272 MET cc_start: 0.8001 (mmm) cc_final: 0.7468 (mmm) REVERT: G 129 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7255 (mttp) REVERT: G 272 MET cc_start: 0.7870 (mmm) cc_final: 0.7584 (mmm) REVERT: G 283 LYS cc_start: 0.8215 (tppt) cc_final: 0.7849 (ttpt) REVERT: G 338 TYR cc_start: 0.8084 (t80) cc_final: 0.7770 (t80) REVERT: J 129 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7265 (mttp) REVERT: J 135 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7319 (tpp) REVERT: J 272 MET cc_start: 0.7882 (mmm) cc_final: 0.7466 (mmm) REVERT: J 283 LYS cc_start: 0.8073 (tppt) cc_final: 0.7815 (ttpt) REVERT: M 135 MET cc_start: 0.7887 (tpp) cc_final: 0.7304 (tpp) REVERT: M 345 THR cc_start: 0.8169 (m) cc_final: 0.7753 (m) REVERT: P 135 MET cc_start: 0.7654 (tpp) cc_final: 0.7317 (tpp) REVERT: P 339 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7858 (mtm-85) REVERT: S 112 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7603 (mm-40) REVERT: S 125 GLU cc_start: 0.7583 (mp0) cc_final: 0.6507 (mp0) REVERT: S 272 MET cc_start: 0.7763 (mmm) cc_final: 0.7386 (mmm) REVERT: S 339 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7810 (mtp180) REVERT: V 135 MET cc_start: 0.7650 (ttm) cc_final: 0.7209 (tpp) REVERT: V 272 MET cc_start: 0.7945 (mmm) cc_final: 0.7609 (mmm) REVERT: V 339 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7848 (mtp180) REVERT: Y 10 ASP cc_start: 0.7902 (m-30) cc_final: 0.7505 (m-30) REVERT: Y 272 MET cc_start: 0.7850 (mmm) cc_final: 0.7538 (mmm) REVERT: 1 258 MET cc_start: 0.8363 (mmm) cc_final: 0.8035 (mmm) REVERT: 1 272 MET cc_start: 0.7845 (mmm) cc_final: 0.7527 (mmm) REVERT: 4 272 MET cc_start: 0.7799 (mmm) cc_final: 0.7304 (mmm) REVERT: 4 283 LYS cc_start: 0.8235 (tppt) cc_final: 0.7863 (ttpt) outliers start: 61 outliers final: 50 residues processed: 455 average time/residue: 0.1827 time to fit residues: 138.1880 Evaluate side-chains 452 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 302 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 142 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141430 restraints weight = 40522.545| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.54 r_work: 0.3230 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33803 Z= 0.123 Angle : 0.485 6.010 45881 Z= 0.257 Chirality : 0.039 0.144 5412 Planarity : 0.003 0.026 5555 Dihedral : 11.075 74.057 5621 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.70 % Allowed : 12.95 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.14), residues: 4004 helix: 1.88 (0.10), residues: 2552 sheet: -1.28 (0.34), residues: 231 loop : -0.32 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 185 TYR 0.011 0.001 TYR S 69 PHE 0.012 0.002 PHE 1 169 TRP 0.004 0.001 TRP S 123 HIS 0.004 0.001 HIS G 56 Details of bonding type rmsd covalent geometry : bond 0.00281 (33792) covalent geometry : angle 0.48475 (45881) hydrogen bonds : bond 0.03711 ( 1826) hydrogen bonds : angle 3.74374 ( 5346) Misc. bond : bond 0.00217 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8068 (tt0) cc_final: 0.7769 (pt0) REVERT: A 272 MET cc_start: 0.7889 (mmm) cc_final: 0.7386 (mmm) REVERT: C 135 MET cc_start: 0.7838 (tpp) cc_final: 0.7443 (tpp) REVERT: C 272 MET cc_start: 0.8025 (mmm) cc_final: 0.7500 (mmm) REVERT: G 129 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7166 (mttp) REVERT: G 272 MET cc_start: 0.7929 (mmm) cc_final: 0.7662 (mmm) REVERT: G 283 LYS cc_start: 0.8173 (tppt) cc_final: 0.7726 (ttpt) REVERT: G 338 TYR cc_start: 0.8024 (t80) cc_final: 0.7743 (t80) REVERT: J 129 LYS cc_start: 0.7682 (ttpt) cc_final: 0.7207 (mttp) REVERT: J 272 MET cc_start: 0.7939 (mmm) cc_final: 0.7506 (mmm) REVERT: J 283 LYS cc_start: 0.8061 (tppt) cc_final: 0.7749 (ttpt) REVERT: J 338 TYR cc_start: 0.8032 (t80) cc_final: 0.7792 (t80) REVERT: M 135 MET cc_start: 0.7909 (tpp) cc_final: 0.7314 (tpp) REVERT: M 249 MET cc_start: 0.8253 (mmm) cc_final: 0.7962 (mmm) REVERT: M 272 MET cc_start: 0.7911 (mmm) cc_final: 0.7411 (mmm) REVERT: M 338 TYR cc_start: 0.7894 (t80) cc_final: 0.7492 (t80) REVERT: M 345 THR cc_start: 0.8131 (m) cc_final: 0.7719 (m) REVERT: P 135 MET cc_start: 0.7697 (tpp) cc_final: 0.7369 (tpp) REVERT: P 339 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7789 (mtm-85) REVERT: S 112 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7541 (mm-40) REVERT: S 272 MET cc_start: 0.7817 (mmm) cc_final: 0.7552 (mmm) REVERT: S 339 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7789 (mtp180) REVERT: V 135 MET cc_start: 0.7629 (ttm) cc_final: 0.7148 (tpp) REVERT: V 272 MET cc_start: 0.8030 (mmm) cc_final: 0.7643 (mmm) REVERT: V 339 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7789 (mtp180) REVERT: Y 10 ASP cc_start: 0.7942 (m-30) cc_final: 0.7557 (m-30) REVERT: Y 135 MET cc_start: 0.7901 (tpp) cc_final: 0.7285 (tpp) REVERT: Y 272 MET cc_start: 0.7915 (mmm) cc_final: 0.7247 (mmm) REVERT: 1 258 MET cc_start: 0.8405 (mmm) cc_final: 0.8083 (mmm) REVERT: 1 272 MET cc_start: 0.7930 (mmm) cc_final: 0.7593 (mmm) REVERT: 4 283 LYS cc_start: 0.8094 (tppt) cc_final: 0.7709 (ttpt) outliers start: 59 outliers final: 49 residues processed: 454 average time/residue: 0.1767 time to fit residues: 133.3347 Evaluate side-chains 458 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 409 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 282 LEU Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 223 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 322 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141386 restraints weight = 40336.228| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.54 r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33803 Z= 0.121 Angle : 0.492 9.650 45881 Z= 0.259 Chirality : 0.039 0.143 5412 Planarity : 0.003 0.026 5555 Dihedral : 11.087 74.029 5621 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.55 % Allowed : 13.41 % Favored : 85.04 % 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: 1.60 (0.14), residues: 4004 helix: 1.94 (0.10), residues: 2552 sheet: -1.29 (0.34), residues: 231 loop : -0.28 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 185 TYR 0.011 0.001 TYR S 69 PHE 0.012 0.002 PHE 1 169 TRP 0.003 0.001 TRP A 123 HIS 0.003 0.001 HIS S 15 Details of bonding type rmsd covalent geometry : bond 0.00277 (33792) covalent geometry : angle 0.49167 (45881) hydrogen bonds : bond 0.03655 ( 1826) hydrogen bonds : angle 3.71598 ( 5346) Misc. bond : bond 0.00211 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 420 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8333 (tt0) cc_final: 0.7981 (pt0) REVERT: A 272 MET cc_start: 0.8026 (mmm) cc_final: 0.7523 (mmm) REVERT: C 10 ASP cc_start: 0.8236 (m-30) cc_final: 0.7913 (m-30) REVERT: C 135 MET cc_start: 0.7872 (tpp) cc_final: 0.7520 (tpp) REVERT: G 129 LYS cc_start: 0.7677 (ttmt) cc_final: 0.7172 (mttp) REVERT: G 272 MET cc_start: 0.8052 (mmm) cc_final: 0.7776 (mmm) REVERT: G 283 LYS cc_start: 0.8309 (tppt) cc_final: 0.7764 (ttpt) REVERT: G 338 TYR cc_start: 0.8227 (t80) cc_final: 0.7717 (t80) REVERT: J 129 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7185 (mttp) REVERT: J 272 MET cc_start: 0.8081 (mmm) cc_final: 0.7722 (mmm) REVERT: J 283 LYS cc_start: 0.8152 (tppt) cc_final: 0.7742 (ttpt) REVERT: J 338 TYR cc_start: 0.8222 (t80) cc_final: 0.7854 (t80) REVERT: M 135 MET cc_start: 0.7904 (tpp) cc_final: 0.7327 (tpp) REVERT: M 272 MET cc_start: 0.8056 (mmm) cc_final: 0.7547 (mmm) REVERT: M 338 TYR cc_start: 0.8103 (t80) cc_final: 0.7475 (t80) REVERT: M 345 THR cc_start: 0.8048 (m) cc_final: 0.7621 (m) REVERT: P 135 MET cc_start: 0.7704 (tpp) cc_final: 0.7404 (tpp) REVERT: P 339 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.7997 (mtm-85) REVERT: S 10 ASP cc_start: 0.8109 (m-30) cc_final: 0.7635 (m-30) REVERT: S 112 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7449 (mm-40) REVERT: S 272 MET cc_start: 0.7987 (mmm) cc_final: 0.7729 (mmm) REVERT: S 339 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.8050 (mtp180) REVERT: V 22 GLN cc_start: 0.7946 (pm20) cc_final: 0.7624 (pm20) REVERT: V 135 MET cc_start: 0.7663 (ttm) cc_final: 0.7167 (tpp) REVERT: V 272 MET cc_start: 0.8116 (mmm) cc_final: 0.7726 (mmm) REVERT: V 339 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8009 (mtp180) REVERT: Y 129 LYS cc_start: 0.7389 (ttmm) cc_final: 0.7105 (mttp) REVERT: Y 135 MET cc_start: 0.7905 (tpp) cc_final: 0.7612 (tpp) REVERT: Y 272 MET cc_start: 0.8046 (mmm) cc_final: 0.7360 (mmm) REVERT: Y 283 LYS cc_start: 0.8293 (tppt) cc_final: 0.7844 (ttpt) REVERT: 1 258 MET cc_start: 0.8459 (mmm) cc_final: 0.8133 (mmm) REVERT: 1 272 MET cc_start: 0.7973 (mmm) cc_final: 0.7564 (mmm) REVERT: 1 283 LYS cc_start: 0.8332 (tppt) cc_final: 0.7557 (mttm) REVERT: 4 272 MET cc_start: 0.7962 (mmm) cc_final: 0.7731 (mmm) REVERT: 4 283 LYS cc_start: 0.8189 (tppt) cc_final: 0.7713 (ttpt) outliers start: 54 outliers final: 49 residues processed: 460 average time/residue: 0.1841 time to fit residues: 140.5698 Evaluate side-chains 462 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 413 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 375 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 373 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 370 optimal weight: 0.5980 chunk 354 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 247 optimal weight: 0.9990 chunk 103 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.171752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145995 restraints weight = 40695.177| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.39 r_work: 0.3317 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33803 Z= 0.115 Angle : 0.490 8.688 45881 Z= 0.257 Chirality : 0.039 0.143 5412 Planarity : 0.003 0.025 5555 Dihedral : 11.112 73.956 5621 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.55 % Allowed : 13.43 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.14), residues: 4004 helix: 1.97 (0.10), residues: 2563 sheet: -1.28 (0.34), residues: 231 loop : -0.30 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.010 0.001 TYR A 69 PHE 0.011 0.001 PHE P 169 TRP 0.002 0.001 TRP A 123 HIS 0.004 0.001 HIS P 56 Details of bonding type rmsd covalent geometry : bond 0.00262 (33792) covalent geometry : angle 0.48984 (45881) hydrogen bonds : bond 0.03580 ( 1826) hydrogen bonds : angle 3.68934 ( 5346) Misc. bond : bond 0.00218 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 422 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8139 (tt0) cc_final: 0.7868 (pt0) REVERT: A 272 MET cc_start: 0.7847 (mmm) cc_final: 0.7407 (mmm) REVERT: C 10 ASP cc_start: 0.8014 (m-30) cc_final: 0.7580 (m-30) REVERT: C 135 MET cc_start: 0.7807 (tpp) cc_final: 0.7446 (tpp) REVERT: C 272 MET cc_start: 0.7972 (mmm) cc_final: 0.7318 (mmm) REVERT: G 129 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7162 (mttp) REVERT: G 272 MET cc_start: 0.7870 (mmm) cc_final: 0.7624 (mmm) REVERT: G 283 LYS cc_start: 0.8175 (tppt) cc_final: 0.7765 (ttpt) REVERT: J 31 THR cc_start: 0.7240 (p) cc_final: 0.6693 (t) REVERT: J 129 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7275 (mttp) REVERT: J 272 MET cc_start: 0.7920 (mmm) cc_final: 0.7654 (mmm) REVERT: J 283 LYS cc_start: 0.8083 (tppt) cc_final: 0.7792 (ttpt) REVERT: J 338 TYR cc_start: 0.7982 (t80) cc_final: 0.7726 (t80) REVERT: M 272 MET cc_start: 0.7872 (mmm) cc_final: 0.7415 (mmm) REVERT: M 338 TYR cc_start: 0.7845 (t80) cc_final: 0.7357 (t80) REVERT: M 345 THR cc_start: 0.8102 (m) cc_final: 0.7674 (m) REVERT: P 135 MET cc_start: 0.7740 (tpp) cc_final: 0.7535 (tpp) REVERT: P 339 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7821 (mtm-85) REVERT: S 10 ASP cc_start: 0.7880 (m-30) cc_final: 0.7370 (m-30) REVERT: S 272 MET cc_start: 0.7835 (mmm) cc_final: 0.7456 (mmm) REVERT: V 22 GLN cc_start: 0.7599 (pm20) cc_final: 0.7268 (pm20) REVERT: V 135 MET cc_start: 0.7599 (ttm) cc_final: 0.7220 (tpp) REVERT: V 272 MET cc_start: 0.7999 (mmm) cc_final: 0.7632 (mmm) REVERT: V 339 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7784 (mtp180) REVERT: Y 129 LYS cc_start: 0.7358 (ttmm) cc_final: 0.7100 (mttp) REVERT: Y 135 MET cc_start: 0.7885 (tpp) cc_final: 0.7386 (tpp) REVERT: Y 283 LYS cc_start: 0.8168 (tppt) cc_final: 0.7851 (ttpt) REVERT: 1 258 MET cc_start: 0.8381 (mmm) cc_final: 0.8066 (mmm) REVERT: 1 272 MET cc_start: 0.7790 (mmm) cc_final: 0.7442 (mmm) REVERT: 1 283 LYS cc_start: 0.8211 (tppt) cc_final: 0.7667 (mttm) REVERT: 4 22 GLN cc_start: 0.7776 (pm20) cc_final: 0.7456 (pm20) REVERT: 4 129 LYS cc_start: 0.7697 (ttpt) cc_final: 0.7284 (mttp) REVERT: 4 283 LYS cc_start: 0.8097 (tppt) cc_final: 0.7756 (ttpt) outliers start: 54 outliers final: 53 residues processed: 459 average time/residue: 0.1817 time to fit residues: 137.6372 Evaluate side-chains 470 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 417 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 282 LEU Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 139 optimal weight: 0.2980 chunk 167 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 267 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 394 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS C 284 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141640 restraints weight = 40484.325| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.54 r_work: 0.3302 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33803 Z= 0.126 Angle : 0.498 8.764 45881 Z= 0.260 Chirality : 0.039 0.142 5412 Planarity : 0.003 0.026 5555 Dihedral : 11.098 74.073 5621 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.61 % Allowed : 13.55 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.61 (0.14), residues: 4004 helix: 1.95 (0.10), residues: 2563 sheet: -1.31 (0.34), residues: 231 loop : -0.28 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 185 TYR 0.012 0.001 TYR 4 69 PHE 0.013 0.002 PHE 1 169 TRP 0.002 0.001 TRP A 123 HIS 0.003 0.001 HIS Y 15 Details of bonding type rmsd covalent geometry : bond 0.00292 (33792) covalent geometry : angle 0.49789 (45881) hydrogen bonds : bond 0.03689 ( 1826) hydrogen bonds : angle 3.70764 ( 5346) Misc. bond : bond 0.00210 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6456.69 seconds wall clock time: 112 minutes 6.64 seconds (6726.64 seconds total)