Starting phenix.real_space_refine on Sat Jun 28 09:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdq_17618/06_2025/8pdq_17618.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33176 Number of models: 1 Model: "" Number of chains: 3 Chain: "0" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "1" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Restraints were copied for chains: 3, 6, E, F, I, L, O, R, U, X, 5, B, D, H, K, N, Q, T, W, Z, 4, A, C, G, J, M, P, S, V, Y Time building chain proxies: 10.85, per 1000 atoms: 0.33 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: 8.58 Conformation dependent library (CDL) restraints added in 3.8 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: 11.05 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: 11.22 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10681 1.34 - 1.46: 6694 1.46 - 1.58: 16021 1.58 - 1.69: 143 1.69 - 1.81: 253 Bond restraints: 33792 Sorted by residual: bond pdb=" CA ILE J 203 " pdb=" CB ILE J 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.33e-01 bond pdb=" CA ILE Y 203 " pdb=" CB ILE Y 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.09e-01 bond pdb=" CA ILE M 203 " pdb=" CB ILE M 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.78e-01 bond pdb=" CA ILE S 203 " pdb=" CB ILE S 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.55e-01 bond pdb=" CA ILE 4 203 " pdb=" CB ILE 4 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.45e-01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 43908 1.20 - 2.39: 1549 2.39 - 3.59: 359 3.59 - 4.78: 41 4.78 - 5.98: 24 Bond angle restraints: 45881 Sorted by residual: angle pdb=" N GLU Y 125 " pdb=" CA GLU Y 125 " pdb=" CB GLU Y 125 " ideal model delta sigma weight residual 110.28 113.47 -3.19 1.55e+00 4.16e-01 4.24e+00 angle pdb=" N GLU J 125 " pdb=" CA GLU J 125 " pdb=" CB GLU J 125 " ideal model delta sigma weight residual 110.28 113.46 -3.18 1.55e+00 4.16e-01 4.21e+00 angle pdb=" N GLU P 125 " pdb=" CA GLU P 125 " pdb=" CB GLU P 125 " ideal model delta sigma weight residual 110.28 113.45 -3.17 1.55e+00 4.16e-01 4.19e+00 angle pdb=" N GLU C 125 " pdb=" CA GLU C 125 " pdb=" CB GLU C 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.17e+00 angle pdb=" N GLU A 125 " pdb=" CA GLU A 125 " pdb=" CB GLU A 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.16e+00 ... (remaining 45876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 18198 15.55 - 31.10: 1877 31.10 - 46.65: 550 46.65 - 62.20: 99 62.20 - 77.75: 132 Dihedral angle restraints: 20856 sinusoidal: 9075 harmonic: 11781 Sorted by residual: dihedral pdb=" CA LEU G 52 " pdb=" C LEU G 52 " pdb=" N TYR G 53 " pdb=" CA TYR G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU 4 52 " pdb=" C LEU 4 52 " pdb=" N TYR 4 53 " pdb=" CA TYR 4 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU Y 52 " pdb=" C LEU Y 52 " pdb=" N TYR Y 53 " pdb=" CA TYR Y 53 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3117 0.027 - 0.055: 1345 0.055 - 0.082: 714 0.082 - 0.110: 153 0.110 - 0.137: 83 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CA THR C 157 " pdb=" N THR C 157 " pdb=" C THR C 157 " pdb=" CB THR C 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA THR S 157 " pdb=" N THR S 157 " pdb=" C THR S 157 " pdb=" CB THR S 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA THR V 157 " pdb=" N THR V 157 " pdb=" C THR V 157 " pdb=" CB THR V 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 5409 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " 0.027 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 C U 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C U 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C U 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.05e+00 pdb=" N1 C X 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C X 73 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C X 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C X 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C X 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C X 73 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C O 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C O 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C O 73 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C O 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C O 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C O 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 73 " -0.006 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 0.37 - 1.28: 88 1.28 - 2.18: 231 2.18 - 3.09: 24036 3.09 - 3.99: 90489 3.99 - 4.90: 167287 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282131 Sorted by model distance: nonbonded pdb=" NE ARG J 78 " pdb=" CD2 TYR M 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG P 78 " pdb=" CD2 TYR S 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG G 78 " pdb=" CD2 TYR J 23 " model vdw 0.371 3.420 nonbonded pdb=" NE ARG A 78 " pdb=" CD2 TYR C 23 " model vdw 0.371 3.420 nonbonded pdb=" CD2 TYR A 23 " pdb=" NE ARG 4 78 " model vdw 0.371 3.420 ... (remaining 282126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.32 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '6' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.460 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 70.190 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.195 33803 Z= 2.161 Angle : 0.566 5.976 45881 Z= 0.324 Chirality : 0.040 0.137 5412 Planarity : 0.004 0.040 5555 Dihedral : 15.289 77.749 13288 Min Nonbonded Distance : 0.371 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.002 0.001 TRP J 123 HIS 0.003 0.001 HIS S 15 PHE 0.014 0.002 PHE M 169 TYR 0.013 0.001 TYR C 69 ARG 0.003 0.000 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.12847 ( 1826) hydrogen bonds : angle 5.23660 ( 5346) covalent geometry : bond 0.00381 (33792) covalent geometry : angle 0.56575 (45881) Misc. bond : bond 1.19416 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 3.803 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: 0.4510 time to fit residues: 343.0426 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 : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.5980 chunk 300 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 231 optimal weight: 0.0020 chunk 359 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 GLN V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 284 GLN Y 306 GLN ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 306 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 306 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143682 restraints weight = 40562.960| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.37 r_work: 0.3250 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33803 Z= 0.136 Angle : 0.529 8.683 45881 Z= 0.287 Chirality : 0.040 0.145 5412 Planarity : 0.006 0.101 5555 Dihedral : 11.747 74.255 5621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.72 % Allowed : 7.80 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 4004 helix: 1.42 (0.10), residues: 2519 sheet: -1.34 (0.29), residues: 231 loop : -0.61 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 56 PHE 0.011 0.001 PHE Y 224 TYR 0.020 0.002 TYR S 23 ARG 0.014 0.001 ARG J 78 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 1826) hydrogen bonds : angle 4.16525 ( 5346) covalent geometry : bond 0.00303 (33792) covalent geometry : angle 0.52925 (45881) Misc. bond : bond 0.00387 ( 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 : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7677 (ttmt) cc_final: 0.6930 (ttpp) REVERT: A 135 MET cc_start: 0.7538 (ttm) cc_final: 0.7312 (tpp) REVERT: A 181 GLU cc_start: 0.8370 (tt0) cc_final: 0.7974 (pt0) REVERT: A 272 MET cc_start: 0.7791 (mmm) cc_final: 0.7430 (mmm) REVERT: A 279 GLN cc_start: 0.7305 (mm110) cc_final: 0.6751 (mm-40) REVERT: C 129 LYS cc_start: 0.7666 (ttmt) cc_final: 0.6973 (ttpp) REVERT: C 272 MET cc_start: 0.7930 (mmm) cc_final: 0.7367 (mmm) REVERT: G 129 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7101 (mttp) REVERT: J 23 TYR cc_start: 0.7622 (m-80) cc_final: 0.7380 (m-80) REVERT: J 272 MET cc_start: 0.7907 (mmm) cc_final: 0.7584 (mmm) REVERT: M 249 MET cc_start: 0.8493 (mmm) cc_final: 0.8248 (mmm) REVERT: M 279 GLN cc_start: 0.7293 (mm110) cc_final: 0.6955 (mm-40) REVERT: P 135 MET cc_start: 0.7511 (ttm) cc_final: 0.7207 (tpp) REVERT: P 272 MET cc_start: 0.8053 (mmm) cc_final: 0.7614 (mmm) REVERT: P 339 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8130 (mtp180) REVERT: S 94 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7985 (mp) REVERT: S 125 GLU cc_start: 0.7573 (mp0) cc_final: 0.6450 (mp0) REVERT: S 135 MET cc_start: 0.7405 (ttm) cc_final: 0.6809 (tpp) REVERT: S 339 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.8024 (mtp180) REVERT: V 135 MET cc_start: 0.7544 (ttm) cc_final: 0.7273 (tpp) REVERT: Y 129 LYS cc_start: 0.7400 (ttmm) cc_final: 0.6693 (ttpp) REVERT: Y 272 MET cc_start: 0.7838 (mmm) cc_final: 0.7509 (mmm) REVERT: Y 339 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.8208 (mtp180) REVERT: 1 129 LYS cc_start: 0.7602 (ttmt) cc_final: 0.6818 (ttpp) REVERT: 1 135 MET cc_start: 0.7639 (ttm) cc_final: 0.7330 (tpp) REVERT: 1 272 MET cc_start: 0.7993 (mmm) cc_final: 0.7558 (mmm) REVERT: 4 337 MET cc_start: 0.8327 (mmm) cc_final: 0.8073 (tmm) outliers start: 25 outliers final: 17 residues processed: 439 average time/residue: 0.4532 time to fit residues: 324.4483 Evaluate side-chains 400 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 382 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C 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 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 94 LEU 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 101 optimal weight: 0.8980 chunk 314 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 392 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 234 optimal weight: 0.6980 chunk 331 optimal weight: 0.9980 chunk 158 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144327 restraints weight = 40589.378| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.36 r_work: 0.3259 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33803 Z= 0.125 Angle : 0.483 5.815 45881 Z= 0.262 Chirality : 0.039 0.140 5412 Planarity : 0.004 0.066 5555 Dihedral : 11.238 74.043 5621 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.38 % Allowed : 8.43 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.13), residues: 4004 helix: 1.66 (0.10), residues: 2530 sheet: -1.30 (0.30), residues: 231 loop : -0.51 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.005 0.001 HIS P 7 PHE 0.012 0.002 PHE P 169 TYR 0.013 0.001 TYR Y 23 ARG 0.007 0.000 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 1826) hydrogen bonds : angle 3.93911 ( 5346) covalent geometry : bond 0.00282 (33792) covalent geometry : angle 0.48327 (45881) Misc. bond : bond 0.00288 ( 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 461 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 413 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7680 (ttmt) cc_final: 0.6931 (ttpp) REVERT: A 181 GLU cc_start: 0.8336 (tt0) cc_final: 0.7994 (pt0) REVERT: A 272 MET cc_start: 0.7822 (mmm) cc_final: 0.7530 (mmm) REVERT: C 129 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7036 (ttpp) REVERT: C 272 MET cc_start: 0.8049 (mmm) cc_final: 0.7388 (mmm) REVERT: G 129 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7121 (mttp) REVERT: G 272 MET cc_start: 0.7880 (mmm) cc_final: 0.7542 (mmm) REVERT: G 283 LYS cc_start: 0.8302 (tppt) cc_final: 0.7828 (ttpt) REVERT: G 337 MET cc_start: 0.8375 (mmm) cc_final: 0.8120 (tmm) REVERT: G 338 TYR cc_start: 0.8228 (t80) cc_final: 0.7670 (t80) REVERT: J 23 TYR cc_start: 0.7695 (m-80) cc_final: 0.7434 (m-80) REVERT: J 129 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7092 (mttp) REVERT: J 135 MET cc_start: 0.7457 (ttm) cc_final: 0.6973 (tpp) REVERT: J 272 MET cc_start: 0.8054 (mmm) cc_final: 0.7776 (mmm) REVERT: M 272 MET cc_start: 0.7979 (mmm) cc_final: 0.7541 (mmm) REVERT: M 345 THR cc_start: 0.8052 (m) cc_final: 0.7632 (m) REVERT: P 135 MET cc_start: 0.7624 (ttm) cc_final: 0.7299 (tpp) REVERT: P 339 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8039 (mtp180) REVERT: S 138 LEU cc_start: 0.8023 (mm) cc_final: 0.7725 (mm) REVERT: S 272 MET cc_start: 0.7856 (mmm) cc_final: 0.7467 (mmm) REVERT: S 339 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8036 (mtp180) REVERT: V 125 GLU cc_start: 0.7389 (mp0) cc_final: 0.7189 (mp0) REVERT: V 272 MET cc_start: 0.8000 (mmm) cc_final: 0.7571 (mmm) REVERT: V 339 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8103 (mtp180) REVERT: Y 138 LEU cc_start: 0.8063 (mm) cc_final: 0.7838 (mm) REVERT: Y 272 MET cc_start: 0.7986 (mmm) cc_final: 0.7764 (mmt) REVERT: Y 283 LYS cc_start: 0.8202 (tppt) cc_final: 0.7785 (ttpt) REVERT: Y 339 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8090 (mtp180) REVERT: 1 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: 1 135 MET cc_start: 0.7649 (ttm) cc_final: 0.7432 (tpp) REVERT: 1 272 MET cc_start: 0.7878 (mmm) cc_final: 0.7376 (mmm) REVERT: 4 10 ASP cc_start: 0.8227 (m-30) cc_final: 0.7665 (m-30) REVERT: 4 112 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7150 (mm-40) REVERT: 4 272 MET cc_start: 0.7758 (mmm) cc_final: 0.7293 (mmm) REVERT: 4 283 LYS cc_start: 0.8464 (tppt) cc_final: 0.7935 (ttpt) REVERT: 4 337 MET cc_start: 0.8310 (mmm) cc_final: 0.8064 (tmm) outliers start: 48 outliers final: 24 residues processed: 445 average time/residue: 0.4390 time to fit residues: 321.5951 Evaluate side-chains 416 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 391 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 31 THR 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 176 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 176 ILE 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 235 SER Chi-restraints excluded: chain 4 residue 94 LEU 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 234 optimal weight: 0.0770 chunk 356 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 273 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143150 restraints weight = 40687.091| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.39 r_work: 0.3301 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33803 Z= 0.136 Angle : 0.486 5.776 45881 Z= 0.259 Chirality : 0.040 0.141 5412 Planarity : 0.004 0.049 5555 Dihedral : 11.101 74.160 5621 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.73 % Allowed : 9.03 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 4004 helix: 1.73 (0.10), residues: 2530 sheet: -1.26 (0.32), residues: 231 loop : -0.43 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 123 HIS 0.004 0.001 HIS A 56 PHE 0.014 0.002 PHE 1 169 TYR 0.013 0.001 TYR S 69 ARG 0.004 0.000 ARG V 78 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1826) hydrogen bonds : angle 3.84607 ( 5346) covalent geometry : bond 0.00312 (33792) covalent geometry : angle 0.48638 (45881) Misc. bond : bond 0.00236 ( 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 472 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 412 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8058 (tt0) cc_final: 0.7771 (pt0) REVERT: A 272 MET cc_start: 0.7745 (mmm) cc_final: 0.7450 (mmm) REVERT: C 129 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7082 (ttpp) REVERT: C 272 MET cc_start: 0.7935 (mmm) cc_final: 0.7327 (mmm) REVERT: G 129 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7173 (mttp) REVERT: G 283 LYS cc_start: 0.8171 (tppt) cc_final: 0.7803 (ttpt) REVERT: G 338 TYR cc_start: 0.8036 (t80) cc_final: 0.7692 (t80) REVERT: J 129 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7180 (mttp) REVERT: J 135 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7300 (tpp) REVERT: J 272 MET cc_start: 0.7920 (mmm) cc_final: 0.7390 (mmm) REVERT: M 249 MET cc_start: 0.8205 (mmm) cc_final: 0.7817 (mmm) REVERT: M 272 MET cc_start: 0.7820 (mmm) cc_final: 0.7402 (mmm) REVERT: M 345 THR cc_start: 0.8131 (m) cc_final: 0.7723 (m) REVERT: P 339 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7852 (mtp180) REVERT: S 272 MET cc_start: 0.7781 (mmm) cc_final: 0.7431 (mmm) REVERT: S 339 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7730 (mtp180) REVERT: V 135 MET cc_start: 0.7781 (tpp) cc_final: 0.7046 (tpp) REVERT: V 272 MET cc_start: 0.7916 (mmm) cc_final: 0.7539 (mmm) REVERT: V 339 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7844 (mtp180) REVERT: Y 10 ASP cc_start: 0.7914 (m-30) cc_final: 0.7567 (m-30) REVERT: Y 125 GLU cc_start: 0.7793 (mp0) cc_final: 0.6859 (mp0) REVERT: Y 138 LEU cc_start: 0.8254 (mm) cc_final: 0.8005 (mm) REVERT: Y 272 MET cc_start: 0.7885 (mmm) cc_final: 0.7665 (mmt) REVERT: Y 339 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7873 (mtp180) REVERT: 1 125 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: 1 272 MET cc_start: 0.7696 (mmm) cc_final: 0.7300 (mmm) REVERT: 4 10 ASP cc_start: 0.8042 (m-30) cc_final: 0.7502 (m-30) REVERT: 4 94 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (mp) REVERT: 4 112 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7218 (mm-40) REVERT: 4 272 MET cc_start: 0.7757 (mmm) cc_final: 0.7168 (mmm) REVERT: 4 283 LYS cc_start: 0.8366 (tppt) cc_final: 0.7897 (ttpt) outliers start: 60 outliers final: 30 residues processed: 452 average time/residue: 0.4290 time to fit residues: 319.3999 Evaluate side-chains 420 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 387 time to evaluate : 3.567 ------------------------------------------------------------------------------- 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 31 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 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 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 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 190 VAL 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 94 LEU 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 196 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 249 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.171278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145008 restraints weight = 40577.832| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.34 r_work: 0.3287 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33803 Z= 0.116 Angle : 0.467 7.305 45881 Z= 0.250 Chirality : 0.039 0.141 5412 Planarity : 0.003 0.035 5555 Dihedral : 11.126 73.994 5621 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.84 % Allowed : 10.04 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.14), residues: 4004 helix: 1.83 (0.10), residues: 2541 sheet: -1.20 (0.33), residues: 231 loop : -0.46 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.003 0.001 HIS S 15 PHE 0.011 0.001 PHE P 169 TYR 0.021 0.001 TYR J 23 ARG 0.003 0.000 ARG 4 78 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1826) hydrogen bonds : angle 3.76125 ( 5346) covalent geometry : bond 0.00261 (33792) covalent geometry : angle 0.46698 (45881) Misc. bond : bond 0.00198 ( 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 468 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 3.577 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 181 GLU cc_start: 0.8367 (tt0) cc_final: 0.8033 (pt0) REVERT: A 272 MET cc_start: 0.7961 (mmm) cc_final: 0.7686 (mmm) REVERT: C 129 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7066 (ttpp) REVERT: C 272 MET cc_start: 0.8096 (mmm) cc_final: 0.7788 (mmt) REVERT: G 129 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7146 (mttp) REVERT: J 129 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7178 (mttp) REVERT: J 135 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7166 (tpp) REVERT: J 272 MET cc_start: 0.8070 (mmm) cc_final: 0.7650 (mmm) REVERT: M 135 MET cc_start: 0.7890 (tpp) cc_final: 0.7199 (tpp) REVERT: M 272 MET cc_start: 0.8021 (mmm) cc_final: 0.7514 (mmm) REVERT: M 345 THR cc_start: 0.8051 (m) cc_final: 0.7630 (m) REVERT: P 339 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.8054 (mtp180) REVERT: S 112 GLN cc_start: 0.7574 (mm110) cc_final: 0.7362 (mm-40) REVERT: S 272 MET cc_start: 0.7887 (mmm) cc_final: 0.7484 (mmm) REVERT: S 339 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8088 (mtp180) REVERT: V 135 MET cc_start: 0.7808 (tpp) cc_final: 0.7137 (tpp) REVERT: V 272 MET cc_start: 0.8086 (mmm) cc_final: 0.7696 (mmm) REVERT: V 339 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8041 (mtp180) REVERT: Y 10 ASP cc_start: 0.8051 (m-30) cc_final: 0.7680 (m-30) REVERT: Y 125 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: Y 138 LEU cc_start: 0.8078 (mm) cc_final: 0.7805 (mm) REVERT: Y 272 MET cc_start: 0.8047 (mmm) cc_final: 0.7778 (mmt) REVERT: Y 283 LYS cc_start: 0.8083 (tppt) cc_final: 0.7614 (mttp) REVERT: Y 339 ARG cc_start: 0.8338 (mmm-85) cc_final: 0.8129 (mtp180) REVERT: 1 272 MET cc_start: 0.7853 (mmm) cc_final: 0.7418 (mmm) REVERT: 4 94 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8239 (mp) REVERT: 4 112 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7200 (mm-40) REVERT: 4 272 MET cc_start: 0.7963 (mmm) cc_final: 0.7408 (mmm) REVERT: 4 283 LYS cc_start: 0.8410 (tppt) cc_final: 0.7905 (ttpt) outliers start: 64 outliers final: 41 residues processed: 452 average time/residue: 0.4310 time to fit residues: 322.2499 Evaluate side-chains 440 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 396 time to evaluate : 3.755 ------------------------------------------------------------------------------- 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 176 ILE 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 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 134 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 342 VAL Chi-restraints excluded: chain 4 residue 94 LEU 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 350 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 216 GLN ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.169794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143422 restraints weight = 40576.917| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.38 r_work: 0.3245 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33803 Z= 0.140 Angle : 0.487 5.724 45881 Z= 0.258 Chirality : 0.039 0.141 5412 Planarity : 0.003 0.039 5555 Dihedral : 11.105 74.207 5621 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 11.45 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 4004 helix: 1.80 (0.10), residues: 2552 sheet: -1.24 (0.33), residues: 231 loop : -0.32 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 56 PHE 0.014 0.002 PHE 1 169 TYR 0.014 0.001 TYR C 23 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1826) hydrogen bonds : angle 3.78024 ( 5346) covalent geometry : bond 0.00324 (33792) covalent geometry : angle 0.48719 (45881) Misc. bond : bond 0.00213 ( 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 473 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 407 time to evaluate : 3.735 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 181 GLU cc_start: 0.7977 (tt0) cc_final: 0.7699 (pt0) REVERT: A 272 MET cc_start: 0.7774 (mmm) cc_final: 0.7515 (mmm) REVERT: C 129 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7067 (ttpp) REVERT: C 272 MET cc_start: 0.7942 (mmm) cc_final: 0.7395 (mmm) REVERT: G 129 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7209 (mttp) REVERT: G 283 LYS cc_start: 0.8196 (tppt) cc_final: 0.7782 (ttpt) REVERT: G 338 TYR cc_start: 0.7976 (t80) cc_final: 0.7710 (t80) REVERT: J 129 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7220 (mttp) REVERT: J 135 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7372 (tpp) REVERT: J 272 MET cc_start: 0.7874 (mmm) cc_final: 0.7445 (mmm) REVERT: M 135 MET cc_start: 0.7868 (tpp) cc_final: 0.7233 (tpp) REVERT: M 249 MET cc_start: 0.8211 (mmm) cc_final: 0.7912 (mmm) REVERT: M 272 MET cc_start: 0.7912 (mmm) cc_final: 0.7404 (mmm) REVERT: M 345 THR cc_start: 0.8144 (m) cc_final: 0.7727 (m) REVERT: P 339 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7760 (mtm-85) REVERT: S 125 GLU cc_start: 0.7567 (mp0) cc_final: 0.6526 (mp0) REVERT: S 272 MET cc_start: 0.7737 (mmm) cc_final: 0.7343 (mmm) REVERT: S 339 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7751 (mtp180) REVERT: V 135 MET cc_start: 0.7929 (tpp) cc_final: 0.7383 (tpp) REVERT: V 272 MET cc_start: 0.7934 (mmm) cc_final: 0.7588 (mmm) REVERT: V 339 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7773 (mtp180) REVERT: Y 10 ASP cc_start: 0.7928 (m-30) cc_final: 0.7568 (m-30) REVERT: Y 138 LEU cc_start: 0.8304 (mm) cc_final: 0.8056 (mm) REVERT: Y 272 MET cc_start: 0.7998 (mmm) cc_final: 0.7755 (mmt) REVERT: 1 258 MET cc_start: 0.8403 (mmm) cc_final: 0.8071 (mmm) REVERT: 1 272 MET cc_start: 0.7798 (mmm) cc_final: 0.7455 (mmm) REVERT: 1 279 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7431 (mm-40) REVERT: 4 272 MET cc_start: 0.7779 (mmm) cc_final: 0.7268 (mmm) outliers start: 66 outliers final: 57 residues processed: 446 average time/residue: 0.4292 time to fit residues: 316.8601 Evaluate side-chains 451 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 393 time to evaluate : 3.510 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL 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 G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 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 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 134 THR Chi-restraints excluded: chain Y residue 135 MET 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 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 364 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 268 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.169717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144312 restraints weight = 40500.246| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.37 r_work: 0.3323 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1824 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= 0.140 Angle : 0.492 5.879 45881 Z= 0.260 Chirality : 0.039 0.142 5412 Planarity : 0.003 0.028 5555 Dihedral : 11.091 74.175 5621 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 12.20 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.14), residues: 4004 helix: 1.83 (0.10), residues: 2563 sheet: -1.27 (0.33), residues: 231 loop : -0.29 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 123 HIS 0.004 0.001 HIS P 56 PHE 0.014 0.002 PHE 1 169 TYR 0.013 0.001 TYR S 69 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1826) hydrogen bonds : angle 3.77117 ( 5346) covalent geometry : bond 0.00324 (33792) covalent geometry : angle 0.49174 (45881) Misc. bond : bond 0.00205 ( 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 471 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 409 time to evaluate : 3.548 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: 0.8338 (tt0) cc_final: 0.8020 (pt0) REVERT: A 272 MET cc_start: 0.7962 (mmm) cc_final: 0.7682 (mmm) REVERT: C 249 MET cc_start: 0.8363 (mmm) cc_final: 0.8151 (mmm) REVERT: C 272 MET cc_start: 0.8116 (mmm) cc_final: 0.7604 (mmm) REVERT: G 129 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7237 (mttp) REVERT: G 272 MET cc_start: 0.7897 (mmm) cc_final: 0.7395 (mmm) REVERT: G 283 LYS cc_start: 0.8320 (tppt) cc_final: 0.7848 (ttpt) REVERT: G 338 TYR cc_start: 0.8263 (t80) cc_final: 0.7794 (t80) REVERT: J 129 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7241 (mttp) REVERT: J 135 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7255 (tpp) REVERT: J 272 MET cc_start: 0.8076 (mmm) cc_final: 0.7636 (mmm) REVERT: J 338 TYR cc_start: 0.7879 (t80) cc_final: 0.7533 (t80) REVERT: M 135 MET cc_start: 0.8012 (tpp) cc_final: 0.7385 (tpp) REVERT: M 345 THR cc_start: 0.8141 (m) cc_final: 0.7721 (m) REVERT: P 112 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7372 (mm-40) REVERT: P 339 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8008 (mtm-85) REVERT: S 272 MET cc_start: 0.7878 (mmm) cc_final: 0.7478 (mmm) REVERT: S 339 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.8052 (mtp180) REVERT: V 135 MET cc_start: 0.8005 (tpp) cc_final: 0.7433 (tpp) REVERT: V 272 MET cc_start: 0.8080 (mmm) cc_final: 0.7697 (mmm) REVERT: V 339 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7955 (mtp180) REVERT: Y 10 ASP cc_start: 0.8145 (m-30) cc_final: 0.7789 (m-30) REVERT: Y 94 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8254 (mp) REVERT: Y 135 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7363 (tpp) REVERT: Y 138 LEU cc_start: 0.8177 (mm) cc_final: 0.7874 (mm) REVERT: Y 272 MET cc_start: 0.8143 (mmm) cc_final: 0.7867 (mmm) REVERT: 1 272 MET cc_start: 0.7944 (mmm) cc_final: 0.7558 (mmm) REVERT: 4 272 MET cc_start: 0.7906 (mmm) cc_final: 0.7444 (mmm) REVERT: 4 283 LYS cc_start: 0.8418 (tppt) cc_final: 0.7849 (ttpt) outliers start: 62 outliers final: 51 residues processed: 446 average time/residue: 0.4423 time to fit residues: 326.9064 Evaluate side-chains 458 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 404 time to evaluate : 3.942 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 31 THR 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 342 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 135 MET 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 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 362 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 HIS M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 HIS ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 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 = 0.3891 r_free = 0.3891 target = 0.168596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139239 restraints weight = 40557.646| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.67 r_work: 0.3253 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33803 Z= 0.159 Angle : 0.513 8.600 45881 Z= 0.269 Chirality : 0.040 0.150 5412 Planarity : 0.003 0.030 5555 Dihedral : 11.075 74.324 5621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.70 % Allowed : 12.80 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.13), residues: 4004 helix: 1.79 (0.10), residues: 2563 sheet: -1.31 (0.33), residues: 231 loop : -0.32 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.003 0.001 HIS V 56 PHE 0.016 0.002 PHE 1 169 TYR 0.015 0.001 TYR S 69 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1826) hydrogen bonds : angle 3.80897 ( 5346) covalent geometry : bond 0.00373 (33792) covalent geometry : angle 0.51260 (45881) Misc. bond : bond 0.00207 ( 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 474 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 415 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7385 (mm110) cc_final: 0.7132 (mm-40) REVERT: A 135 MET cc_start: 0.7720 (tpp) cc_final: 0.7435 (tpp) REVERT: A 181 GLU cc_start: 0.8038 (tt0) cc_final: 0.7709 (pt0) REVERT: A 272 MET cc_start: 0.7883 (mmm) cc_final: 0.7606 (mmm) REVERT: C 272 MET cc_start: 0.8030 (mmm) cc_final: 0.7520 (mmm) REVERT: G 129 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7188 (mttp) REVERT: G 272 MET cc_start: 0.7739 (mmm) cc_final: 0.7254 (mmm) REVERT: G 283 LYS cc_start: 0.8200 (tppt) cc_final: 0.7761 (ttpt) REVERT: J 129 LYS cc_start: 0.7657 (ttpt) cc_final: 0.7183 (mttp) REVERT: J 135 MET cc_start: 0.7495 (ttm) cc_final: 0.7265 (tpp) REVERT: J 272 MET cc_start: 0.7950 (mmm) cc_final: 0.7492 (mmm) REVERT: M 135 MET cc_start: 0.7946 (tpp) cc_final: 0.7354 (tpp) REVERT: M 249 MET cc_start: 0.8313 (mmm) cc_final: 0.8103 (mmm) REVERT: M 272 MET cc_start: 0.7932 (mmm) cc_final: 0.7422 (mmm) REVERT: M 345 THR cc_start: 0.8102 (m) cc_final: 0.7681 (m) REVERT: P 112 GLN cc_start: 0.7784 (mm110) cc_final: 0.7483 (mm-40) REVERT: P 339 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7790 (mtm-85) REVERT: S 112 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7576 (mm-40) REVERT: S 125 GLU cc_start: 0.7550 (mp0) cc_final: 0.6355 (mp0) REVERT: S 272 MET cc_start: 0.7814 (mmm) cc_final: 0.7414 (mmm) REVERT: S 339 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7780 (mtp180) REVERT: V 135 MET cc_start: 0.7985 (tpp) cc_final: 0.7408 (tpp) REVERT: V 272 MET cc_start: 0.8032 (mmm) cc_final: 0.7623 (mmm) REVERT: V 339 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7792 (mtp180) REVERT: Y 10 ASP cc_start: 0.8008 (m-30) cc_final: 0.7624 (m-30) REVERT: Y 135 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7099 (tpp) REVERT: Y 138 LEU cc_start: 0.8183 (mm) cc_final: 0.7925 (mm) REVERT: Y 272 MET cc_start: 0.8066 (mmm) cc_final: 0.7792 (mmm) REVERT: Y 283 LYS cc_start: 0.8253 (tppt) cc_final: 0.7844 (ttpt) REVERT: 1 258 MET cc_start: 0.8428 (mmm) cc_final: 0.8105 (mmm) REVERT: 1 272 MET cc_start: 0.7921 (mmm) cc_final: 0.7543 (mmm) REVERT: 4 10 ASP cc_start: 0.8134 (m-30) cc_final: 0.7584 (m-30) REVERT: 4 22 GLN cc_start: 0.7966 (pm20) cc_final: 0.7731 (pm20) REVERT: 4 283 LYS cc_start: 0.8306 (tppt) cc_final: 0.7690 (ttpt) outliers start: 59 outliers final: 51 residues processed: 454 average time/residue: 0.4571 time to fit residues: 347.3102 Evaluate side-chains 464 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 412 time to evaluate : 3.843 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 135 MET 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 182 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 395 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 310 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 HIS 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 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 = 0.3852 r_free = 0.3852 target = 0.164987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133427 restraints weight = 40678.581| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.06 r_work: 0.3099 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 33803 Z= 0.256 Angle : 0.605 7.576 45881 Z= 0.312 Chirality : 0.044 0.167 5412 Planarity : 0.004 0.047 5555 Dihedral : 11.053 74.866 5621 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.84 % Allowed : 12.97 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.13), residues: 4004 helix: 1.50 (0.10), residues: 2552 sheet: -1.51 (0.32), residues: 231 loop : -0.36 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 261 HIS 0.004 0.001 HIS V 56 PHE 0.019 0.002 PHE 1 169 TYR 0.020 0.002 TYR S 69 ARG 0.004 0.001 ARG M 27 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 1826) hydrogen bonds : angle 4.04591 ( 5346) covalent geometry : bond 0.00607 (33792) covalent geometry : angle 0.60547 (45881) Misc. bond : bond 0.00214 ( 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 480 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 416 time to evaluate : 4.018 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 135 MET cc_start: 0.8058 (tpp) cc_final: 0.7687 (tpp) REVERT: A 272 MET cc_start: 0.7948 (mmm) cc_final: 0.7714 (mmm) REVERT: C 135 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6583 (tpp) REVERT: C 272 MET cc_start: 0.8152 (mmm) cc_final: 0.7678 (mmm) REVERT: G 129 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7426 (ttmm) REVERT: G 283 LYS cc_start: 0.8393 (tppt) cc_final: 0.7790 (ttpt) REVERT: J 272 MET cc_start: 0.8102 (mmm) cc_final: 0.7540 (mmm) REVERT: M 135 MET cc_start: 0.7972 (tpp) cc_final: 0.7405 (tpp) REVERT: M 249 MET cc_start: 0.8647 (mmm) cc_final: 0.8401 (mmm) REVERT: M 272 MET cc_start: 0.8061 (mmm) cc_final: 0.7546 (mmm) REVERT: P 112 GLN cc_start: 0.7792 (mm110) cc_final: 0.7432 (mm-40) REVERT: P 339 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8118 (mtm-85) REVERT: S 112 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7449 (mm-40) REVERT: S 272 MET cc_start: 0.7970 (mmm) cc_final: 0.7579 (mmm) REVERT: S 339 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8062 (mtp180) REVERT: V 135 MET cc_start: 0.8047 (tpp) cc_final: 0.7486 (tpp) REVERT: V 272 MET cc_start: 0.8045 (mmm) cc_final: 0.7600 (mmm) REVERT: V 339 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.8084 (mtp180) REVERT: Y 135 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7266 (tpp) REVERT: Y 138 LEU cc_start: 0.8021 (mm) cc_final: 0.7757 (mm) REVERT: Y 272 MET cc_start: 0.8165 (mmm) cc_final: 0.7860 (mmt) REVERT: 1 272 MET cc_start: 0.8107 (mmm) cc_final: 0.7651 (mmm) REVERT: 4 283 LYS cc_start: 0.8395 (tppt) cc_final: 0.7709 (ttpt) outliers start: 64 outliers final: 54 residues processed: 457 average time/residue: 0.4287 time to fit residues: 325.8741 Evaluate side-chains 465 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 409 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 31 THR 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 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 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 342 VAL 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 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 94 LEU 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 94 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 135 MET 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 135 MET 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 317 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 384 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 HIS 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 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 = 0.3894 r_free = 0.3894 target = 0.168878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139296 restraints weight = 40471.484| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.67 r_work: 0.3169 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33803 Z= 0.136 Angle : 0.512 7.487 45881 Z= 0.271 Chirality : 0.040 0.146 5412 Planarity : 0.003 0.026 5555 Dihedral : 11.074 74.166 5621 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 13.29 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4004 helix: 1.71 (0.10), residues: 2563 sheet: -1.50 (0.32), residues: 231 loop : -0.42 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 123 HIS 0.003 0.001 HIS J 15 PHE 0.013 0.002 PHE C 169 TYR 0.013 0.001 TYR A 69 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1826) hydrogen bonds : angle 3.85729 ( 5346) covalent geometry : bond 0.00312 (33792) covalent geometry : angle 0.51245 (45881) Misc. bond : bond 0.00223 ( 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 475 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 417 time to evaluate : 4.146 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: 0.7415 (mm110) cc_final: 0.7160 (mm-40) REVERT: A 135 MET cc_start: 0.7972 (tpp) cc_final: 0.7414 (tpp) REVERT: A 181 GLU cc_start: 0.8108 (tt0) cc_final: 0.7792 (pt0) REVERT: A 272 MET cc_start: 0.7917 (mmm) cc_final: 0.7423 (mmm) REVERT: G 283 LYS cc_start: 0.8200 (tppt) cc_final: 0.7726 (ttpt) REVERT: J 272 MET cc_start: 0.7991 (mmm) cc_final: 0.7557 (mmm) REVERT: M 135 MET cc_start: 0.7949 (tpp) cc_final: 0.7442 (tpp) REVERT: M 249 MET cc_start: 0.8292 (mmm) cc_final: 0.8044 (mmm) REVERT: M 272 MET cc_start: 0.7942 (mmm) cc_final: 0.7450 (mmm) REVERT: P 112 GLN cc_start: 0.7829 (mm110) cc_final: 0.7565 (mm-40) REVERT: P 339 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7868 (mtm-85) REVERT: S 112 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7589 (mm-40) REVERT: S 272 MET cc_start: 0.7896 (mmm) cc_final: 0.7450 (mmm) REVERT: S 339 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7882 (mtp180) REVERT: V 22 GLN cc_start: 0.7815 (pm20) cc_final: 0.7466 (pm20) REVERT: V 135 MET cc_start: 0.7927 (tpp) cc_final: 0.7367 (tpp) REVERT: V 272 MET cc_start: 0.8021 (mmm) cc_final: 0.7609 (mmm) REVERT: Y 135 MET cc_start: 0.7382 (ttm) cc_final: 0.7095 (tpp) REVERT: Y 138 LEU cc_start: 0.8160 (mm) cc_final: 0.7925 (mm) REVERT: Y 272 MET cc_start: 0.8070 (mmm) cc_final: 0.7839 (mmm) REVERT: Y 283 LYS cc_start: 0.8220 (tppt) cc_final: 0.7558 (mttp) REVERT: 1 272 MET cc_start: 0.7948 (mmm) cc_final: 0.7573 (mmm) REVERT: 4 10 ASP cc_start: 0.8097 (m-30) cc_final: 0.7526 (m-30) REVERT: 4 22 GLN cc_start: 0.7817 (pm20) cc_final: 0.7536 (pm20) REVERT: 4 283 LYS cc_start: 0.8308 (tppt) cc_final: 0.7761 (ttpt) outliers start: 58 outliers final: 51 residues processed: 457 average time/residue: 0.6128 time to fit residues: 471.7392 Evaluate side-chains 459 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 408 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 282 LEU Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 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 135 MET 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 307 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 341 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 342 optimal weight: 0.0570 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 284 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 GLN ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.167653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140716 restraints weight = 40616.086| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.55 r_work: 0.3247 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33803 Z= 0.166 Angle : 0.533 7.258 45881 Z= 0.278 Chirality : 0.040 0.153 5412 Planarity : 0.003 0.032 5555 Dihedral : 11.079 74.370 5621 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.58 % Allowed : 13.52 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.13), residues: 4004 helix: 1.69 (0.10), residues: 2563 sheet: -1.56 (0.32), residues: 231 loop : -0.44 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 123 HIS 0.003 0.001 HIS V 56 PHE 0.016 0.002 PHE 1 169 TYR 0.015 0.001 TYR Y 69 ARG 0.005 0.000 ARG S 185 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1826) hydrogen bonds : angle 3.87135 ( 5346) covalent geometry : bond 0.00390 (33792) covalent geometry : angle 0.53305 (45881) Misc. bond : bond 0.00216 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16931.27 seconds wall clock time: 296 minutes 5.88 seconds (17765.88 seconds total)