Starting phenix.real_space_refine on Sun Aug 9 05:17:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_17618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdq_17618/08_2026/8pdq_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 2.86, per 1000 atoms: 0.09 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.39 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: 5.39 Time building geometry restraints manager: 3.41 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=" O3' C R 73 " pdb=" P C R 74 " ideal model delta sigma weight residual 1.607 1.596 0.011 1.20e-02 6.94e+03 8.55e-01 bond pdb=" O3' C I 73 " pdb=" P C I 74 " ideal model delta sigma weight residual 1.607 1.596 0.011 1.20e-02 6.94e+03 8.44e-01 bond pdb=" O3' C E 73 " pdb=" P C E 74 " ideal model delta sigma weight residual 1.607 1.596 0.011 1.20e-02 6.94e+03 8.43e-01 bond pdb=" O3' C F 73 " pdb=" P C F 74 " ideal model delta sigma weight residual 1.607 1.596 0.011 1.20e-02 6.94e+03 8.35e-01 bond pdb=" O3' C U 73 " pdb=" P C U 74 " ideal model delta sigma weight residual 1.607 1.596 0.011 1.20e-02 6.94e+03 8.30e-01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 43701 1.20 - 2.39: 1608 2.39 - 3.59: 474 3.59 - 4.78: 74 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: 18077 15.55 - 31.10: 1921 31.10 - 46.65: 572 46.65 - 62.20: 143 62.20 - 77.75: 143 Dihedral angle restraints: 20856 sinusoidal: 9075 harmonic: 11781 Sorted by residual: dihedral pdb=" C4' C I 74 " pdb=" C3' C I 74 " pdb=" C2' C I 74 " pdb=" C1' C I 74 " ideal model delta sinusoidal sigma weight residual 36.35 -33.80 70.15 1 3.10e+00 1.04e-01 6.60e+02 dihedral pdb=" C4' C X 74 " pdb=" C3' C X 74 " pdb=" C2' C X 74 " pdb=" C1' C X 74 " ideal model delta sinusoidal sigma weight residual 36.34 -33.79 70.14 1 3.10e+00 1.04e-01 6.60e+02 dihedral pdb=" C4' C O 74 " pdb=" C3' C O 74 " pdb=" C2' C O 74 " pdb=" C1' C O 74 " ideal model delta sinusoidal sigma weight residual 36.34 -33.76 70.11 1 3.10e+00 1.04e-01 6.59e+02 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4401 0.056 - 0.112: 849 0.112 - 0.168: 74 0.168 - 0.224: 24 0.224 - 0.280: 64 Chirality restraints: 5412 Sorted by residual: chirality pdb=" C2' C R 74 " pdb=" C3' C R 74 " pdb=" O2' C R 74 " pdb=" C1' C R 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2' C 0 74 " pdb=" C3' C 0 74 " pdb=" O2' C 0 74 " pdb=" C1' C 0 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' C L 74 " pdb=" C3' C L 74 " pdb=" O2' C L 74 " pdb=" C1' C L 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (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: 0.08 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.280 Find NCS groups from input model: 0.240 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.601 5.976 45881 Z= 0.325 Chirality : 0.050 0.280 5412 Planarity : 0.004 0.040 5555 Dihedral : 15.865 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 are 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/Z covalent geometry : bond 0.00384 / 0.17 (33792) covalent geometry : angle 0.60057 / 0.32 (45881) hydrogen bonds : bond 0.12847 / 8.57 ( 1826) hydrogen bonds : angle 5.23660 / 3.70 ( 5346) Misc. bond : bond 1.19416 / 69.21 ( 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 : 1.204 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: 0.1938 time to fit residues: 148.5482 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 : 1.256 ------------------------------------------------------------------------------- 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... A 15 HIS ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN 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 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN S 306 GLN ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** 1 279 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 = 0.3882 r_free = 0.3882 target = 0.167933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137686 restraints weight = 40904.736| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.67 r_work: 0.3241 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33803 Z= 0.189 Angle : 0.730 9.031 45881 Z= 0.338 Chirality : 0.054 0.552 5412 Planarity : 0.006 0.111 5555 Dihedral : 12.217 73.866 5621 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.72 % Allowed : 8.29 % Favored : 91.00 % 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 are not related in a simple way. whole: 0.69 (0.13), residues: 4004 helix: 1.24 (0.10), residues: 2519 sheet: -1.42 (0.29), residues: 231 loop : -0.68 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 78 TYR 0.017 0.002 TYR G 23 PHE 0.016 0.002 PHE Y 224 TRP 0.005 0.001 TRP 4 123 HIS 0.005 0.001 HIS V 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (33792) covalent geometry : angle 0.73016 / 0.34 (45881) hydrogen bonds : bond 0.04578 / 3.08 ( 1826) hydrogen bonds : angle 4.20450 / 2.95 ( 5346) Misc. bond : bond 0.00457 / 0.27 ( 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 451 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 426 time to evaluate : 1.114 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 181 GLU cc_start: 0.7996 (tt0) cc_final: 0.7665 (pt0) REVERT: A 272 MET cc_start: 0.7746 (mmm) cc_final: 0.7376 (mmm) REVERT: C 129 LYS cc_start: 0.7676 (ttmt) cc_final: 0.6939 (ttpp) REVERT: C 272 MET cc_start: 0.7920 (mmm) cc_final: 0.7272 (mmm) REVERT: G 129 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7142 (mttp) REVERT: J 23 TYR cc_start: 0.7697 (m-80) cc_final: 0.7459 (m-80) REVERT: J 272 MET cc_start: 0.7827 (mmm) cc_final: 0.7504 (mmm) REVERT: M 249 MET cc_start: 0.8385 (mmm) cc_final: 0.8121 (mmm) REVERT: M 279 GLN cc_start: 0.7274 (mm110) cc_final: 0.6933 (mm-40) REVERT: P 135 MET cc_start: 0.7474 (ttm) cc_final: 0.7148 (tpp) REVERT: P 272 MET cc_start: 0.8051 (mmm) cc_final: 0.7572 (mmm) REVERT: P 339 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7987 (mtt180) REVERT: S 125 GLU cc_start: 0.7574 (mp0) cc_final: 0.6465 (mp0) REVERT: S 135 MET cc_start: 0.7391 (ttm) cc_final: 0.6739 (tpp) REVERT: S 138 LEU cc_start: 0.8104 (mm) cc_final: 0.7876 (mm) REVERT: S 272 MET cc_start: 0.7810 (mmm) cc_final: 0.7414 (mmm) REVERT: S 339 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7770 (mtp180) REVERT: Y 272 MET cc_start: 0.7800 (mmm) cc_final: 0.7103 (mmm) REVERT: 1 129 LYS cc_start: 0.7646 (ttmt) cc_final: 0.6819 (ttpp) REVERT: 1 135 MET cc_start: 0.7711 (ttm) cc_final: 0.7499 (tpp) REVERT: 4 337 MET cc_start: 0.8190 (mmm) cc_final: 0.7923 (tmm) REVERT: 4 341 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7370 (mtm180) outliers start: 25 outliers final: 19 residues processed: 440 average time/residue: 0.2021 time to fit residues: 146.4739 Evaluate side-chains 408 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 389 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 G residue 235 SER 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 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: 0.7980 chunk 24 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 390 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 313 optimal weight: 0.6980 chunk 311 optimal weight: 2.9990 chunk 375 optimal weight: 0.8980 chunk 335 optimal weight: 0.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 284 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144739 restraints weight = 40786.570| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.38 r_work: 0.3325 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33803 Z= 0.136 Angle : 0.585 9.012 45881 Z= 0.277 Chirality : 0.046 0.275 5412 Planarity : 0.004 0.067 5555 Dihedral : 12.489 107.012 5621 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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 are not related in a simple way. whole: 1.08 (0.13), residues: 4004 helix: 1.57 (0.10), residues: 2530 sheet: -1.37 (0.30), residues: 231 loop : -0.57 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 78 TYR 0.013 0.001 TYR Y 23 PHE 0.012 0.002 PHE P 169 TRP 0.005 0.001 TRP 4 123 HIS 0.005 0.001 HIS V 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (33792) covalent geometry : angle 0.58482 / 0.28 (45881) hydrogen bonds : bond 0.04026 / 2.69 ( 1826) hydrogen bonds : angle 3.96118 / 2.78 ( 5346) Misc. bond : bond 0.00320 / 0.19 ( 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 444 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 397 time to evaluate : 1.218 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: 0.7662 (mmm) cc_final: 0.7372 (mmm) REVERT: C 129 LYS cc_start: 0.7703 (ttmt) cc_final: 0.7089 (ttpp) REVERT: C 272 MET cc_start: 0.7917 (mmm) cc_final: 0.7233 (mmm) REVERT: G 129 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7218 (mttp) REVERT: G 272 MET cc_start: 0.7675 (mmm) cc_final: 0.7266 (mmm) REVERT: G 283 LYS cc_start: 0.8119 (tppt) cc_final: 0.7766 (ttpt) REVERT: J 129 LYS cc_start: 0.7563 (ttpt) cc_final: 0.7146 (mttp) REVERT: J 135 MET cc_start: 0.7440 (ttm) cc_final: 0.6919 (tpp) REVERT: J 272 MET cc_start: 0.7899 (mmm) cc_final: 0.7624 (mmm) REVERT: M 272 MET cc_start: 0.7774 (mmm) cc_final: 0.7331 (mmm) REVERT: M 345 THR cc_start: 0.8182 (m) cc_final: 0.7779 (m) REVERT: P 339 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7805 (mtp180) REVERT: S 272 MET cc_start: 0.7699 (mmm) cc_final: 0.7321 (mmm) REVERT: S 339 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7704 (mtp180) REVERT: V 125 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: V 135 MET cc_start: 0.7516 (ttm) cc_final: 0.7141 (tpp) REVERT: V 272 MET cc_start: 0.7805 (mmm) cc_final: 0.7429 (mmm) REVERT: Y 125 GLU cc_start: 0.7785 (mp0) cc_final: 0.6911 (mp0) REVERT: 1 125 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: 1 272 MET cc_start: 0.7741 (mmm) cc_final: 0.7426 (mmm) REVERT: 4 10 ASP cc_start: 0.8010 (m-30) cc_final: 0.7471 (m-30) REVERT: 4 272 MET cc_start: 0.7575 (mmm) cc_final: 0.7135 (mmm) REVERT: 4 283 LYS cc_start: 0.8375 (tppt) cc_final: 0.7936 (ttpt) outliers start: 47 outliers final: 25 residues processed: 435 average time/residue: 0.2130 time to fit residues: 153.6914 Evaluate side-chains 414 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 387 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 190 VAL 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 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 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: 2.9990 chunk 154 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 336 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 344 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.140542 restraints weight = 40741.816| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.46 r_work: 0.3258 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33803 Z= 0.186 Angle : 0.603 7.331 45881 Z= 0.289 Chirality : 0.047 0.286 5412 Planarity : 0.004 0.072 5555 Dihedral : 12.606 122.264 5621 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.07 % Allowed : 9.15 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4004 helix: 1.53 (0.10), residues: 2530 sheet: -1.41 (0.31), residues: 231 loop : -0.54 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 4 78 TYR 0.016 0.002 TYR S 69 PHE 0.017 0.002 PHE 1 169 TRP 0.006 0.001 TRP 4 123 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (33792) covalent geometry : angle 0.60324 / 0.29 (45881) hydrogen bonds : bond 0.04349 / 2.92 ( 1826) hydrogen bonds : angle 3.97390 / 2.79 ( 5346) Misc. bond : bond 0.00221 / 0.13 ( 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 474 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 402 time to evaluate : 1.268 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: A 272 MET cc_start: 0.7797 (mmm) cc_final: 0.7522 (mmm) REVERT: C 129 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7101 (ttpp) REVERT: C 272 MET cc_start: 0.7952 (mmm) cc_final: 0.7339 (mmm) REVERT: G 129 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7298 (mttp) REVERT: G 272 MET cc_start: 0.7748 (mmm) cc_final: 0.7448 (mmm) REVERT: J 135 MET cc_start: 0.7583 (ttm) cc_final: 0.7361 (tpp) REVERT: J 272 MET cc_start: 0.7951 (mmm) cc_final: 0.7309 (mmm) REVERT: M 249 MET cc_start: 0.8301 (mmm) cc_final: 0.7938 (mmm) REVERT: M 272 MET cc_start: 0.7855 (mmm) cc_final: 0.7412 (mmm) REVERT: M 345 THR cc_start: 0.8200 (m) cc_final: 0.7793 (m) REVERT: P 135 MET cc_start: 0.7644 (tpp) cc_final: 0.7132 (tpp) REVERT: P 339 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7866 (mtt180) REVERT: S 112 GLN cc_start: 0.7809 (mm110) cc_final: 0.7510 (mm-40) REVERT: S 135 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6971 (tpp) REVERT: S 138 LEU cc_start: 0.8183 (mm) cc_final: 0.7937 (mm) REVERT: S 272 MET cc_start: 0.7826 (mmm) cc_final: 0.7448 (mmm) REVERT: S 339 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7787 (mtp180) REVERT: V 125 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: V 135 MET cc_start: 0.7678 (ttm) cc_final: 0.7390 (tpp) REVERT: V 272 MET cc_start: 0.7908 (mmm) cc_final: 0.7517 (mmm) REVERT: 1 125 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: 4 10 ASP cc_start: 0.8120 (m-30) cc_final: 0.7587 (m-30) REVERT: 4 272 MET cc_start: 0.7755 (mmm) cc_final: 0.7173 (mmm) REVERT: 4 283 LYS cc_start: 0.8347 (tppt) cc_final: 0.7864 (ttpt) outliers start: 72 outliers final: 34 residues processed: 447 average time/residue: 0.2107 time to fit residues: 156.4420 Evaluate side-chains 421 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 31 THR 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 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 235 SER 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 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 94 LEU 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 31 THR 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 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 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 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: 0.5980 chunk 86 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 305 optimal weight: 0.7980 chunk 329 optimal weight: 0.0030 chunk 312 optimal weight: 0.7980 chunk 306 optimal weight: 0.8980 chunk 390 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** V 7 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141456 restraints weight = 40559.194| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.52 r_work: 0.3250 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1772 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= 0.117 Angle : 0.552 8.352 45881 Z= 0.261 Chirality : 0.046 0.303 5412 Planarity : 0.003 0.035 5555 Dihedral : 12.584 133.271 5621 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.58 % Allowed : 11.05 % Favored : 87.37 % 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 are not related in a simple way. whole: 1.31 (0.14), residues: 4004 helix: 1.78 (0.10), residues: 2519 sheet: -1.26 (0.32), residues: 231 loop : -0.54 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 78 TYR 0.018 0.001 TYR M 23 PHE 0.010 0.001 PHE C 169 TRP 0.004 0.001 TRP A 123 HIS 0.004 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (33792) covalent geometry : angle 0.55158 / 0.26 (45881) hydrogen bonds : bond 0.03702 / 2.47 ( 1826) hydrogen bonds : angle 3.80857 / 2.67 ( 5346) Misc. bond : bond 0.00239 / 0.14 ( 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 473 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 418 time to evaluate : 1.253 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: 0.7968 (mmm) cc_final: 0.7697 (mmm) REVERT: C 129 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6971 (ttpp) REVERT: C 272 MET cc_start: 0.8070 (mmm) cc_final: 0.7496 (mmm) REVERT: G 129 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7202 (mttp) REVERT: G 272 MET cc_start: 0.7981 (mmm) cc_final: 0.7697 (mmm) REVERT: G 283 LYS cc_start: 0.8303 (tppt) cc_final: 0.7786 (ttpt) REVERT: J 129 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7180 (mttp) REVERT: J 135 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6992 (tpp) REVERT: J 272 MET cc_start: 0.8086 (mmm) cc_final: 0.7652 (mmm) REVERT: M 135 MET cc_start: 0.7582 (ttm) cc_final: 0.7314 (tpp) REVERT: M 272 MET cc_start: 0.8055 (mmm) cc_final: 0.7523 (mmm) REVERT: M 345 THR cc_start: 0.8062 (m) cc_final: 0.7658 (m) REVERT: P 135 MET cc_start: 0.7583 (tpp) cc_final: 0.7116 (tpp) REVERT: P 283 LYS cc_start: 0.8146 (tppt) cc_final: 0.7772 (ttpt) REVERT: P 339 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8023 (mtm-85) REVERT: S 112 GLN cc_start: 0.7758 (mm110) cc_final: 0.7424 (mm-40) REVERT: S 135 MET cc_start: 0.7601 (ttm) cc_final: 0.7272 (tpp) REVERT: S 272 MET cc_start: 0.7909 (mmm) cc_final: 0.7508 (mmm) REVERT: S 339 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.8061 (mtp180) REVERT: V 125 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: V 135 MET cc_start: 0.7569 (ttm) cc_final: 0.7121 (tpp) REVERT: V 272 MET cc_start: 0.8054 (mmm) cc_final: 0.7641 (mmm) REVERT: Y 10 ASP cc_start: 0.8055 (m-30) cc_final: 0.7668 (m-30) REVERT: Y 272 MET cc_start: 0.8054 (mmm) cc_final: 0.7842 (mmm) REVERT: Y 283 LYS cc_start: 0.8142 (tppt) cc_final: 0.7819 (ttpt) REVERT: 1 279 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7595 (mm-40) REVERT: 4 272 MET cc_start: 0.7907 (mmm) cc_final: 0.7359 (mmm) REVERT: 4 283 LYS cc_start: 0.8337 (tppt) cc_final: 0.7817 (ttpt) outliers start: 55 outliers final: 38 residues processed: 462 average time/residue: 0.2058 time to fit residues: 158.4521 Evaluate side-chains 434 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 394 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU 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 125 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER 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: 2.9990 chunk 343 optimal weight: 4.9990 chunk 234 optimal weight: 0.2980 chunk 339 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 7 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140124 restraints weight = 40502.629| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.51 r_work: 0.3272 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33803 Z= 0.150 Angle : 0.569 7.562 45881 Z= 0.272 Chirality : 0.047 0.291 5412 Planarity : 0.003 0.035 5555 Dihedral : 12.592 134.324 5621 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.70 % Allowed : 12.34 % Favored : 85.96 % 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 are not related in a simple way. whole: 1.36 (0.13), residues: 4004 helix: 1.73 (0.10), residues: 2552 sheet: -1.33 (0.33), residues: 231 loop : -0.33 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 78 TYR 0.014 0.001 TYR S 69 PHE 0.016 0.002 PHE 1 169 TRP 0.004 0.001 TRP 4 123 HIS 0.003 0.001 HIS S 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (33792) covalent geometry : angle 0.56919 / 0.27 (45881) hydrogen bonds : bond 0.03961 / 2.66 ( 1826) hydrogen bonds : angle 3.82745 / 2.68 ( 5346) Misc. bond : bond 0.00200 / 0.12 ( 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 464 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 405 time to evaluate : 1.206 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: 0.8042 (tt0) cc_final: 0.7741 (pt0) REVERT: A 272 MET cc_start: 0.7862 (mmm) cc_final: 0.7595 (mmm) REVERT: C 129 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7033 (ttpp) REVERT: C 272 MET cc_start: 0.8000 (mmm) cc_final: 0.7453 (mmm) REVERT: G 129 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7242 (mttp) REVERT: G 272 MET cc_start: 0.7884 (mmm) cc_final: 0.7583 (mmm) REVERT: G 283 LYS cc_start: 0.8235 (tppt) cc_final: 0.7786 (ttpt) REVERT: J 135 MET cc_start: 0.7570 (ttm) cc_final: 0.7136 (tpp) REVERT: J 272 MET cc_start: 0.7908 (mmm) cc_final: 0.7427 (mmm) REVERT: M 112 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7433 (mm-40) REVERT: M 135 MET cc_start: 0.7508 (ttm) cc_final: 0.7056 (tpp) REVERT: M 249 MET cc_start: 0.8305 (mmm) cc_final: 0.8008 (mmm) REVERT: M 272 MET cc_start: 0.7963 (mmm) cc_final: 0.7422 (mmm) REVERT: M 345 THR cc_start: 0.8144 (m) cc_final: 0.7717 (m) REVERT: P 135 MET cc_start: 0.7505 (tpp) cc_final: 0.7130 (tpp) REVERT: P 283 LYS cc_start: 0.8057 (tppt) cc_final: 0.7763 (ttpt) REVERT: P 339 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7787 (mtm-85) REVERT: S 112 GLN cc_start: 0.7797 (mm110) cc_final: 0.7459 (mm-40) REVERT: S 125 GLU cc_start: 0.7581 (mp0) cc_final: 0.6465 (mp0) REVERT: S 135 MET cc_start: 0.7490 (ttm) cc_final: 0.7238 (tpp) REVERT: S 272 MET cc_start: 0.7796 (mmm) cc_final: 0.7384 (mmm) REVERT: S 339 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7770 (mtp180) REVERT: V 135 MET cc_start: 0.7449 (ttm) cc_final: 0.7238 (tpp) REVERT: V 272 MET cc_start: 0.7961 (mmm) cc_final: 0.7572 (mmm) REVERT: V 339 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7810 (mtp180) REVERT: Y 10 ASP cc_start: 0.7943 (m-30) cc_final: 0.7548 (m-30) REVERT: Y 283 LYS cc_start: 0.8107 (tppt) cc_final: 0.7822 (ttpt) REVERT: 1 272 MET cc_start: 0.7686 (mmm) cc_final: 0.7325 (mmm) REVERT: 4 272 MET cc_start: 0.7831 (mmm) cc_final: 0.7311 (mmm) REVERT: 4 283 LYS cc_start: 0.8298 (tppt) cc_final: 0.7837 (ttpt) outliers start: 59 outliers final: 46 residues processed: 447 average time/residue: 0.1962 time to fit residues: 146.7777 Evaluate side-chains 448 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 135 MET 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 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 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 94 LEU 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 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 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: 0.9980 chunk 230 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 333 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 7 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140680 restraints weight = 40619.162| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.49 r_work: 0.3285 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1878 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= 0.137 Angle : 0.563 7.774 45881 Z= 0.267 Chirality : 0.047 0.294 5412 Planarity : 0.003 0.030 5555 Dihedral : 12.577 134.652 5621 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.96 % Allowed : 12.60 % Favored : 85.44 % 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 are not related in a simple way. whole: 1.44 (0.14), residues: 4004 helix: 1.81 (0.10), residues: 2552 sheet: -1.33 (0.33), residues: 231 loop : -0.33 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 78 TYR 0.013 0.001 TYR S 69 PHE 0.014 0.002 PHE 1 169 TRP 0.004 0.001 TRP A 123 HIS 0.003 0.001 HIS S 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (33792) covalent geometry : angle 0.56311 / 0.27 (45881) hydrogen bonds : bond 0.03818 / 2.56 ( 1826) hydrogen bonds : angle 3.78009 / 2.65 ( 5346) Misc. bond : bond 0.00203 / 0.12 ( 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 483 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 415 time to evaluate : 1.223 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 181 GLU cc_start: 0.8018 (tt0) cc_final: 0.7725 (pt0) REVERT: A 272 MET cc_start: 0.7860 (mmm) cc_final: 0.7598 (mmm) REVERT: C 272 MET cc_start: 0.8009 (mmm) cc_final: 0.7468 (mmm) REVERT: G 129 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7233 (mttp) REVERT: G 272 MET cc_start: 0.7915 (mmm) cc_final: 0.7618 (mmm) REVERT: G 283 LYS cc_start: 0.8197 (tppt) cc_final: 0.7766 (ttpt) REVERT: J 135 MET cc_start: 0.7550 (ttm) cc_final: 0.7241 (tpp) REVERT: J 272 MET cc_start: 0.7912 (mmm) cc_final: 0.7455 (mmm) REVERT: M 135 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7209 (tpp) REVERT: M 345 THR cc_start: 0.8148 (m) cc_final: 0.7729 (m) REVERT: P 135 MET cc_start: 0.7647 (tpp) cc_final: 0.7330 (tpp) REVERT: P 283 LYS cc_start: 0.8040 (tppt) cc_final: 0.7743 (ttpt) REVERT: P 339 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7757 (mtm-85) REVERT: S 272 MET cc_start: 0.7794 (mmm) cc_final: 0.7390 (mmm) REVERT: S 339 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7740 (mtp180) REVERT: V 135 MET cc_start: 0.7521 (ttm) cc_final: 0.6964 (tpp) REVERT: V 272 MET cc_start: 0.7996 (mmm) cc_final: 0.7579 (mmm) REVERT: Y 10 ASP cc_start: 0.7921 (m-30) cc_final: 0.7514 (m-30) REVERT: Y 135 MET cc_start: 0.7462 (ttm) cc_final: 0.7259 (tpp) REVERT: Y 283 LYS cc_start: 0.8079 (tppt) cc_final: 0.7818 (ttpt) REVERT: 1 272 MET cc_start: 0.7772 (mmm) cc_final: 0.7436 (mmm) REVERT: 4 272 MET cc_start: 0.7800 (mmm) cc_final: 0.7377 (mmm) REVERT: 4 283 LYS cc_start: 0.8216 (tppt) cc_final: 0.7779 (ttpt) outliers start: 68 outliers final: 51 residues processed: 458 average time/residue: 0.1980 time to fit residues: 151.0702 Evaluate side-chains 459 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 135 MET 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 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 135 MET Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 94 LEU 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 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 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 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: 3.9990 chunk 72 optimal weight: 0.0970 chunk 328 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 142 optimal weight: 0.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 7 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141944 restraints weight = 40539.133| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.52 r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33803 Z= 0.116 Angle : 0.553 8.001 45881 Z= 0.260 Chirality : 0.046 0.303 5412 Planarity : 0.003 0.026 5555 Dihedral : 12.554 134.139 5621 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.75 % Allowed : 12.97 % Favored : 85.27 % 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 are not related in a simple way. whole: 1.57 (0.14), residues: 4004 helix: 1.93 (0.10), residues: 2552 sheet: -1.30 (0.34), residues: 231 loop : -0.31 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 78 TYR 0.011 0.001 TYR J 69 PHE 0.012 0.002 PHE P 169 TRP 0.003 0.001 TRP A 123 HIS 0.004 0.001 HIS V 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (33792) covalent geometry : angle 0.55294 / 0.26 (45881) hydrogen bonds : bond 0.03622 / 2.42 ( 1826) hydrogen bonds : angle 3.71875 / 2.61 ( 5346) Misc. bond : bond 0.00209 / 0.12 ( 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 483 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 0.882 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 112 GLN cc_start: 0.7348 (mm110) cc_final: 0.7092 (mm-40) REVERT: A 181 GLU cc_start: 0.8328 (tt0) cc_final: 0.7998 (pt0) REVERT: A 272 MET cc_start: 0.8013 (mmm) cc_final: 0.7726 (mmm) REVERT: G 10 ASP cc_start: 0.8194 (m-30) cc_final: 0.7716 (m-30) REVERT: G 129 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7166 (mttp) REVERT: G 272 MET cc_start: 0.8038 (mmm) cc_final: 0.7766 (mmm) REVERT: G 283 LYS cc_start: 0.8310 (tppt) cc_final: 0.7808 (ttpt) REVERT: J 129 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7198 (mttp) REVERT: J 135 MET cc_start: 0.7515 (ttm) cc_final: 0.7239 (tpp) REVERT: J 272 MET cc_start: 0.8104 (mmm) cc_final: 0.7673 (mmm) REVERT: J 338 TYR cc_start: 0.8286 (t80) cc_final: 0.8034 (t80) REVERT: M 135 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7241 (tpp) REVERT: M 272 MET cc_start: 0.8006 (mmm) cc_final: 0.7493 (mmm) REVERT: M 345 THR cc_start: 0.8118 (m) cc_final: 0.7695 (m) REVERT: P 112 GLN cc_start: 0.7662 (mm110) cc_final: 0.7396 (mm-40) REVERT: P 135 MET cc_start: 0.7718 (tpp) cc_final: 0.7445 (tpp) REVERT: P 283 LYS cc_start: 0.8126 (tppt) cc_final: 0.7787 (ttpt) REVERT: P 339 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8070 (mtm-85) REVERT: S 112 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7555 (mm-40) REVERT: S 125 GLU cc_start: 0.7626 (mp0) cc_final: 0.6455 (mp0) REVERT: S 272 MET cc_start: 0.7979 (mmm) cc_final: 0.7709 (mmm) REVERT: S 339 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8085 (mtp180) REVERT: V 135 MET cc_start: 0.7597 (ttm) cc_final: 0.7088 (tpp) REVERT: V 272 MET cc_start: 0.8117 (mmm) cc_final: 0.7706 (mmm) REVERT: V 339 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.8050 (mtp180) REVERT: Y 135 MET cc_start: 0.7516 (ttm) cc_final: 0.7152 (tpp) REVERT: Y 283 LYS cc_start: 0.8090 (tppt) cc_final: 0.7795 (ttpt) REVERT: 1 272 MET cc_start: 0.7994 (mmm) cc_final: 0.7601 (mmm) REVERT: 4 283 LYS cc_start: 0.8175 (tppt) cc_final: 0.7708 (ttpt) outliers start: 61 outliers final: 49 residues processed: 464 average time/residue: 0.1947 time to fit residues: 150.4625 Evaluate side-chains 465 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 415 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 294 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 135 MET 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 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 135 MET Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL 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 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 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: 0.6980 chunk 149 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** 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 7 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135974 restraints weight = 40558.605| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.75 r_work: 0.3177 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33803 Z= 0.258 Angle : 0.670 7.567 45881 Z= 0.319 Chirality : 0.051 0.318 5412 Planarity : 0.004 0.045 5555 Dihedral : 12.647 137.556 5621 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.70 % Allowed : 13.46 % 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 are not related in a simple way. whole: 1.13 (0.13), residues: 4004 helix: 1.55 (0.10), residues: 2552 sheet: -1.54 (0.32), residues: 231 loop : -0.39 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 27 TYR 0.021 0.002 TYR S 69 PHE 0.019 0.002 PHE J 169 TRP 0.007 0.002 TRP V 261 HIS 0.004 0.001 HIS V 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (33792) covalent geometry : angle 0.66966 / 0.32 (45881) hydrogen bonds : bond 0.04710 / 3.18 ( 1826) hydrogen bonds : angle 4.01128 / 2.81 ( 5346) Misc. bond : bond 0.00209 / 0.12 ( 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 477 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 418 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: A 181 GLU cc_start: 0.8094 (tt0) cc_final: 0.7770 (pt0) REVERT: A 241 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7501 (mt-10) REVERT: A 272 MET cc_start: 0.7850 (mmm) cc_final: 0.7614 (mmm) REVERT: C 272 MET cc_start: 0.8053 (mmm) cc_final: 0.7448 (mmm) REVERT: G 129 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7381 (ttmm) REVERT: G 272 MET cc_start: 0.7861 (mmm) cc_final: 0.7601 (mmm) REVERT: G 283 LYS cc_start: 0.8244 (tppt) cc_final: 0.7744 (ttpt) REVERT: J 135 MET cc_start: 0.7555 (ttm) cc_final: 0.7305 (tpp) REVERT: J 272 MET cc_start: 0.7977 (mmm) cc_final: 0.7482 (mmm) REVERT: M 135 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7300 (tpp) REVERT: M 272 MET cc_start: 0.7946 (mmm) cc_final: 0.7431 (mmm) REVERT: P 112 GLN cc_start: 0.7734 (mm110) cc_final: 0.7467 (mm-40) REVERT: P 135 MET cc_start: 0.7782 (tpp) cc_final: 0.7542 (tpp) REVERT: P 283 LYS cc_start: 0.8126 (tppt) cc_final: 0.7770 (ttpt) REVERT: P 339 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7884 (mtm-85) REVERT: S 112 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7672 (mm-40) REVERT: S 125 GLU cc_start: 0.7608 (mp0) cc_final: 0.6366 (mp0) REVERT: S 272 MET cc_start: 0.7842 (mmm) cc_final: 0.7430 (mmm) REVERT: S 339 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7792 (mtp180) REVERT: V 135 MET cc_start: 0.7672 (ttm) cc_final: 0.7428 (tpp) REVERT: V 272 MET cc_start: 0.7920 (mmm) cc_final: 0.7495 (mmm) REVERT: Y 283 LYS cc_start: 0.8068 (tppt) cc_final: 0.7774 (ttpt) REVERT: 4 22 GLN cc_start: 0.7977 (pm20) cc_final: 0.7746 (pm20) REVERT: 4 283 LYS cc_start: 0.8147 (tppt) cc_final: 0.7713 (ttpt) outliers start: 59 outliers final: 51 residues processed: 457 average time/residue: 0.1970 time to fit residues: 150.1841 Evaluate side-chains 465 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 413 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 MET 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 282 LEU 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 135 MET Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL 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 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 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 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 31 THR 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: 0.7980 chunk 6 optimal weight: 0.7980 chunk 373 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 107 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS ** 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.169984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140865 restraints weight = 40697.663| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.59 r_work: 0.3274 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33803 Z= 0.122 Angle : 0.576 8.342 45881 Z= 0.272 Chirality : 0.047 0.321 5412 Planarity : 0.003 0.027 5555 Dihedral : 12.579 135.083 5621 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.50 % Allowed : 13.49 % 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 are not related in a simple way. whole: 1.42 (0.14), residues: 4004 helix: 1.81 (0.10), residues: 2552 sheet: -1.49 (0.32), residues: 231 loop : -0.36 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 78 TYR 0.011 0.001 TYR 4 69 PHE 0.013 0.002 PHE P 169 TRP 0.003 0.001 TRP G 123 HIS 0.004 0.001 HIS 4 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33792) covalent geometry : angle 0.57649 / 0.27 (45881) hydrogen bonds : bond 0.03728 / 2.49 ( 1826) hydrogen bonds : angle 3.80183 / 2.66 ( 5346) Misc. bond : bond 0.00224 / 0.13 ( 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 470 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 418 time to evaluate : 0.828 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 112 GLN cc_start: 0.7386 (mm110) cc_final: 0.7127 (mm-40) REVERT: A 181 GLU cc_start: 0.8328 (tt0) cc_final: 0.7976 (pt0) REVERT: A 272 MET cc_start: 0.8043 (mmm) cc_final: 0.7542 (mmm) REVERT: C 272 MET cc_start: 0.8107 (mmm) cc_final: 0.7488 (mmm) REVERT: G 112 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6996 (mm-40) REVERT: G 129 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7218 (mttp) REVERT: G 272 MET cc_start: 0.8043 (mmm) cc_final: 0.7776 (mmm) REVERT: G 283 LYS cc_start: 0.8306 (tppt) cc_final: 0.7769 (ttpt) REVERT: J 135 MET cc_start: 0.7448 (ttm) cc_final: 0.7246 (tpp) REVERT: J 272 MET cc_start: 0.8127 (mmm) cc_final: 0.7778 (mmm) REVERT: J 338 TYR cc_start: 0.8287 (t80) cc_final: 0.7944 (t80) REVERT: M 135 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7283 (tpp) REVERT: M 272 MET cc_start: 0.8054 (mmm) cc_final: 0.7544 (mmm) REVERT: M 345 THR cc_start: 0.8079 (m) cc_final: 0.7621 (m) REVERT: P 112 GLN cc_start: 0.7866 (mm110) cc_final: 0.7599 (mm-40) REVERT: P 135 MET cc_start: 0.7673 (tpp) cc_final: 0.7433 (tpp) REVERT: P 283 LYS cc_start: 0.8153 (tppt) cc_final: 0.7760 (ttpt) REVERT: P 337 MET cc_start: 0.8409 (mmm) cc_final: 0.7923 (tmm) REVERT: P 339 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8044 (mtm-85) REVERT: S 112 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7592 (mm-40) REVERT: S 125 GLU cc_start: 0.7604 (mp0) cc_final: 0.6440 (mp0) REVERT: S 272 MET cc_start: 0.7982 (mmm) cc_final: 0.7706 (mmm) REVERT: S 339 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8082 (mtp180) REVERT: V 22 GLN cc_start: 0.7987 (pm20) cc_final: 0.7641 (pm20) REVERT: V 135 MET cc_start: 0.7577 (ttm) cc_final: 0.7118 (tpp) REVERT: V 272 MET cc_start: 0.8130 (mmm) cc_final: 0.7715 (mmm) REVERT: Y 10 ASP cc_start: 0.8117 (m-30) cc_final: 0.7788 (m-30) REVERT: Y 283 LYS cc_start: 0.8058 (tppt) cc_final: 0.7733 (ttpt) REVERT: 1 272 MET cc_start: 0.7886 (mmm) cc_final: 0.7583 (mmm) REVERT: 4 10 ASP cc_start: 0.8302 (m-30) cc_final: 0.7754 (m-30) REVERT: 4 22 GLN cc_start: 0.7976 (pm20) cc_final: 0.7710 (pm20) REVERT: 4 125 GLU cc_start: 0.7524 (mp0) cc_final: 0.7315 (mp0) REVERT: 4 283 LYS cc_start: 0.8188 (tppt) cc_final: 0.7700 (ttpt) outliers start: 52 outliers final: 47 residues processed: 454 average time/residue: 0.1865 time to fit residues: 140.9704 Evaluate side-chains 463 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 415 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 MET 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 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 135 MET Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL 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 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL 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 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: 1.9990 chunk 167 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 394 optimal weight: 0.0870 chunk 308 optimal weight: 0.2980 chunk 301 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 284 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 216 GLN ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143311 restraints weight = 40533.816| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.55 r_work: 0.3301 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2063 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= 0.118 Angle : 0.564 8.137 45881 Z= 0.265 Chirality : 0.046 0.300 5412 Planarity : 0.003 0.026 5555 Dihedral : 12.542 134.731 5621 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.55 % Allowed : 13.69 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.14), residues: 4004 helix: 1.95 (0.10), residues: 2552 sheet: -1.44 (0.33), residues: 231 loop : -0.34 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 78 TYR 0.011 0.001 TYR J 69 PHE 0.012 0.002 PHE P 169 TRP 0.002 0.001 TRP J 123 HIS 0.004 0.001 HIS 4 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33792) covalent geometry : angle 0.56432 / 0.27 (45881) hydrogen bonds : bond 0.03654 / 2.45 ( 1826) hydrogen bonds : angle 3.72616 / 2.61 ( 5346) Misc. bond : bond 0.00220 / 0.13 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.80 seconds wall clock time: 129 minutes 4.56 seconds (7744.56 seconds total)