Starting phenix.real_space_refine on Tue Sep 24 10:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opl_17072/09_2024/8opl_17072.cif" } resolution = 2.41 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= 0.024 sd= 0.551 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 135 5.49 5 S 405 5.16 5 C 31293 2.51 5 N 8667 2.21 5 O 10179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50679 Number of models: 1 Model: "" Number of chains: 2 Chain: "Ba" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1777 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 211} Chain: "Bd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Restraints were copied for chains: Bl, Bm, Bn, Bo, Bk, Bp, Bq, Br, Bs, Aa, Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, As, Au, At, Aw, Av, Ay, Ax, Az, Be, Bf, Bg, Bb, Bc, Bh, Bi, Bj, Bt, Bu, Bv, Bw, Bx, By, Bz, Ak, Aj, Am, Al, Ao, An, Aq, Ap, Ar, Ca, Cb Time building chain proxies: 8.12, per 1000 atoms: 0.16 Number of scatterers: 50679 At special positions: 0 Unit cell: (143.45, 143.45, 222.3, 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 405 16.00 P 135 15.00 O 10179 8.00 N 8667 7.00 C 31293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.82 Conformation dependent library (CDL) restraints added in 4.5 seconds 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11448 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 27 sheets defined 48.7% alpha, 4.5% beta 0 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 11.27 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 73 Processing helix chain 'Aa' and resid 76 through 80 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAa 151 " --> pdb=" O PROAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 178 removed outlier: 3.876A pdb=" N LYSAa 177 " --> pdb=" O METAa 173 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAa 195 " --> pdb=" O ASPAa 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 226 Processing helix chain 'Ab' and resid 66 through 73 Processing helix chain 'Ab' and resid 76 through 80 Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 123 removed outlier: 3.509A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAb 151 " --> pdb=" O PROAb 147 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAb 177 " --> pdb=" O METAb 173 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 188 Processing helix chain 'Ab' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAb 195 " --> pdb=" O ASPAb 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 226 Processing helix chain 'Ac' and resid 66 through 73 Processing helix chain 'Ac' and resid 76 through 80 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNAc 151 " --> pdb=" O PROAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 178 removed outlier: 3.873A pdb=" N LYSAc 177 " --> pdb=" O METAc 173 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAc 195 " --> pdb=" O ASPAc 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 226 Processing helix chain 'Ad' and resid 66 through 73 Processing helix chain 'Ad' and resid 76 through 80 Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAd 151 " --> pdb=" O PROAd 147 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSAd 177 " --> pdb=" O METAd 173 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 188 Processing helix chain 'Ad' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAd 195 " --> pdb=" O ASPAd 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 226 Processing helix chain 'Ae' and resid 66 through 73 Processing helix chain 'Ae' and resid 76 through 80 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNAe 151 " --> pdb=" O PROAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAe 177 " --> pdb=" O METAe 173 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAe 195 " --> pdb=" O ASPAe 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 226 Processing helix chain 'Af' and resid 66 through 73 Processing helix chain 'Af' and resid 76 through 80 Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAf 151 " --> pdb=" O PROAf 147 " (cutoff:3.500A) Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 178 removed outlier: 3.873A pdb=" N LYSAf 177 " --> pdb=" O METAf 173 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 188 Processing helix chain 'Af' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAf 195 " --> pdb=" O ASPAf 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 226 Processing helix chain 'Ag' and resid 66 through 73 Processing helix chain 'Ag' and resid 76 through 80 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNAg 151 " --> pdb=" O PROAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAg 177 " --> pdb=" O METAg 173 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAg 195 " --> pdb=" O ASPAg 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 226 Processing helix chain 'Ah' and resid 66 through 73 Processing helix chain 'Ah' and resid 76 through 80 Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAh 151 " --> pdb=" O PROAh 147 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAh 177 " --> pdb=" O METAh 173 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 188 Processing helix chain 'Ah' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAh 195 " --> pdb=" O ASPAh 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 226 Processing helix chain 'Ai' and resid 66 through 73 Processing helix chain 'Ai' and resid 76 through 80 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNAi 151 " --> pdb=" O PROAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSAi 177 " --> pdb=" O METAi 173 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAi 195 " --> pdb=" O ASPAi 192 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 226 Processing helix chain 'As' and resid 66 through 73 Processing helix chain 'As' and resid 76 through 80 Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAs 151 " --> pdb=" O PROAs 147 " (cutoff:3.500A) Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 178 removed outlier: 3.873A pdb=" N LYSAs 177 " --> pdb=" O METAs 173 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAs 195 " --> pdb=" O ASPAs 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 226 Processing helix chain 'At' and resid 66 through 73 Processing helix chain 'At' and resid 76 through 80 Processing helix chain 'At' and resid 86 through 102 Processing helix chain 'At' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAt 111 " --> pdb=" O GLUAt 107 " (cutoff:3.500A) Processing helix chain 'At' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAt 151 " --> pdb=" O PROAt 147 " (cutoff:3.500A) Processing helix chain 'At' and resid 155 through 161 Processing helix chain 'At' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSAt 177 " --> pdb=" O METAt 173 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 188 Processing helix chain 'At' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAt 195 " --> pdb=" O ASPAt 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAt 197 " --> pdb=" O SERAt 194 " (cutoff:3.500A) Processing helix chain 'At' and resid 210 through 226 Processing helix chain 'Au' and resid 66 through 73 Processing helix chain 'Au' and resid 76 through 80 Processing helix chain 'Au' and resid 86 through 102 Processing helix chain 'Au' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAu 151 " --> pdb=" O PROAu 147 " (cutoff:3.500A) Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAu 177 " --> pdb=" O METAu 173 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAu 195 " --> pdb=" O ASPAu 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 226 Processing helix chain 'Av' and resid 66 through 73 Processing helix chain 'Av' and resid 76 through 80 Processing helix chain 'Av' and resid 86 through 102 Processing helix chain 'Av' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAv 111 " --> pdb=" O GLUAv 107 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAv 151 " --> pdb=" O PROAv 147 " (cutoff:3.500A) Processing helix chain 'Av' and resid 155 through 161 Processing helix chain 'Av' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAv 177 " --> pdb=" O METAv 173 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 188 Processing helix chain 'Av' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUAv 195 " --> pdb=" O ASPAv 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAv 197 " --> pdb=" O SERAv 194 " (cutoff:3.500A) Processing helix chain 'Av' and resid 210 through 226 Processing helix chain 'Aw' and resid 66 through 73 Processing helix chain 'Aw' and resid 76 through 80 Processing helix chain 'Aw' and resid 86 through 102 Processing helix chain 'Aw' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNAw 151 " --> pdb=" O PROAw 147 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSAw 177 " --> pdb=" O METAw 173 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUAw 195 " --> pdb=" O ASPAw 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 226 Processing helix chain 'Ax' and resid 66 through 73 Processing helix chain 'Ax' and resid 76 through 80 Processing helix chain 'Ax' and resid 86 through 102 Processing helix chain 'Ax' and resid 107 through 123 removed outlier: 3.512A pdb=" N VALAx 111 " --> pdb=" O GLUAx 107 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAx 151 " --> pdb=" O PROAx 147 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 155 through 161 Processing helix chain 'Ax' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSAx 177 " --> pdb=" O METAx 173 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 182 through 188 Processing helix chain 'Ax' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUAx 195 " --> pdb=" O ASPAx 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAx 197 " --> pdb=" O SERAx 194 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 210 through 226 Processing helix chain 'Ay' and resid 66 through 73 Processing helix chain 'Ay' and resid 76 through 80 Processing helix chain 'Ay' and resid 86 through 102 Processing helix chain 'Ay' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALAy 111 " --> pdb=" O GLUAy 107 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNAy 151 " --> pdb=" O PROAy 147 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 155 through 161 Processing helix chain 'Ay' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAy 177 " --> pdb=" O METAy 173 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAy 195 " --> pdb=" O ASPAy 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGAy 197 " --> pdb=" O SERAy 194 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 210 through 226 Processing helix chain 'Az' and resid 66 through 73 Processing helix chain 'Az' and resid 76 through 80 Processing helix chain 'Az' and resid 86 through 102 Processing helix chain 'Az' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALAz 111 " --> pdb=" O GLUAz 107 " (cutoff:3.500A) Processing helix chain 'Az' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNAz 151 " --> pdb=" O PROAz 147 " (cutoff:3.500A) Processing helix chain 'Az' and resid 155 through 161 Processing helix chain 'Az' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSAz 177 " --> pdb=" O METAz 173 " (cutoff:3.500A) Processing helix chain 'Az' and resid 182 through 188 Processing helix chain 'Az' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUAz 195 " --> pdb=" O ASPAz 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGAz 197 " --> pdb=" O SERAz 194 " (cutoff:3.500A) Processing helix chain 'Az' and resid 210 through 226 Processing helix chain 'Ba' and resid 66 through 73 Processing helix chain 'Ba' and resid 76 through 80 Processing helix chain 'Ba' and resid 86 through 102 Processing helix chain 'Ba' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALBa 111 " --> pdb=" O GLUBa 107 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNBa 151 " --> pdb=" O PROBa 147 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 155 through 161 Processing helix chain 'Ba' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBa 177 " --> pdb=" O METBa 173 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBa 195 " --> pdb=" O ASPBa 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGBa 197 " --> pdb=" O SERBa 194 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 210 through 226 Processing helix chain 'Bk' and resid 66 through 73 Processing helix chain 'Bk' and resid 76 through 80 Processing helix chain 'Bk' and resid 86 through 102 Processing helix chain 'Bk' and resid 107 through 123 removed outlier: 3.512A pdb=" N VALBk 111 " --> pdb=" O GLUBk 107 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNBk 151 " --> pdb=" O PROBk 147 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 155 through 161 Processing helix chain 'Bk' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSBk 177 " --> pdb=" O METBk 173 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 182 through 188 Processing helix chain 'Bk' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBk 195 " --> pdb=" O ASPBk 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGBk 197 " --> pdb=" O SERBk 194 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 210 through 226 Processing helix chain 'Bl' and resid 66 through 73 Processing helix chain 'Bl' and resid 76 through 80 Processing helix chain 'Bl' and resid 86 through 102 Processing helix chain 'Bl' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALBl 111 " --> pdb=" O GLUBl 107 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNBl 151 " --> pdb=" O PROBl 147 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 155 through 161 Processing helix chain 'Bl' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSBl 177 " --> pdb=" O METBl 173 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 182 through 188 Processing helix chain 'Bl' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBl 195 " --> pdb=" O ASPBl 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGBl 197 " --> pdb=" O SERBl 194 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 210 through 226 Processing helix chain 'Bm' and resid 66 through 73 Processing helix chain 'Bm' and resid 76 through 80 Processing helix chain 'Bm' and resid 86 through 102 Processing helix chain 'Bm' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALBm 111 " --> pdb=" O GLUBm 107 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNBm 151 " --> pdb=" O PROBm 147 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 155 through 161 Processing helix chain 'Bm' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBm 177 " --> pdb=" O METBm 173 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 182 through 188 Processing helix chain 'Bm' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUBm 195 " --> pdb=" O ASPBm 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGBm 197 " --> pdb=" O SERBm 194 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 210 through 226 Processing helix chain 'Bn' and resid 66 through 73 Processing helix chain 'Bn' and resid 76 through 80 Processing helix chain 'Bn' and resid 86 through 102 Processing helix chain 'Bn' and resid 107 through 123 removed outlier: 3.510A pdb=" N VALBn 111 " --> pdb=" O GLUBn 107 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNBn 151 " --> pdb=" O PROBn 147 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 155 through 161 Processing helix chain 'Bn' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBn 177 " --> pdb=" O METBn 173 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 182 through 188 Processing helix chain 'Bn' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBn 195 " --> pdb=" O ASPBn 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGBn 197 " --> pdb=" O SERBn 194 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 210 through 226 Processing helix chain 'Bo' and resid 66 through 73 Processing helix chain 'Bo' and resid 76 through 80 Processing helix chain 'Bo' and resid 86 through 102 Processing helix chain 'Bo' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALBo 111 " --> pdb=" O GLUBo 107 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNBo 151 " --> pdb=" O PROBo 147 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 155 through 161 Processing helix chain 'Bo' and resid 163 through 178 removed outlier: 3.874A pdb=" N LYSBo 177 " --> pdb=" O METBo 173 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 182 through 188 Processing helix chain 'Bo' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUBo 195 " --> pdb=" O ASPBo 192 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARGBo 197 " --> pdb=" O SERBo 194 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 210 through 226 Processing helix chain 'Bp' and resid 66 through 73 Processing helix chain 'Bp' and resid 76 through 80 Processing helix chain 'Bp' and resid 86 through 102 Processing helix chain 'Bp' and resid 107 through 123 removed outlier: 3.509A pdb=" N VALBp 111 " --> pdb=" O GLUBp 107 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 145 through 151 removed outlier: 3.581A pdb=" N ASNBp 151 " --> pdb=" O PROBp 147 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 155 through 161 Processing helix chain 'Bp' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBp 177 " --> pdb=" O METBp 173 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 182 through 188 Processing helix chain 'Bp' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUBp 195 " --> pdb=" O ASPBp 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGBp 197 " --> pdb=" O SERBp 194 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 210 through 226 Processing helix chain 'Bq' and resid 66 through 73 Processing helix chain 'Bq' and resid 76 through 80 Processing helix chain 'Bq' and resid 86 through 102 Processing helix chain 'Bq' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALBq 111 " --> pdb=" O GLUBq 107 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNBq 151 " --> pdb=" O PROBq 147 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 155 through 161 Processing helix chain 'Bq' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBq 177 " --> pdb=" O METBq 173 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 182 through 188 Processing helix chain 'Bq' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBq 195 " --> pdb=" O ASPBq 192 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGBq 197 " --> pdb=" O SERBq 194 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 210 through 226 Processing helix chain 'Br' and resid 66 through 73 Processing helix chain 'Br' and resid 76 through 80 Processing helix chain 'Br' and resid 86 through 102 Processing helix chain 'Br' and resid 107 through 123 removed outlier: 3.512A pdb=" N VALBr 111 " --> pdb=" O GLUBr 107 " (cutoff:3.500A) Processing helix chain 'Br' and resid 145 through 151 removed outlier: 3.580A pdb=" N ASNBr 151 " --> pdb=" O PROBr 147 " (cutoff:3.500A) Processing helix chain 'Br' and resid 155 through 161 Processing helix chain 'Br' and resid 163 through 178 removed outlier: 3.875A pdb=" N LYSBr 177 " --> pdb=" O METBr 173 " (cutoff:3.500A) Processing helix chain 'Br' and resid 182 through 188 Processing helix chain 'Br' and resid 192 through 199 removed outlier: 3.591A pdb=" N LEUBr 195 " --> pdb=" O ASPBr 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGBr 197 " --> pdb=" O SERBr 194 " (cutoff:3.500A) Processing helix chain 'Br' and resid 210 through 226 Processing helix chain 'Bs' and resid 66 through 73 Processing helix chain 'Bs' and resid 76 through 80 Processing helix chain 'Bs' and resid 86 through 102 Processing helix chain 'Bs' and resid 107 through 123 removed outlier: 3.511A pdb=" N VALBs 111 " --> pdb=" O GLUBs 107 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 145 through 151 removed outlier: 3.582A pdb=" N ASNBs 151 " --> pdb=" O PROBs 147 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 155 through 161 Processing helix chain 'Bs' and resid 163 through 178 removed outlier: 3.873A pdb=" N LYSBs 177 " --> pdb=" O METBs 173 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 182 through 188 Processing helix chain 'Bs' and resid 192 through 199 removed outlier: 3.592A pdb=" N LEUBs 195 " --> pdb=" O ASPBs 192 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARGBs 197 " --> pdb=" O SERBs 194 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 210 through 226 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 136 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 136 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'As' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'At' and resid 131 through 136 Processing sheet with id=AB3, first strand: chain 'Au' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'Av' and resid 131 through 136 Processing sheet with id=AB5, first strand: chain 'Aw' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'Ax' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'Ay' and resid 131 through 136 Processing sheet with id=AB8, first strand: chain 'Az' and resid 131 through 136 Processing sheet with id=AB9, first strand: chain 'Ba' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'Bk' and resid 131 through 136 Processing sheet with id=AC2, first strand: chain 'Bl' and resid 131 through 136 Processing sheet with id=AC3, first strand: chain 'Bm' and resid 131 through 136 Processing sheet with id=AC4, first strand: chain 'Bn' and resid 131 through 136 Processing sheet with id=AC5, first strand: chain 'Bo' and resid 131 through 136 Processing sheet with id=AC6, first strand: chain 'Bp' and resid 131 through 136 Processing sheet with id=AC7, first strand: chain 'Bq' and resid 131 through 136 Processing sheet with id=AC8, first strand: chain 'Br' and resid 131 through 136 Processing sheet with id=AC9, first strand: chain 'Bs' and resid 131 through 136 1944 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 54 stacking parallelities Total time for adding SS restraints: 12.58 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12919 1.33 - 1.45: 9676 1.45 - 1.57: 28300 1.57 - 1.69: 243 1.69 - 1.81: 756 Bond restraints: 51894 Sorted by residual: bond pdb=" C LYSAb 177 " pdb=" N GLUAb 178 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.05e-02 9.07e+03 1.59e+01 bond pdb=" C LYSAi 177 " pdb=" N GLUAi 178 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.05e-02 9.07e+03 1.58e+01 bond pdb=" C LYSAe 177 " pdb=" N GLUAe 178 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.05e-02 9.07e+03 1.56e+01 bond pdb=" C LYSAv 177 " pdb=" N GLUAv 178 " ideal model delta sigma weight residual 1.327 1.285 0.041 1.05e-02 9.07e+03 1.56e+01 bond pdb=" C LYSAw 177 " pdb=" N GLUAw 178 " ideal model delta sigma weight residual 1.327 1.285 0.041 1.05e-02 9.07e+03 1.56e+01 ... (remaining 51889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 66119 0.96 - 1.93: 3538 1.93 - 2.89: 675 2.89 - 3.85: 219 3.85 - 4.82: 189 Bond angle restraints: 70740 Sorted by residual: angle pdb=" N VALAc 264 " pdb=" CA VALAc 264 " pdb=" C VALAc 264 " ideal model delta sigma weight residual 109.30 113.89 -4.59 1.25e+00 6.40e-01 1.35e+01 angle pdb=" N VALAe 264 " pdb=" CA VALAe 264 " pdb=" C VALAe 264 " ideal model delta sigma weight residual 109.30 113.88 -4.58 1.25e+00 6.40e-01 1.34e+01 angle pdb=" N VALAs 264 " pdb=" CA VALAs 264 " pdb=" C VALAs 264 " ideal model delta sigma weight residual 109.30 113.88 -4.58 1.25e+00 6.40e-01 1.34e+01 angle pdb=" N VALBr 264 " pdb=" CA VALBr 264 " pdb=" C VALBr 264 " ideal model delta sigma weight residual 109.30 113.88 -4.58 1.25e+00 6.40e-01 1.34e+01 angle pdb=" N VALAz 264 " pdb=" CA VALAz 264 " pdb=" C VALAz 264 " ideal model delta sigma weight residual 109.30 113.88 -4.58 1.25e+00 6.40e-01 1.34e+01 ... (remaining 70735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 30697 34.86 - 69.72: 1406 69.72 - 104.58: 54 104.58 - 139.44: 0 139.44 - 174.30: 27 Dihedral angle restraints: 32184 sinusoidal: 14472 harmonic: 17712 Sorted by residual: dihedral pdb=" O4' UBw 4 " pdb=" C1' UBw 4 " pdb=" N1 UBw 4 " pdb=" C2 UBw 4 " ideal model delta sinusoidal sigma weight residual -128.00 46.30 -174.30 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' UBf 4 " pdb=" C1' UBf 4 " pdb=" N1 UBf 4 " pdb=" C2 UBf 4 " ideal model delta sinusoidal sigma weight residual -128.00 46.25 -174.25 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' UBv 4 " pdb=" C1' UBv 4 " pdb=" N1 UBv 4 " pdb=" C2 UBv 4 " ideal model delta sinusoidal sigma weight residual -128.00 46.25 -174.25 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 32181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4729 0.031 - 0.062: 2429 0.062 - 0.092: 579 0.092 - 0.123: 228 0.123 - 0.154: 27 Chirality restraints: 7992 Sorted by residual: chirality pdb=" C1' UAj 2 " pdb=" O4' UAj 2 " pdb=" C2' UAj 2 " pdb=" N1 UAj 2 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" C1' UBv 2 " pdb=" O4' UBv 2 " pdb=" C2' UBv 2 " pdb=" N1 UBv 2 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" C1' UBd 2 " pdb=" O4' UBd 2 " pdb=" C2' UBd 2 " pdb=" N1 UBd 2 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 7989 not shown) Planarity restraints: 8748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUAi 262 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C LEUAi 262 " -0.035 2.00e-02 2.50e+03 pdb=" O LEUAi 262 " 0.013 2.00e-02 2.50e+03 pdb=" N GLYAi 263 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUBk 262 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEUBk 262 " -0.034 2.00e-02 2.50e+03 pdb=" O LEUBk 262 " 0.013 2.00e-02 2.50e+03 pdb=" N GLYBk 263 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUBr 262 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C LEUBr 262 " -0.034 2.00e-02 2.50e+03 pdb=" O LEUBr 262 " 0.013 2.00e-02 2.50e+03 pdb=" N GLYBr 263 " 0.012 2.00e-02 2.50e+03 ... (remaining 8745 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 15947 2.83 - 3.35: 46420 3.35 - 3.87: 91234 3.87 - 4.38: 106821 4.38 - 4.90: 170863 Nonbonded interactions: 431285 Sorted by model distance: nonbonded pdb=" OD2 ASPBm 192 " pdb=" NH2 ARGBm 212 " model vdw 2.317 3.120 nonbonded pdb=" OD2 ASPAe 192 " pdb=" NH2 ARGAe 212 " model vdw 2.317 3.120 nonbonded pdb=" OD2 ASPAz 192 " pdb=" NH2 ARGAz 212 " model vdw 2.317 3.120 nonbonded pdb=" OD2 ASPAb 192 " pdb=" NH2 ARGAb 212 " model vdw 2.317 3.120 nonbonded pdb=" OD2 ASPAd 192 " pdb=" NH2 ARGAd 212 " model vdw 2.317 3.120 ... (remaining 431280 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: 0.00 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' selection = chain 'Bk' selection = chain 'Bl' selection = chain 'Bm' selection = chain 'Bn' selection = chain 'Bo' selection = chain 'Bp' selection = chain 'Bq' selection = chain 'Br' selection = chain 'Bs' } ncs_group { reference = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bh' selection = chain 'Bi' selection = chain 'Bj' selection = chain 'Bt' selection = chain 'Bu' selection = chain 'Bv' selection = chain 'Bw' selection = chain 'Bx' selection = chain 'By' selection = chain 'Bz' selection = chain 'Ca' selection = chain 'Cb' } 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: 1.060 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: 0.040 Extract box with map and model: 1.460 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 71.650 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 51894 Z= 0.259 Angle : 0.568 4.816 70740 Z= 0.349 Chirality : 0.040 0.154 7992 Planarity : 0.005 0.040 8748 Dihedral : 18.294 174.302 20736 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.71 % Allowed : 17.33 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.52 (0.11), residues: 5994 helix: 1.08 (0.11), residues: 2646 sheet: 0.30 (0.30), residues: 270 loop : -0.23 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBp 132 HIS 0.002 0.001 HISAe 69 PHE 0.013 0.002 PHEAy 200 TYR 0.013 0.001 TYRBp 94 ARG 0.004 0.000 ARGAd 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1012 time to evaluate : 4.274 Fit side-chains REVERT: Aa 134 MET cc_start: 0.9212 (mtp) cc_final: 0.8998 (mtp) REVERT: Aa 176 LYS cc_start: 0.8405 (mttp) cc_final: 0.8081 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7979 (mttm) cc_final: 0.7758 (mttp) REVERT: Aa 208 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8341 (mtt-85) REVERT: Aa 258 MET cc_start: 0.8949 (mmm) cc_final: 0.8650 (mmt) REVERT: Ab 54 MET cc_start: 0.7713 (ptp) cc_final: 0.7513 (ptp) REVERT: Ab 107 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7161 (mm-30) REVERT: Ab 108 MET cc_start: 0.8652 (tpt) cc_final: 0.8423 (tpt) REVERT: Ab 134 MET cc_start: 0.9189 (mtp) cc_final: 0.8964 (ttt) REVERT: Ab 136 CYS cc_start: 0.7863 (t) cc_final: 0.7455 (m) REVERT: Ab 160 MET cc_start: 0.9278 (mmm) cc_final: 0.8951 (mmm) REVERT: Ab 176 LYS cc_start: 0.8403 (mttp) cc_final: 0.7992 (mtmt) REVERT: Ab 177 LYS cc_start: 0.8052 (mttm) cc_final: 0.7821 (mttp) REVERT: Ac 135 MET cc_start: 0.8817 (mmm) cc_final: 0.8517 (mmm) REVERT: Ac 136 CYS cc_start: 0.7652 (t) cc_final: 0.7200 (m) REVERT: Ac 243 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7060 (tp30) REVERT: Ad 56 MET cc_start: 0.8499 (mmm) cc_final: 0.8062 (mmm) REVERT: Ad 108 MET cc_start: 0.8586 (tpt) cc_final: 0.8282 (tpt) REVERT: Ad 110 THR cc_start: 0.8806 (m) cc_final: 0.8488 (m) REVERT: Ad 134 MET cc_start: 0.9203 (mtp) cc_final: 0.8800 (ttt) REVERT: Ad 177 LYS cc_start: 0.8223 (mttm) cc_final: 0.7949 (mttp) REVERT: Ad 208 ARG cc_start: 0.8502 (mtt90) cc_final: 0.8291 (mtt-85) REVERT: Ae 56 MET cc_start: 0.8400 (mmm) cc_final: 0.7998 (mmm) REVERT: Ae 136 CYS cc_start: 0.7897 (t) cc_final: 0.7405 (p) REVERT: Ae 176 LYS cc_start: 0.8439 (mttp) cc_final: 0.8049 (mtmt) REVERT: Ae 220 MET cc_start: 0.9390 (mtm) cc_final: 0.9051 (mtp) REVERT: Af 54 MET cc_start: 0.8009 (ptp) cc_final: 0.7111 (ttp) REVERT: Af 56 MET cc_start: 0.8513 (mmm) cc_final: 0.7741 (mmm) REVERT: Af 108 MET cc_start: 0.8622 (tpt) cc_final: 0.8278 (tpp) REVERT: Af 136 CYS cc_start: 0.7847 (t) cc_final: 0.7272 (m) REVERT: Af 139 GLU cc_start: 0.7728 (tp30) cc_final: 0.7400 (tt0) REVERT: Af 176 LYS cc_start: 0.8418 (mttp) cc_final: 0.8033 (mtmt) REVERT: Af 177 LYS cc_start: 0.8119 (mttm) cc_final: 0.7906 (mttp) REVERT: Af 258 MET cc_start: 0.8909 (mmm) cc_final: 0.8681 (mmt) REVERT: Ag 134 MET cc_start: 0.9210 (mtp) cc_final: 0.9006 (ttt) REVERT: Ag 136 CYS cc_start: 0.7725 (t) cc_final: 0.7362 (m) REVERT: Ah 54 MET cc_start: 0.7606 (ptp) cc_final: 0.7001 (ptp) REVERT: Ah 107 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6704 (mm-30) REVERT: Ah 135 MET cc_start: 0.8763 (mmm) cc_final: 0.8448 (mmm) REVERT: Ah 136 CYS cc_start: 0.7681 (t) cc_final: 0.7206 (m) REVERT: Ah 139 GLU cc_start: 0.7700 (tp30) cc_final: 0.7446 (tt0) REVERT: Ai 54 MET cc_start: 0.7735 (ptp) cc_final: 0.7517 (ptp) REVERT: Ai 56 MET cc_start: 0.8543 (mmm) cc_final: 0.7784 (mpt) REVERT: Ai 110 THR cc_start: 0.8662 (m) cc_final: 0.8445 (m) REVERT: Ai 136 CYS cc_start: 0.7822 (t) cc_final: 0.7419 (m) REVERT: Ai 160 MET cc_start: 0.9234 (mmm) cc_final: 0.8922 (mmm) REVERT: Ai 173 MET cc_start: 0.8655 (tmm) cc_final: 0.8392 (tmm) REVERT: Ai 177 LYS cc_start: 0.8178 (mttm) cc_final: 0.7953 (mttp) REVERT: Ai 244 GLU cc_start: 0.8261 (tt0) cc_final: 0.7983 (tt0) REVERT: Ai 258 MET cc_start: 0.8934 (mmm) cc_final: 0.8681 (mmm) REVERT: As 56 MET cc_start: 0.8583 (mmm) cc_final: 0.8305 (mmm) REVERT: As 134 MET cc_start: 0.9208 (mtp) cc_final: 0.8979 (ttt) REVERT: As 136 CYS cc_start: 0.7748 (t) cc_final: 0.7294 (m) REVERT: As 176 LYS cc_start: 0.8453 (mttp) cc_final: 0.8063 (mtmt) REVERT: As 177 LYS cc_start: 0.8169 (mttm) cc_final: 0.7936 (mttp) REVERT: Au 54 MET cc_start: 0.7802 (ptp) cc_final: 0.7522 (ptm) REVERT: Au 134 MET cc_start: 0.9119 (mtp) cc_final: 0.8902 (ttt) REVERT: Au 135 MET cc_start: 0.8794 (mmm) cc_final: 0.8214 (mmm) REVERT: Au 173 MET cc_start: 0.8684 (tmm) cc_final: 0.8236 (tmm) REVERT: Au 176 LYS cc_start: 0.8455 (mttp) cc_final: 0.8082 (mtmt) REVERT: Au 177 LYS cc_start: 0.8179 (mttm) cc_final: 0.7965 (mttp) REVERT: Av 107 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6701 (mm-30) REVERT: Av 108 MET cc_start: 0.8553 (tpt) cc_final: 0.8223 (tpt) REVERT: Av 176 LYS cc_start: 0.8484 (mttp) cc_final: 0.8080 (mtmt) REVERT: Aw 54 MET cc_start: 0.7711 (ptp) cc_final: 0.7168 (ptp) REVERT: Aw 56 MET cc_start: 0.8496 (mmm) cc_final: 0.8045 (mmm) REVERT: Aw 153 LYS cc_start: 0.9185 (mptp) cc_final: 0.8961 (mmtm) REVERT: Ax 56 MET cc_start: 0.8585 (mmm) cc_final: 0.8095 (mmm) REVERT: Ax 134 MET cc_start: 0.9249 (mtp) cc_final: 0.8995 (ttt) REVERT: Ax 136 CYS cc_start: 0.7892 (t) cc_final: 0.7306 (m) REVERT: Ax 160 MET cc_start: 0.9286 (mmm) cc_final: 0.9077 (mmm) REVERT: Ax 176 LYS cc_start: 0.8509 (mttp) cc_final: 0.8130 (mtmt) REVERT: Ay 54 MET cc_start: 0.7958 (ptp) cc_final: 0.7141 (ttp) REVERT: Ay 134 MET cc_start: 0.9205 (mtp) cc_final: 0.8999 (ttt) REVERT: Ay 136 CYS cc_start: 0.7853 (t) cc_final: 0.7313 (m) REVERT: Az 54 MET cc_start: 0.7724 (ptp) cc_final: 0.7210 (ptm) REVERT: Az 56 MET cc_start: 0.8536 (mmm) cc_final: 0.8296 (mmm) REVERT: Az 108 MET cc_start: 0.8591 (tpt) cc_final: 0.7980 (tpt) REVERT: Az 134 MET cc_start: 0.9189 (mtp) cc_final: 0.8901 (ttt) REVERT: Az 136 CYS cc_start: 0.7688 (t) cc_final: 0.7112 (m) REVERT: Az 176 LYS cc_start: 0.8381 (mttp) cc_final: 0.7991 (mtmt) REVERT: Ba 108 MET cc_start: 0.8507 (tpt) cc_final: 0.7871 (tpt) REVERT: Ba 134 MET cc_start: 0.9218 (mtp) cc_final: 0.8824 (ttt) REVERT: Ba 160 MET cc_start: 0.9286 (mmm) cc_final: 0.9046 (mmm) REVERT: Ba 176 LYS cc_start: 0.8424 (mttp) cc_final: 0.8078 (mtmt) REVERT: Ba 258 MET cc_start: 0.8971 (mmm) cc_final: 0.8761 (mmt) REVERT: Bk 54 MET cc_start: 0.7743 (ptp) cc_final: 0.7434 (ptp) REVERT: Bk 176 LYS cc_start: 0.8389 (mttp) cc_final: 0.7973 (mtmt) REVERT: Bl 134 MET cc_start: 0.9203 (mtp) cc_final: 0.8992 (ttt) REVERT: Bl 136 CYS cc_start: 0.7907 (t) cc_final: 0.7412 (m) REVERT: Bl 139 GLU cc_start: 0.7725 (tp30) cc_final: 0.7297 (tt0) REVERT: Bl 176 LYS cc_start: 0.8457 (mttp) cc_final: 0.8248 (mttp) REVERT: Bm 54 MET cc_start: 0.7640 (ptp) cc_final: 0.7330 (ptm) REVERT: Bm 134 MET cc_start: 0.9190 (mtp) cc_final: 0.8687 (ttt) REVERT: Bm 265 LYS cc_start: 0.7925 (mptm) cc_final: 0.7696 (mmtt) REVERT: Bn 54 MET cc_start: 0.7551 (ptp) cc_final: 0.6978 (ptm) REVERT: Bn 56 MET cc_start: 0.8505 (mmm) cc_final: 0.7871 (mpt) REVERT: Bn 63 THR cc_start: 0.8673 (p) cc_final: 0.8455 (t) REVERT: Bn 160 MET cc_start: 0.9269 (mmm) cc_final: 0.8776 (mmm) REVERT: Bo 79 ASP cc_start: 0.8815 (m-30) cc_final: 0.8612 (m-30) REVERT: Bo 136 CYS cc_start: 0.7915 (t) cc_final: 0.7433 (m) REVERT: Bo 139 GLU cc_start: 0.7804 (tp30) cc_final: 0.7439 (tt0) REVERT: Bo 173 MET cc_start: 0.8672 (tmm) cc_final: 0.8370 (tmm) REVERT: Bo 178 GLU cc_start: 0.7951 (pt0) cc_final: 0.7728 (pt0) REVERT: Bo 220 MET cc_start: 0.9445 (mtm) cc_final: 0.9092 (mtp) REVERT: Bp 56 MET cc_start: 0.8446 (mmm) cc_final: 0.7995 (mmm) REVERT: Bp 134 MET cc_start: 0.9208 (mtp) cc_final: 0.9008 (mtp) REVERT: Bp 267 MET cc_start: 0.5514 (mtt) cc_final: 0.5171 (mtp) REVERT: Bq 54 MET cc_start: 0.7784 (ptp) cc_final: 0.7490 (ptp) REVERT: Bq 134 MET cc_start: 0.9197 (mtp) cc_final: 0.8973 (ttt) REVERT: Bq 139 GLU cc_start: 0.7788 (tp30) cc_final: 0.7503 (tt0) REVERT: Bq 177 LYS cc_start: 0.8123 (mttm) cc_final: 0.7905 (mttp) REVERT: Bq 220 MET cc_start: 0.9456 (mtm) cc_final: 0.9238 (mtm) REVERT: Br 108 MET cc_start: 0.8476 (tpt) cc_final: 0.7750 (tpt) REVERT: Br 134 MET cc_start: 0.9139 (mtp) cc_final: 0.8818 (ttt) REVERT: Br 160 MET cc_start: 0.9224 (mmm) cc_final: 0.8974 (mmm) REVERT: Br 176 LYS cc_start: 0.8417 (mttp) cc_final: 0.7991 (mtmt) REVERT: Bs 54 MET cc_start: 0.7710 (ptp) cc_final: 0.7432 (ptp) REVERT: Bs 56 MET cc_start: 0.8374 (mmm) cc_final: 0.7915 (mmm) REVERT: Bs 76 GLN cc_start: 0.8719 (mt0) cc_final: 0.8490 (mt0) REVERT: Bs 107 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6774 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7777 (t) cc_final: 0.7328 (m) REVERT: Bs 139 GLU cc_start: 0.7866 (tp30) cc_final: 0.7658 (tt0) REVERT: Bs 176 LYS cc_start: 0.8468 (mttp) cc_final: 0.8011 (mtmt) REVERT: Bs 220 MET cc_start: 0.9437 (mtm) cc_final: 0.9115 (mtp) outliers start: 37 outliers final: 24 residues processed: 1039 average time/residue: 1.6450 time to fit residues: 2079.7984 Evaluate side-chains 968 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 944 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Af residue 211 VAL Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 211 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 211 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 9.9990 chunk 450 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 465 optimal weight: 0.0870 chunk 180 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 346 optimal weight: 0.0070 chunk 539 optimal weight: 5.9990 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 113 ASN Ax 113 ASN Bk 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 51894 Z= 0.209 Angle : 0.494 4.917 70740 Z= 0.266 Chirality : 0.040 0.165 7992 Planarity : 0.005 0.039 8748 Dihedral : 14.573 176.605 8745 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.87 % Allowed : 15.23 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.02 (0.11), residues: 5994 helix: 1.51 (0.11), residues: 2484 sheet: 0.62 (0.31), residues: 270 loop : 0.10 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBa 132 HIS 0.003 0.001 HISAd 217 PHE 0.015 0.002 PHEAg 200 TYR 0.012 0.001 TYRAs 94 ARG 0.004 0.000 ARGAz 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 961 time to evaluate : 4.196 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8646 (tmm) cc_final: 0.8213 (tmm) REVERT: Aa 176 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8082 (mtmt) REVERT: Aa 258 MET cc_start: 0.8822 (mmm) cc_final: 0.8520 (mmt) REVERT: Ab 108 MET cc_start: 0.8680 (tpt) cc_final: 0.8453 (tpt) REVERT: Ab 134 MET cc_start: 0.9168 (mtp) cc_final: 0.8925 (ttt) REVERT: Ab 136 CYS cc_start: 0.7889 (t) cc_final: 0.7453 (m) REVERT: Ab 176 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8012 (mtmt) REVERT: Ab 177 LYS cc_start: 0.7781 (mttm) cc_final: 0.7576 (mttp) REVERT: Ac 60 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7659 (mmtt) REVERT: Ac 135 MET cc_start: 0.8881 (mmm) cc_final: 0.8407 (mmm) REVERT: Ac 136 CYS cc_start: 0.7632 (t) cc_final: 0.7166 (m) REVERT: Ac 178 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: Ac 243 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7084 (tp30) REVERT: Ad 56 MET cc_start: 0.8461 (mmm) cc_final: 0.8138 (mmm) REVERT: Ad 108 MET cc_start: 0.8635 (tpt) cc_final: 0.8275 (tpt) REVERT: Ad 110 THR cc_start: 0.8788 (m) cc_final: 0.8536 (m) REVERT: Ad 134 MET cc_start: 0.9208 (mtp) cc_final: 0.8833 (ttt) REVERT: Ad 177 LYS cc_start: 0.8007 (mttm) cc_final: 0.7776 (mttp) REVERT: Ad 208 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8270 (mtt-85) REVERT: Ae 56 MET cc_start: 0.8346 (mmm) cc_final: 0.7909 (mmm) REVERT: Ae 67 LEU cc_start: 0.8167 (tp) cc_final: 0.7928 (tp) REVERT: Ae 136 CYS cc_start: 0.7963 (t) cc_final: 0.7624 (m) REVERT: Ae 176 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7939 (mtmt) REVERT: Af 54 MET cc_start: 0.7864 (ptp) cc_final: 0.7160 (ttp) REVERT: Af 136 CYS cc_start: 0.7912 (t) cc_final: 0.7287 (m) REVERT: Af 176 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8024 (mtmt) REVERT: Ag 60 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7982 (mmtt) REVERT: Ag 136 CYS cc_start: 0.7737 (t) cc_final: 0.7265 (m) REVERT: Ag 265 LYS cc_start: 0.8216 (mptm) cc_final: 0.7847 (mmtm) REVERT: Ah 54 MET cc_start: 0.7532 (ptp) cc_final: 0.6895 (ptp) REVERT: Ah 107 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6813 (mm-30) REVERT: Ah 135 MET cc_start: 0.8849 (mmm) cc_final: 0.8336 (mmm) REVERT: Ah 136 CYS cc_start: 0.7786 (t) cc_final: 0.7261 (m) REVERT: Ah 146 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8439 (ttmt) REVERT: Ah 177 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7670 (mttp) REVERT: Ai 54 MET cc_start: 0.7694 (ptp) cc_final: 0.7483 (ptp) REVERT: Ai 56 MET cc_start: 0.8546 (mmm) cc_final: 0.7850 (mpt) REVERT: Ai 136 CYS cc_start: 0.7834 (t) cc_final: 0.7398 (m) REVERT: Ai 146 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8084 (ttmt) REVERT: Ai 160 MET cc_start: 0.9184 (mmm) cc_final: 0.8881 (mmm) REVERT: Ai 177 LYS cc_start: 0.7905 (mttm) cc_final: 0.7699 (mttp) REVERT: As 136 CYS cc_start: 0.7755 (t) cc_final: 0.7406 (m) REVERT: As 176 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (mtmt) REVERT: As 177 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7701 (mttp) REVERT: As 197 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8410 (ptm160) REVERT: At 176 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8023 (mtmt) REVERT: Au 54 MET cc_start: 0.7742 (ptp) cc_final: 0.7534 (ptm) REVERT: Au 63 THR cc_start: 0.8718 (p) cc_final: 0.8486 (t) REVERT: Au 134 MET cc_start: 0.9125 (mtp) cc_final: 0.8838 (ttt) REVERT: Au 135 MET cc_start: 0.8876 (mmm) cc_final: 0.8156 (mmm) REVERT: Au 173 MET cc_start: 0.8618 (tmm) cc_final: 0.8300 (tmm) REVERT: Av 60 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7902 (mmtt) REVERT: Av 107 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6622 (mm-30) REVERT: Av 108 MET cc_start: 0.8618 (tpt) cc_final: 0.8282 (tpt) REVERT: Av 176 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8056 (mtmt) REVERT: Aw 54 MET cc_start: 0.7568 (ptp) cc_final: 0.7330 (ptp) REVERT: Aw 56 MET cc_start: 0.8471 (mmm) cc_final: 0.7942 (mmm) REVERT: Ax 56 MET cc_start: 0.8519 (mmm) cc_final: 0.8197 (mmm) REVERT: Ax 134 MET cc_start: 0.9223 (mtp) cc_final: 0.9006 (ttt) REVERT: Ax 136 CYS cc_start: 0.7881 (t) cc_final: 0.7291 (m) REVERT: Ax 176 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8100 (mtmt) REVERT: Ay 54 MET cc_start: 0.7710 (ptp) cc_final: 0.7161 (ptp) REVERT: Ay 134 MET cc_start: 0.9182 (mtp) cc_final: 0.8956 (ttt) REVERT: Ay 136 CYS cc_start: 0.7844 (t) cc_final: 0.7391 (m) REVERT: Ay 178 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6995 (pt0) REVERT: Az 54 MET cc_start: 0.7755 (ptp) cc_final: 0.7482 (ptm) REVERT: Az 108 MET cc_start: 0.8641 (tpt) cc_final: 0.8041 (tpt) REVERT: Az 134 MET cc_start: 0.9229 (mtp) cc_final: 0.8988 (ttt) REVERT: Az 136 CYS cc_start: 0.7758 (t) cc_final: 0.7155 (m) REVERT: Az 177 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7527 (mttm) REVERT: Ba 60 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7913 (mmtt) REVERT: Ba 91 ASP cc_start: 0.8766 (m-30) cc_final: 0.8517 (m-30) REVERT: Ba 160 MET cc_start: 0.9251 (mmm) cc_final: 0.9016 (mmm) REVERT: Ba 176 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8096 (mtmt) REVERT: Ba 177 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7603 (mttm) REVERT: Bk 176 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7936 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7886 (t0) cc_final: 0.7675 (t70) REVERT: Bl 108 MET cc_start: 0.8592 (tpt) cc_final: 0.7822 (tpt) REVERT: Bl 134 MET cc_start: 0.9198 (mtp) cc_final: 0.8995 (ttt) REVERT: Bl 136 CYS cc_start: 0.7981 (t) cc_final: 0.7458 (m) REVERT: Bl 176 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8016 (mtmt) REVERT: Bl 177 LYS cc_start: 0.7912 (mttm) cc_final: 0.7677 (mttp) REVERT: Bl 265 LYS cc_start: 0.8151 (mptm) cc_final: 0.7932 (mmtt) REVERT: Bm 134 MET cc_start: 0.9222 (mtp) cc_final: 0.8828 (ttt) REVERT: Bm 176 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8100 (mptm) cc_final: 0.7819 (mmtt) REVERT: Bn 56 MET cc_start: 0.8440 (mmm) cc_final: 0.8195 (mmm) REVERT: Bn 60 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7767 (mmtt) REVERT: Bn 63 THR cc_start: 0.8694 (p) cc_final: 0.8432 (t) REVERT: Bn 160 MET cc_start: 0.9285 (mmm) cc_final: 0.8841 (mmm) REVERT: Bn 176 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7995 (mtmt) REVERT: Bo 79 ASP cc_start: 0.8847 (m-30) cc_final: 0.8545 (m-30) REVERT: Bo 136 CYS cc_start: 0.7895 (t) cc_final: 0.7388 (m) REVERT: Bo 173 MET cc_start: 0.8614 (tmm) cc_final: 0.8284 (tmm) REVERT: Bo 220 MET cc_start: 0.9435 (mtm) cc_final: 0.9037 (mtp) REVERT: Bo 265 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7960 (mmtt) REVERT: Bp 56 MET cc_start: 0.8390 (mmm) cc_final: 0.7768 (mmm) REVERT: Bp 134 MET cc_start: 0.9093 (mtp) cc_final: 0.8830 (ttt) REVERT: Bp 176 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: Bp 267 MET cc_start: 0.5876 (mtt) cc_final: 0.5664 (mtm) REVERT: Bq 54 MET cc_start: 0.7477 (ptp) cc_final: 0.7137 (ptp) REVERT: Bq 134 MET cc_start: 0.9208 (mtp) cc_final: 0.9000 (ttt) REVERT: Bq 139 GLU cc_start: 0.7627 (tp30) cc_final: 0.7284 (tt0) REVERT: Bq 153 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8967 (mmtm) REVERT: Br 108 MET cc_start: 0.8546 (tpt) cc_final: 0.7768 (tpt) REVERT: Br 160 MET cc_start: 0.9289 (mmm) cc_final: 0.9021 (mmm) REVERT: Br 176 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7902 (mtmt) REVERT: Br 177 LYS cc_start: 0.8037 (mttm) cc_final: 0.7814 (mtpp) REVERT: Bs 56 MET cc_start: 0.8379 (mmm) cc_final: 0.7919 (mmm) REVERT: Bs 76 GLN cc_start: 0.8686 (mt0) cc_final: 0.8430 (mt0) REVERT: Bs 107 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6743 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7833 (t) cc_final: 0.7430 (m) REVERT: Bs 139 GLU cc_start: 0.7809 (tp30) cc_final: 0.7599 (tp30) REVERT: Bs 176 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7962 (mtmt) REVERT: Bs 220 MET cc_start: 0.9474 (mtm) cc_final: 0.9171 (mtp) outliers start: 98 outliers final: 37 residues processed: 996 average time/residue: 1.7424 time to fit residues: 2096.6454 Evaluate side-chains 995 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 933 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 178 GLU Chi-restraints excluded: chain Ad residue 165 ASP Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Ah residue 44 VAL Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 153 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain As residue 176 LYS Chi-restraints excluded: chain As residue 177 LYS Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 176 LYS Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Av residue 176 LYS Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 165 ASP Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ay residue 176 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Az residue 177 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 176 LYS Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bn residue 176 LYS Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bp residue 177 LYS Chi-restraints excluded: chain Bp residue 211 VAL Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 176 LYS Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 448 optimal weight: 0.9980 chunk 367 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 540 optimal weight: 7.9990 chunk 583 optimal weight: 10.0000 chunk 481 optimal weight: 0.0570 chunk 535 optimal weight: 6.9990 chunk 184 optimal weight: 0.0030 chunk 433 optimal weight: 4.9990 overall best weight: 2.0112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ax 77 GLN Ba 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 51894 Z= 0.158 Angle : 0.456 4.872 70740 Z= 0.245 Chirality : 0.039 0.152 7992 Planarity : 0.004 0.040 8748 Dihedral : 14.413 176.444 8729 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.10 % Allowed : 15.04 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.99 (0.11), residues: 5994 helix: 1.34 (0.11), residues: 2646 sheet: 0.78 (0.31), residues: 270 loop : 0.14 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAh 132 HIS 0.002 0.001 HISBp 69 PHE 0.013 0.002 PHEAg 200 TYR 0.013 0.001 TYRAs 94 ARG 0.005 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 994 time to evaluate : 4.273 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8617 (tmm) cc_final: 0.8205 (tmm) REVERT: Aa 176 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8045 (mtmt) REVERT: Aa 258 MET cc_start: 0.8743 (mmm) cc_final: 0.8490 (mmt) REVERT: Ab 54 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7096 (ttp) REVERT: Ab 108 MET cc_start: 0.8624 (tpt) cc_final: 0.8330 (tpt) REVERT: Ab 134 MET cc_start: 0.9154 (mtp) cc_final: 0.8931 (ttt) REVERT: Ab 136 CYS cc_start: 0.7887 (t) cc_final: 0.7505 (m) REVERT: Ab 176 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (mtmt) REVERT: Ab 177 LYS cc_start: 0.7759 (mttm) cc_final: 0.7559 (mttp) REVERT: Ac 56 MET cc_start: 0.8277 (mmm) cc_final: 0.8067 (mmm) REVERT: Ac 58 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7908 (mmmm) REVERT: Ac 135 MET cc_start: 0.8897 (mmm) cc_final: 0.8471 (mmm) REVERT: Ac 136 CYS cc_start: 0.7632 (t) cc_final: 0.7185 (m) REVERT: Ac 178 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: Ac 243 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7047 (tp30) REVERT: Ad 56 MET cc_start: 0.8474 (mmm) cc_final: 0.8070 (mmm) REVERT: Ad 108 MET cc_start: 0.8567 (tpt) cc_final: 0.8202 (tpt) REVERT: Ad 134 MET cc_start: 0.9189 (mtp) cc_final: 0.8832 (ttt) REVERT: Ad 208 ARG cc_start: 0.8475 (mtt90) cc_final: 0.8256 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8204 (tp) cc_final: 0.7953 (tp) REVERT: Ae 136 CYS cc_start: 0.7932 (t) cc_final: 0.7632 (m) REVERT: Ae 176 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: Ae 220 MET cc_start: 0.9408 (mtm) cc_final: 0.9021 (mtp) REVERT: Af 56 MET cc_start: 0.8288 (mmm) cc_final: 0.7813 (mmm) REVERT: Af 136 CYS cc_start: 0.7897 (t) cc_final: 0.7290 (m) REVERT: Af 176 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (mtmt) REVERT: Ag 136 CYS cc_start: 0.7756 (t) cc_final: 0.7251 (m) REVERT: Ag 265 LYS cc_start: 0.8215 (mptm) cc_final: 0.7854 (mmtm) REVERT: Ah 54 MET cc_start: 0.7432 (ptp) cc_final: 0.6983 (ptp) REVERT: Ah 107 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6753 (mm-30) REVERT: Ah 135 MET cc_start: 0.8880 (mmm) cc_final: 0.8412 (mmm) REVERT: Ah 136 CYS cc_start: 0.7744 (t) cc_final: 0.7240 (m) REVERT: Ah 146 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8475 (ttmt) REVERT: Ai 54 MET cc_start: 0.7633 (ptp) cc_final: 0.7371 (ptp) REVERT: Ai 56 MET cc_start: 0.8516 (mmm) cc_final: 0.7819 (mpt) REVERT: Ai 110 THR cc_start: 0.8628 (m) cc_final: 0.8386 (m) REVERT: Ai 136 CYS cc_start: 0.7779 (t) cc_final: 0.7367 (m) REVERT: Ai 146 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: Ai 173 MET cc_start: 0.8740 (tmm) cc_final: 0.8461 (tmm) REVERT: Ai 177 LYS cc_start: 0.7818 (mttm) cc_final: 0.7600 (mttp) REVERT: Ai 258 MET cc_start: 0.8838 (mmt) cc_final: 0.8538 (mmm) REVERT: As 136 CYS cc_start: 0.7750 (t) cc_final: 0.7422 (m) REVERT: As 176 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: At 63 THR cc_start: 0.8690 (p) cc_final: 0.8469 (t) REVERT: At 176 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (mtmt) REVERT: Au 54 MET cc_start: 0.7606 (ptp) cc_final: 0.7254 (ptm) REVERT: Au 134 MET cc_start: 0.9135 (mtp) cc_final: 0.8848 (ttt) REVERT: Au 135 MET cc_start: 0.8870 (mmm) cc_final: 0.8205 (mmm) REVERT: Au 136 CYS cc_start: 0.7719 (t) cc_final: 0.7371 (m) REVERT: Au 173 MET cc_start: 0.8547 (tmm) cc_final: 0.8283 (tmm) REVERT: Av 60 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7903 (mmtt) REVERT: Av 72 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7162 (pt0) REVERT: Av 107 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6571 (mm-30) REVERT: Av 108 MET cc_start: 0.8559 (tpt) cc_final: 0.8292 (mmp) REVERT: Av 176 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: Av 181 MET cc_start: 0.9365 (tpp) cc_final: 0.9141 (tpp) REVERT: Aw 56 MET cc_start: 0.8440 (mmm) cc_final: 0.8029 (mmm) REVERT: Ax 56 MET cc_start: 0.8408 (mmm) cc_final: 0.8019 (mmm) REVERT: Ax 134 MET cc_start: 0.9193 (mtp) cc_final: 0.8984 (ttt) REVERT: Ax 136 CYS cc_start: 0.7957 (t) cc_final: 0.7396 (m) REVERT: Ax 176 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: Ay 54 MET cc_start: 0.7657 (ptp) cc_final: 0.7249 (ptp) REVERT: Ay 136 CYS cc_start: 0.7831 (t) cc_final: 0.7408 (m) REVERT: Ay 178 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: Az 54 MET cc_start: 0.7560 (ptp) cc_final: 0.7290 (ptm) REVERT: Az 72 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7327 (pt0) REVERT: Az 108 MET cc_start: 0.8615 (tpt) cc_final: 0.7978 (tpt) REVERT: Az 134 MET cc_start: 0.9217 (mtp) cc_final: 0.8873 (ttt) REVERT: Az 136 CYS cc_start: 0.7755 (t) cc_final: 0.7162 (m) REVERT: Ba 91 ASP cc_start: 0.8773 (m-30) cc_final: 0.8503 (m-30) REVERT: Ba 160 MET cc_start: 0.9243 (mmm) cc_final: 0.9006 (mmm) REVERT: Ba 176 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7976 (mtmt) REVERT: Ba 177 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7615 (mttm) REVERT: Bk 176 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7908 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7912 (t0) cc_final: 0.7686 (t70) REVERT: Bl 108 MET cc_start: 0.8554 (tpt) cc_final: 0.8114 (mmt) REVERT: Bl 134 MET cc_start: 0.9179 (mtp) cc_final: 0.8968 (ttt) REVERT: Bl 136 CYS cc_start: 0.7970 (t) cc_final: 0.7451 (m) REVERT: Bl 176 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7882 (mtmt) REVERT: Bl 177 LYS cc_start: 0.7847 (mttm) cc_final: 0.7623 (mttp) REVERT: Bm 134 MET cc_start: 0.9200 (mtp) cc_final: 0.8838 (ttt) REVERT: Bm 176 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7981 (mtmt) REVERT: Bm 197 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8318 (ptm160) REVERT: Bm 265 LYS cc_start: 0.8118 (mptm) cc_final: 0.7820 (mmtt) REVERT: Bn 63 THR cc_start: 0.8728 (p) cc_final: 0.8459 (t) REVERT: Bn 160 MET cc_start: 0.9276 (mmm) cc_final: 0.8786 (mmm) REVERT: Bo 79 ASP cc_start: 0.8837 (m-30) cc_final: 0.8553 (m-30) REVERT: Bo 136 CYS cc_start: 0.7863 (t) cc_final: 0.7403 (m) REVERT: Bo 139 GLU cc_start: 0.7730 (tp30) cc_final: 0.7317 (tt0) REVERT: Bo 173 MET cc_start: 0.8597 (tmm) cc_final: 0.8377 (tmm) REVERT: Bo 220 MET cc_start: 0.9428 (mtm) cc_final: 0.9020 (mtp) REVERT: Bp 56 MET cc_start: 0.8295 (mmm) cc_final: 0.7976 (mmm) REVERT: Bp 134 MET cc_start: 0.9089 (mtp) cc_final: 0.8838 (ttt) REVERT: Bp 176 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8078 (mtmt) REVERT: Bq 54 MET cc_start: 0.7461 (ptp) cc_final: 0.7168 (ptp) REVERT: Bq 153 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8961 (mmtm) REVERT: Br 160 MET cc_start: 0.9276 (mmm) cc_final: 0.8998 (mmm) REVERT: Br 176 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7829 (mtmt) REVERT: Br 177 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7665 (mtpp) REVERT: Bs 56 MET cc_start: 0.8306 (mmm) cc_final: 0.7899 (mmm) REVERT: Bs 76 GLN cc_start: 0.8627 (mt0) cc_final: 0.8368 (mt0) REVERT: Bs 107 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6724 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7804 (t) cc_final: 0.7448 (m) REVERT: Bs 139 GLU cc_start: 0.7803 (tp30) cc_final: 0.7569 (tp30) REVERT: Bs 176 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7930 (mtmt) REVERT: Bs 220 MET cc_start: 0.9463 (mtm) cc_final: 0.9145 (mtp) outliers start: 110 outliers final: 32 residues processed: 1044 average time/residue: 1.7310 time to fit residues: 2189.8326 Evaluate side-chains 1005 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 949 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 178 GLU Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 176 LYS Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 176 LYS Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 176 LYS Chi-restraints excluded: chain Av residue 231 ARG Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 176 LYS Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bm residue 197 ARG Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 177 LYS Chi-restraints excluded: chain Bs residue 176 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 0.9990 chunk 406 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 362 optimal weight: 0.9980 chunk 542 optimal weight: 9.9990 chunk 574 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 513 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ah 77 GLN As 77 GLN Ax 113 ASN Ba 76 GLN Bp 113 ASN Bp 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 51894 Z= 0.246 Angle : 0.512 5.790 70740 Z= 0.274 Chirality : 0.042 0.172 7992 Planarity : 0.005 0.043 8748 Dihedral : 14.540 177.302 8721 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.62 % Allowed : 14.28 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.02 (0.11), residues: 5994 helix: 1.55 (0.11), residues: 2484 sheet: 0.69 (0.31), residues: 270 loop : 0.07 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBa 132 HIS 0.004 0.001 HISAd 217 PHE 0.015 0.002 PHEAg 200 TYR 0.013 0.001 TYRAs 94 ARG 0.004 0.000 ARGAu 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 955 time to evaluate : 4.215 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8689 (tmm) cc_final: 0.8307 (tmm) REVERT: Aa 176 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8110 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7830 (mttp) cc_final: 0.7519 (mtpt) REVERT: Aa 258 MET cc_start: 0.8804 (mmm) cc_final: 0.8482 (mmt) REVERT: Ab 54 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7153 (ttp) REVERT: Ab 134 MET cc_start: 0.9150 (mtp) cc_final: 0.8926 (ttt) REVERT: Ab 136 CYS cc_start: 0.7894 (t) cc_final: 0.7516 (m) REVERT: Ab 176 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7997 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7628 (mmtt) REVERT: Ac 135 MET cc_start: 0.8886 (mmm) cc_final: 0.8402 (mmm) REVERT: Ac 136 CYS cc_start: 0.7631 (t) cc_final: 0.7184 (m) REVERT: Ac 178 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: Ad 56 MET cc_start: 0.8495 (mmm) cc_final: 0.8134 (mmm) REVERT: Ad 108 MET cc_start: 0.8579 (tpt) cc_final: 0.8215 (tpt) REVERT: Ad 134 MET cc_start: 0.9179 (mtp) cc_final: 0.8833 (ttt) REVERT: Ad 178 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: Ad 208 ARG cc_start: 0.8486 (mtt90) cc_final: 0.8275 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8225 (tp) cc_final: 0.7952 (tp) REVERT: Ae 176 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7926 (mtmt) REVERT: Af 54 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7136 (ttp) REVERT: Af 136 CYS cc_start: 0.7959 (t) cc_final: 0.7349 (m) REVERT: Af 176 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: Ag 136 CYS cc_start: 0.7813 (t) cc_final: 0.7243 (m) REVERT: Ag 244 GLU cc_start: 0.8328 (tt0) cc_final: 0.8015 (tt0) REVERT: Ag 265 LYS cc_start: 0.8254 (mptm) cc_final: 0.7872 (mmtm) REVERT: Ah 54 MET cc_start: 0.7422 (ptp) cc_final: 0.6913 (ptp) REVERT: Ah 107 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6820 (mm-30) REVERT: Ah 136 CYS cc_start: 0.7745 (t) cc_final: 0.7215 (m) REVERT: Ah 146 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8491 (ttmt) REVERT: Ai 54 MET cc_start: 0.7582 (ptp) cc_final: 0.7314 (ptp) REVERT: Ai 56 MET cc_start: 0.8534 (mmm) cc_final: 0.7825 (mpt) REVERT: Ai 136 CYS cc_start: 0.7857 (t) cc_final: 0.7404 (m) REVERT: Ai 146 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: Ai 177 LYS cc_start: 0.7880 (mttm) cc_final: 0.7658 (mttp) REVERT: Ai 258 MET cc_start: 0.8859 (mmt) cc_final: 0.8563 (mmm) REVERT: As 136 CYS cc_start: 0.7804 (t) cc_final: 0.7422 (m) REVERT: As 176 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8112 (mtmt) REVERT: At 176 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: At 267 MET cc_start: 0.5268 (OUTLIER) cc_final: 0.5004 (mmt) REVERT: Au 54 MET cc_start: 0.7609 (ptp) cc_final: 0.7285 (ptm) REVERT: Au 134 MET cc_start: 0.9104 (mtp) cc_final: 0.8871 (ttt) REVERT: Av 107 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6585 (mm-30) REVERT: Av 108 MET cc_start: 0.8565 (tpt) cc_final: 0.8293 (mmp) REVERT: Av 176 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8076 (mtmt) REVERT: Aw 56 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8067 (mmm) REVERT: Ax 56 MET cc_start: 0.8476 (mmm) cc_final: 0.8106 (mmm) REVERT: Ax 176 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8121 (mtmt) REVERT: Ay 54 MET cc_start: 0.7567 (ptp) cc_final: 0.7133 (ptp) REVERT: Ay 136 CYS cc_start: 0.7848 (t) cc_final: 0.7379 (m) REVERT: Ay 177 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7743 (mttm) REVERT: Ay 178 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: Az 54 MET cc_start: 0.7637 (ptp) cc_final: 0.7330 (ptm) REVERT: Az 72 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7397 (pt0) REVERT: Az 108 MET cc_start: 0.8683 (tpt) cc_final: 0.8166 (tpt) REVERT: Az 134 MET cc_start: 0.9219 (mtp) cc_final: 0.8868 (ttt) REVERT: Az 136 CYS cc_start: 0.7842 (t) cc_final: 0.7194 (m) REVERT: Ba 58 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7173 (pttm) REVERT: Ba 91 ASP cc_start: 0.8786 (m-30) cc_final: 0.8499 (m-30) REVERT: Ba 165 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7977 (t0) REVERT: Ba 176 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8104 (mtmt) REVERT: Ba 177 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7608 (mttm) REVERT: Bk 176 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7881 (t0) cc_final: 0.7650 (t70) REVERT: Bl 136 CYS cc_start: 0.8004 (t) cc_final: 0.7461 (m) REVERT: Bl 177 LYS cc_start: 0.7847 (mttm) cc_final: 0.7631 (mtmt) REVERT: Bm 134 MET cc_start: 0.9219 (mtp) cc_final: 0.8858 (ttt) REVERT: Bm 176 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8106 (mtmt) REVERT: Bm 197 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8357 (ptm160) REVERT: Bm 265 LYS cc_start: 0.8175 (mptm) cc_final: 0.7878 (mmtm) REVERT: Bn 63 THR cc_start: 0.8756 (p) cc_final: 0.8457 (t) REVERT: Bn 160 MET cc_start: 0.9319 (mmm) cc_final: 0.8707 (mmm) REVERT: Bo 79 ASP cc_start: 0.8838 (m-30) cc_final: 0.8530 (m-30) REVERT: Bo 107 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6896 (mm-30) REVERT: Bo 136 CYS cc_start: 0.7844 (t) cc_final: 0.7428 (m) REVERT: Bo 139 GLU cc_start: 0.7701 (tp30) cc_final: 0.7360 (tt0) REVERT: Bo 173 MET cc_start: 0.8656 (tmm) cc_final: 0.8326 (tmm) REVERT: Bo 220 MET cc_start: 0.9439 (mtm) cc_final: 0.9048 (mtp) REVERT: Bp 134 MET cc_start: 0.9102 (mtp) cc_final: 0.8888 (ttt) REVERT: Bp 176 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8130 (mtmt) REVERT: Bq 54 MET cc_start: 0.7474 (ptp) cc_final: 0.7211 (ptp) REVERT: Bq 99 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8513 (tp) REVERT: Bq 139 GLU cc_start: 0.7566 (tp30) cc_final: 0.7218 (tt0) REVERT: Bq 153 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8963 (mmtm) REVERT: Bq 265 LYS cc_start: 0.8071 (mptm) cc_final: 0.7790 (mmpt) REVERT: Br 54 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7270 (ptp) REVERT: Br 160 MET cc_start: 0.9290 (mmm) cc_final: 0.9017 (mmm) REVERT: Br 176 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7820 (mtmt) REVERT: Br 220 MET cc_start: 0.9466 (mtm) cc_final: 0.9169 (mtm) REVERT: Bs 56 MET cc_start: 0.8292 (mmm) cc_final: 0.7825 (mmm) REVERT: Bs 107 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6752 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7802 (t) cc_final: 0.7443 (m) REVERT: Bs 139 GLU cc_start: 0.7749 (tp30) cc_final: 0.7542 (tp30) REVERT: Bs 176 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8024 (mtmt) REVERT: Bs 220 MET cc_start: 0.9472 (mtm) cc_final: 0.9167 (mtp) outliers start: 137 outliers final: 73 residues processed: 1024 average time/residue: 1.6162 time to fit residues: 1992.7071 Evaluate side-chains 1036 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 933 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ac residue 178 GLU Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 165 ASP Chi-restraints excluded: chain Ad residue 178 GLU Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Af residue 211 VAL Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ah residue 44 VAL Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 176 LYS Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 176 LYS Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain At residue 267 MET Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 176 LYS Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 56 MET Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 165 ASP Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 165 ASP Chi-restraints excluded: chain Ay residue 176 LYS Chi-restraints excluded: chain Ay residue 177 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 88 SER Chi-restraints excluded: chain Az residue 110 THR Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 88 SER Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bm residue 197 ARG Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 134 MET Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 99 LEU Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 176 LYS Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 54 MET Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Br residue 260 THR Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 176 LYS Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 427 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 489 optimal weight: 10.0000 chunk 396 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 293 optimal weight: 5.9990 chunk 515 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 98 GLN Ad 98 GLN Ah 77 GLN Ai 98 GLN Ba 76 GLN Bq 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 51894 Z= 0.449 Angle : 0.635 7.169 70740 Z= 0.338 Chirality : 0.049 0.188 7992 Planarity : 0.006 0.051 8748 Dihedral : 14.759 177.762 8721 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.09 % Allowed : 13.42 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.19 (0.10), residues: 5994 helix: 0.82 (0.10), residues: 2646 sheet: 0.38 (0.30), residues: 270 loop : -0.46 (0.10), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAy 132 HIS 0.007 0.001 HISAd 217 PHE 0.018 0.003 PHEAg 200 TYR 0.014 0.002 TYRAs 94 ARG 0.007 0.001 ARGAt 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 971 time to evaluate : 4.320 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8676 (tmm) cc_final: 0.8305 (tmm) REVERT: Aa 176 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8200 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7881 (mttp) cc_final: 0.7580 (mtpt) REVERT: Aa 258 MET cc_start: 0.8853 (mmm) cc_final: 0.8502 (mmt) REVERT: Ab 54 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7224 (ttp) REVERT: Ab 136 CYS cc_start: 0.7895 (t) cc_final: 0.7496 (m) REVERT: Ab 176 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8107 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7726 (mmtt) REVERT: Ac 135 MET cc_start: 0.8885 (mmm) cc_final: 0.8464 (mmm) REVERT: Ac 178 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7014 (pt0) REVERT: Ad 56 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: Ad 108 MET cc_start: 0.8599 (tpt) cc_final: 0.8260 (tpt) REVERT: Ad 134 MET cc_start: 0.9164 (mtp) cc_final: 0.8854 (ttt) REVERT: Ad 178 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: Ad 208 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8282 (mtt-85) REVERT: Ad 265 LYS cc_start: 0.8184 (mptm) cc_final: 0.7913 (mmtt) REVERT: Ae 67 LEU cc_start: 0.8246 (tp) cc_final: 0.7987 (tp) REVERT: Ae 176 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7983 (mtmt) REVERT: Af 54 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7284 (ttp) REVERT: Af 176 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8140 (mtmt) REVERT: Af 265 LYS cc_start: 0.8237 (mptm) cc_final: 0.8023 (mptt) REVERT: Ag 58 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7991 (mmmm) REVERT: Ag 136 CYS cc_start: 0.7931 (t) cc_final: 0.7307 (m) REVERT: Ag 177 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7731 (mttm) REVERT: Ag 244 GLU cc_start: 0.8363 (tt0) cc_final: 0.8045 (tt0) REVERT: Ag 265 LYS cc_start: 0.8348 (mptm) cc_final: 0.7947 (mmtm) REVERT: Ah 54 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7060 (ptp) REVERT: Ah 107 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6938 (mm-30) REVERT: Ah 136 CYS cc_start: 0.7858 (t) cc_final: 0.7326 (m) REVERT: Ah 146 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8474 (ttmt) REVERT: Ai 56 MET cc_start: 0.8629 (mmm) cc_final: 0.8277 (mmm) REVERT: Ai 136 CYS cc_start: 0.7956 (t) cc_final: 0.7455 (m) REVERT: Ai 244 GLU cc_start: 0.8368 (tt0) cc_final: 0.8094 (tt0) REVERT: Ai 258 MET cc_start: 0.8852 (mmt) cc_final: 0.8617 (mmm) REVERT: At 265 LYS cc_start: 0.8281 (mptm) cc_final: 0.7984 (mmtt) REVERT: At 267 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4887 (mmt) REVERT: Au 54 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7479 (ptm) REVERT: Au 134 MET cc_start: 0.9115 (mtp) cc_final: 0.8898 (ttt) REVERT: Au 176 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8103 (mtmm) REVERT: Au 178 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: Av 107 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6661 (mm-30) REVERT: Av 108 MET cc_start: 0.8660 (tpt) cc_final: 0.8360 (mmp) REVERT: Aw 56 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8263 (mmm) REVERT: Aw 177 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7764 (mttm) REVERT: Aw 244 GLU cc_start: 0.8336 (tt0) cc_final: 0.8094 (tt0) REVERT: Ax 56 MET cc_start: 0.8584 (mmm) cc_final: 0.8216 (mmm) REVERT: Ax 265 LYS cc_start: 0.8326 (mptm) cc_final: 0.8080 (mmtt) REVERT: Ay 136 CYS cc_start: 0.7996 (t) cc_final: 0.7241 (m) REVERT: Ay 177 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7797 (mttp) REVERT: Ay 178 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7110 (pt0) REVERT: Az 54 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7279 (ptm) REVERT: Az 134 MET cc_start: 0.9201 (mtp) cc_final: 0.8865 (ttt) REVERT: Az 136 CYS cc_start: 0.7859 (t) cc_final: 0.7196 (m) REVERT: Az 177 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7576 (mttm) REVERT: Ba 91 ASP cc_start: 0.8812 (m-30) cc_final: 0.8481 (m-30) REVERT: Ba 176 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: Ba 177 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7722 (mttt) REVERT: Bk 176 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7949 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7939 (t0) cc_final: 0.7700 (t70) REVERT: Bl 136 CYS cc_start: 0.8078 (t) cc_final: 0.7485 (m) REVERT: Bl 177 LYS cc_start: 0.7963 (mttm) cc_final: 0.7737 (mttp) REVERT: Bl 265 LYS cc_start: 0.8236 (mmtm) cc_final: 0.8020 (mmtt) REVERT: Bm 134 MET cc_start: 0.9229 (mtp) cc_final: 0.8897 (ttt) REVERT: Bm 176 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8107 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8232 (mptm) cc_final: 0.8018 (mmtt) REVERT: Bn 56 MET cc_start: 0.8398 (mmm) cc_final: 0.7917 (mpt) REVERT: Bn 63 THR cc_start: 0.8807 (p) cc_final: 0.8470 (t) REVERT: Bn 160 MET cc_start: 0.9329 (mmm) cc_final: 0.9004 (mmm) REVERT: Bo 54 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7344 (ptp) REVERT: Bo 79 ASP cc_start: 0.8842 (m-30) cc_final: 0.8539 (m-30) REVERT: Bo 136 CYS cc_start: 0.7877 (t) cc_final: 0.7446 (m) REVERT: Bo 139 GLU cc_start: 0.7669 (tp30) cc_final: 0.7417 (tt0) REVERT: Bo 173 MET cc_start: 0.8683 (tmm) cc_final: 0.8414 (tmm) REVERT: Bo 176 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8063 (mtmm) REVERT: Bo 220 MET cc_start: 0.9445 (mtm) cc_final: 0.9045 (mtp) REVERT: Bp 56 MET cc_start: 0.8402 (mmm) cc_final: 0.7944 (mmm) REVERT: Bp 87 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8518 (tp40) REVERT: Bp 176 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8172 (mtmt) REVERT: Bq 54 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7357 (ptp) REVERT: Bq 153 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8999 (mmtm) REVERT: Bq 265 LYS cc_start: 0.8201 (mptm) cc_final: 0.7934 (mmpt) REVERT: Br 160 MET cc_start: 0.9272 (mmm) cc_final: 0.8919 (mmm) REVERT: Br 176 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: Br 177 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7853 (mttp) REVERT: Bs 56 MET cc_start: 0.8384 (mmm) cc_final: 0.7867 (mmm) REVERT: Bs 107 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6840 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7781 (t) cc_final: 0.7418 (m) REVERT: Bs 139 GLU cc_start: 0.7740 (tp30) cc_final: 0.7502 (tp30) REVERT: Bs 176 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8092 (mttt) REVERT: Bs 220 MET cc_start: 0.9474 (mtm) cc_final: 0.9210 (mtp) outliers start: 162 outliers final: 86 residues processed: 1042 average time/residue: 1.6051 time to fit residues: 2016.9558 Evaluate side-chains 1074 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 954 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ac residue 178 GLU Chi-restraints excluded: chain Ac residue 230 SER Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 56 MET Chi-restraints excluded: chain Ad residue 165 ASP Chi-restraints excluded: chain Ad residue 178 GLU Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 165 ASP Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Af residue 211 VAL Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 176 LYS Chi-restraints excluded: chain Ag residue 177 LYS Chi-restraints excluded: chain Ah residue 44 VAL Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 165 ASP Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain At residue 267 MET Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 54 MET Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Au residue 176 LYS Chi-restraints excluded: chain Au residue 178 GLU Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 56 MET Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 177 LYS Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 165 ASP Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 165 ASP Chi-restraints excluded: chain Ay residue 176 LYS Chi-restraints excluded: chain Ay residue 177 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 230 SER Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 54 MET Chi-restraints excluded: chain Az residue 88 SER Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Az residue 165 ASP Chi-restraints excluded: chain Az residue 177 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 54 MET Chi-restraints excluded: chain Bl residue 88 SER Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 176 LYS Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 230 SER Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 125 SER Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 165 ASP Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 177 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 54 MET Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 176 LYS Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 212 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 1.9990 chunk 517 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 574 optimal weight: 0.9990 chunk 477 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 301 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 98 GLN Ai 98 GLN Ba 76 GLN Bq 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 51894 Z= 0.135 Angle : 0.454 5.900 70740 Z= 0.243 Chirality : 0.038 0.152 7992 Planarity : 0.004 0.044 8748 Dihedral : 14.329 176.180 8721 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.79 % Allowed : 15.01 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.92 (0.11), residues: 5994 helix: 1.16 (0.10), residues: 2700 sheet: 0.82 (0.31), residues: 270 loop : 0.20 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAh 132 HIS 0.002 0.001 HISBk 69 PHE 0.013 0.002 PHEAv 200 TYR 0.017 0.001 TYRAs 94 ARG 0.005 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 979 time to evaluate : 4.319 Fit side-chains REVERT: Aa 136 CYS cc_start: 0.8042 (t) cc_final: 0.7410 (m) REVERT: Aa 173 MET cc_start: 0.8626 (tmm) cc_final: 0.8267 (tmm) REVERT: Aa 176 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8043 (mtmt) REVERT: Aa 258 MET cc_start: 0.8742 (mmm) cc_final: 0.8496 (mmt) REVERT: Ab 54 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7109 (ttp) REVERT: Ab 136 CYS cc_start: 0.7774 (t) cc_final: 0.7431 (m) REVERT: Ab 176 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7745 (mmtt) REVERT: Ac 135 MET cc_start: 0.8918 (mmm) cc_final: 0.8544 (mmm) REVERT: Ac 136 CYS cc_start: 0.7586 (t) cc_final: 0.7157 (m) REVERT: Ac 173 MET cc_start: 0.8662 (tmm) cc_final: 0.8316 (tmm) REVERT: Ad 56 MET cc_start: 0.8397 (mmm) cc_final: 0.8027 (mmm) REVERT: Ad 108 MET cc_start: 0.8536 (tpt) cc_final: 0.8180 (tpt) REVERT: Ad 134 MET cc_start: 0.9148 (mtp) cc_final: 0.8782 (ttt) REVERT: Ad 208 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8274 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8193 (tp) cc_final: 0.7989 (tp) REVERT: Ae 176 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7818 (mtmt) REVERT: Ae 220 MET cc_start: 0.9393 (mtm) cc_final: 0.8999 (mtp) REVERT: Af 136 CYS cc_start: 0.7984 (t) cc_final: 0.7529 (m) REVERT: Af 176 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8007 (mtmt) REVERT: Ag 136 CYS cc_start: 0.7767 (t) cc_final: 0.7206 (m) REVERT: Ag 178 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: Ag 244 GLU cc_start: 0.8293 (tt0) cc_final: 0.7985 (tt0) REVERT: Ag 265 LYS cc_start: 0.8267 (mptm) cc_final: 0.7838 (mmtm) REVERT: Ah 54 MET cc_start: 0.7520 (ptp) cc_final: 0.7039 (ptp) REVERT: Ah 107 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6796 (mm-30) REVERT: Ah 135 MET cc_start: 0.8869 (mmm) cc_final: 0.8402 (mmm) REVERT: Ah 136 CYS cc_start: 0.7748 (t) cc_final: 0.7220 (m) REVERT: Ah 146 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8457 (ttmt) REVERT: Ah 178 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: Ai 56 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7836 (mpt) REVERT: Ai 136 CYS cc_start: 0.7912 (t) cc_final: 0.7483 (m) REVERT: Ai 146 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: Ai 173 MET cc_start: 0.8730 (tmm) cc_final: 0.8527 (tmm) REVERT: Ai 244 GLU cc_start: 0.8371 (tt0) cc_final: 0.8097 (tt0) REVERT: Ai 258 MET cc_start: 0.8817 (mmt) cc_final: 0.8526 (mmm) REVERT: As 108 MET cc_start: 0.8655 (tpt) cc_final: 0.8346 (mmp) REVERT: As 136 CYS cc_start: 0.7840 (t) cc_final: 0.7426 (m) REVERT: Au 54 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7326 (ptm) REVERT: Au 134 MET cc_start: 0.9096 (mtp) cc_final: 0.8868 (ttt) REVERT: Au 135 MET cc_start: 0.8815 (mmm) cc_final: 0.8186 (mmm) REVERT: Au 136 CYS cc_start: 0.7688 (t) cc_final: 0.7408 (m) REVERT: Av 58 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7165 (pttm) REVERT: Av 72 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7127 (pt0) REVERT: Aw 56 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7941 (mmm) REVERT: Aw 244 GLU cc_start: 0.8340 (tt0) cc_final: 0.8128 (tt0) REVERT: Ax 56 MET cc_start: 0.8426 (mmm) cc_final: 0.8010 (mmm) REVERT: Ax 136 CYS cc_start: 0.7763 (t) cc_final: 0.7358 (p) REVERT: Ax 176 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7927 (mtmt) REVERT: Ay 136 CYS cc_start: 0.7940 (t) cc_final: 0.7460 (m) REVERT: Ay 177 LYS cc_start: 0.7877 (mttm) cc_final: 0.7666 (mttp) REVERT: Az 54 MET cc_start: 0.7581 (ptp) cc_final: 0.7338 (ptm) REVERT: Az 63 THR cc_start: 0.8749 (p) cc_final: 0.8530 (t) REVERT: Az 72 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7320 (pt0) REVERT: Az 108 MET cc_start: 0.8635 (tpt) cc_final: 0.8131 (tpt) REVERT: Az 134 MET cc_start: 0.9191 (mtp) cc_final: 0.8876 (ttt) REVERT: Az 136 CYS cc_start: 0.7762 (t) cc_final: 0.7168 (m) REVERT: Ba 91 ASP cc_start: 0.8801 (m-30) cc_final: 0.8476 (m-30) REVERT: Ba 176 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7959 (mtmt) REVERT: Bk 176 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7871 (t0) cc_final: 0.7666 (t70) REVERT: Bl 108 MET cc_start: 0.8590 (tpt) cc_final: 0.8229 (mmt) REVERT: Bl 134 MET cc_start: 0.9069 (ttt) cc_final: 0.8746 (ttt) REVERT: Bl 136 CYS cc_start: 0.8000 (t) cc_final: 0.7475 (m) REVERT: Bl 176 LYS cc_start: 0.8119 (mttp) cc_final: 0.7784 (mtmt) REVERT: Bl 265 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7968 (mmtt) REVERT: Bm 134 MET cc_start: 0.9185 (mtp) cc_final: 0.8861 (ttt) REVERT: Bm 176 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8113 (mptm) cc_final: 0.7795 (mmtm) REVERT: Bn 63 THR cc_start: 0.8760 (p) cc_final: 0.8466 (t) REVERT: Bn 160 MET cc_start: 0.9259 (mmm) cc_final: 0.9021 (mmm) REVERT: Bo 79 ASP cc_start: 0.8822 (m-30) cc_final: 0.8532 (m-30) REVERT: Bo 136 CYS cc_start: 0.7725 (t) cc_final: 0.7422 (m) REVERT: Bo 139 GLU cc_start: 0.7760 (tp30) cc_final: 0.7300 (tt0) REVERT: Bo 173 MET cc_start: 0.8575 (tmm) cc_final: 0.8327 (tmm) REVERT: Bo 220 MET cc_start: 0.9427 (mtm) cc_final: 0.9013 (mtp) REVERT: Bp 108 MET cc_start: 0.8574 (tpt) cc_final: 0.8117 (mmp) REVERT: Bp 176 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8037 (mtmt) REVERT: Bq 54 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7308 (ptp) REVERT: Bq 153 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8892 (mmtm) REVERT: Bq 265 LYS cc_start: 0.8164 (mptm) cc_final: 0.7909 (mmpt) REVERT: Br 72 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7391 (pt0) REVERT: Br 160 MET cc_start: 0.9268 (mmm) cc_final: 0.8983 (mmm) REVERT: Br 176 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: Br 177 LYS cc_start: 0.7862 (mttm) cc_final: 0.7658 (mttp) REVERT: Br 220 MET cc_start: 0.9446 (mtm) cc_final: 0.9165 (mtm) REVERT: Bs 54 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7324 (ttp) REVERT: Bs 56 MET cc_start: 0.8273 (mmm) cc_final: 0.7839 (mmm) REVERT: Bs 72 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7192 (pt0) REVERT: Bs 107 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6742 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7635 (t) cc_final: 0.7408 (m) REVERT: Bs 139 GLU cc_start: 0.7734 (tp30) cc_final: 0.7507 (tp30) REVERT: Bs 220 MET cc_start: 0.9447 (mtm) cc_final: 0.9125 (mtp) outliers start: 94 outliers final: 46 residues processed: 1025 average time/residue: 1.6059 time to fit residues: 1985.6955 Evaluate side-chains 1024 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 957 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 44 VAL Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 178 GLU Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 56 MET Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 54 MET Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 56 MET Chi-restraints excluded: chain Aw residue 58 LYS Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 54 MET Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 54 MET Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 231 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 419 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 483 optimal weight: 0.4980 chunk 320 optimal weight: 9.9990 chunk 572 optimal weight: 20.0000 chunk 358 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 264 optimal weight: 20.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 98 GLN Ad 98 GLN Ah 77 GLN Ai 98 GLN Ax 113 ASN Ay 229 GLN Ba 76 GLN Bl 87 GLN Bp 245 ASN Bq 98 GLN Br 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 51894 Z= 0.281 Angle : 0.538 5.385 70740 Z= 0.286 Chirality : 0.043 0.177 7992 Planarity : 0.005 0.047 8748 Dihedral : 14.576 177.376 8721 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.29 % Allowed : 14.51 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.96 (0.11), residues: 5994 helix: 1.48 (0.11), residues: 2484 sheet: 0.71 (0.31), residues: 270 loop : 0.04 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAf 132 HIS 0.005 0.001 HISAd 217 PHE 0.015 0.002 PHEAg 200 TYR 0.016 0.002 TYRAs 94 ARG 0.005 0.000 ARGAg 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 951 time to evaluate : 4.201 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8665 (tmm) cc_final: 0.8298 (tmm) REVERT: Aa 176 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7765 (mttp) cc_final: 0.7471 (mtpt) REVERT: Aa 258 MET cc_start: 0.8820 (mmm) cc_final: 0.8518 (mmt) REVERT: Ab 54 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7183 (ttp) REVERT: Ab 136 CYS cc_start: 0.7819 (t) cc_final: 0.7448 (m) REVERT: Ab 176 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7710 (mmtt) REVERT: Ac 135 MET cc_start: 0.8888 (mmm) cc_final: 0.8461 (mmm) REVERT: Ac 136 CYS cc_start: 0.7592 (t) cc_final: 0.7160 (m) REVERT: Ad 56 MET cc_start: 0.8495 (mmm) cc_final: 0.8114 (mmm) REVERT: Ad 108 MET cc_start: 0.8571 (tpt) cc_final: 0.8209 (tpt) REVERT: Ad 134 MET cc_start: 0.9161 (mtp) cc_final: 0.8827 (ttt) REVERT: Ad 208 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8235 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8184 (tp) cc_final: 0.7911 (tp) REVERT: Ae 176 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7932 (mtmt) REVERT: Af 54 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7171 (ttp) REVERT: Af 136 CYS cc_start: 0.8004 (t) cc_final: 0.7550 (m) REVERT: Af 139 GLU cc_start: 0.7805 (tp30) cc_final: 0.7405 (tt0) REVERT: Af 176 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8072 (mtmt) REVERT: Ag 58 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7964 (mtpm) REVERT: Ag 136 CYS cc_start: 0.7868 (t) cc_final: 0.7270 (m) REVERT: Ag 178 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: Ag 244 GLU cc_start: 0.8281 (tt0) cc_final: 0.7960 (tt0) REVERT: Ag 265 LYS cc_start: 0.8250 (mptm) cc_final: 0.7837 (mmtm) REVERT: Ah 54 MET cc_start: 0.7475 (ptp) cc_final: 0.6998 (ptp) REVERT: Ah 107 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6832 (mm-30) REVERT: Ah 136 CYS cc_start: 0.7848 (t) cc_final: 0.7303 (m) REVERT: Ah 146 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8482 (ttmt) REVERT: Ah 178 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6927 (pt0) REVERT: Ai 56 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.7876 (mpt) REVERT: Ai 136 CYS cc_start: 0.7923 (t) cc_final: 0.7465 (m) REVERT: Ai 146 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8115 (ttmt) REVERT: Ai 244 GLU cc_start: 0.8373 (tt0) cc_final: 0.8092 (tt0) REVERT: Ai 258 MET cc_start: 0.8859 (mmt) cc_final: 0.8602 (mmm) REVERT: At 265 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7829 (mmtt) REVERT: Au 54 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7250 (ptm) REVERT: Au 134 MET cc_start: 0.9060 (mtp) cc_final: 0.8847 (ttt) REVERT: Av 107 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6618 (mm-30) REVERT: Aw 56 MET cc_start: 0.8445 (mmm) cc_final: 0.8077 (mmm) REVERT: Aw 134 MET cc_start: 0.9192 (mtp) cc_final: 0.8975 (ttt) REVERT: Aw 244 GLU cc_start: 0.8373 (tt0) cc_final: 0.8149 (tt0) REVERT: Ax 56 MET cc_start: 0.8446 (mmm) cc_final: 0.8018 (mmm) REVERT: Ax 136 CYS cc_start: 0.7700 (t) cc_final: 0.7276 (p) REVERT: Ay 136 CYS cc_start: 0.8012 (t) cc_final: 0.7316 (m) REVERT: Ay 177 LYS cc_start: 0.7951 (mttm) cc_final: 0.7731 (mttp) REVERT: Ay 178 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: Az 54 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7338 (ptm) REVERT: Az 72 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7418 (pt0) REVERT: Az 108 MET cc_start: 0.8709 (tpt) cc_final: 0.8088 (tpt) REVERT: Az 134 MET cc_start: 0.9178 (mtp) cc_final: 0.8856 (ttt) REVERT: Az 136 CYS cc_start: 0.7782 (t) cc_final: 0.7149 (m) REVERT: Az 177 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7510 (mttm) REVERT: Ba 91 ASP cc_start: 0.8806 (m-30) cc_final: 0.8491 (m-30) REVERT: Ba 176 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8130 (mtmt) REVERT: Ba 177 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7584 (mttm) REVERT: Bk 176 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7946 (mtmt) REVERT: Bk 177 LYS cc_start: 0.7796 (mttp) cc_final: 0.7547 (mttm) REVERT: Bl 102 ASP cc_start: 0.7863 (t0) cc_final: 0.7635 (t70) REVERT: Bl 108 MET cc_start: 0.8627 (tpt) cc_final: 0.8230 (mmt) REVERT: Bl 134 MET cc_start: 0.9117 (ttt) cc_final: 0.8791 (ttt) REVERT: Bl 136 CYS cc_start: 0.7994 (t) cc_final: 0.7431 (m) REVERT: Bl 265 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7963 (mmtt) REVERT: Bm 134 MET cc_start: 0.9210 (mtp) cc_final: 0.8898 (ttt) REVERT: Bm 176 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8094 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8170 (mptm) cc_final: 0.7853 (mmtm) REVERT: Bn 63 THR cc_start: 0.8774 (p) cc_final: 0.8464 (t) REVERT: Bn 160 MET cc_start: 0.9323 (mmm) cc_final: 0.8990 (mmm) REVERT: Bn 267 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4787 (mmt) REVERT: Bo 79 ASP cc_start: 0.8837 (m-30) cc_final: 0.8543 (m-30) REVERT: Bo 136 CYS cc_start: 0.7753 (t) cc_final: 0.7424 (m) REVERT: Bo 139 GLU cc_start: 0.7663 (tp30) cc_final: 0.7302 (tt0) REVERT: Bo 173 MET cc_start: 0.8654 (tmm) cc_final: 0.8330 (tmm) REVERT: Bo 220 MET cc_start: 0.9442 (mtm) cc_final: 0.9038 (mtp) REVERT: Bo 267 MET cc_start: 0.5532 (mtm) cc_final: 0.5300 (mtt) REVERT: Bp 176 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8140 (mtmt) REVERT: Bq 54 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7337 (ptp) REVERT: Bq 153 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8971 (mmtm) REVERT: Bq 265 LYS cc_start: 0.8208 (mptm) cc_final: 0.7953 (mmpt) REVERT: Br 176 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7881 (mtmt) REVERT: Br 220 MET cc_start: 0.9457 (mtm) cc_final: 0.9183 (mtm) REVERT: Bs 56 MET cc_start: 0.8267 (mmm) cc_final: 0.7792 (mmm) REVERT: Bs 107 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6873 (mm-30) REVERT: Bs 136 CYS cc_start: 0.7685 (t) cc_final: 0.7409 (m) REVERT: Bs 139 GLU cc_start: 0.7727 (tp30) cc_final: 0.7510 (tp30) REVERT: Bs 220 MET cc_start: 0.9465 (mtm) cc_final: 0.9174 (mtp) outliers start: 120 outliers final: 74 residues processed: 1014 average time/residue: 1.6406 time to fit residues: 2000.2823 Evaluate side-chains 1037 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 939 time to evaluate : 4.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 165 ASP Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 165 ASP Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Af residue 211 VAL Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ah residue 44 VAL Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 178 GLU Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 56 MET Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 54 MET Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Au residue 165 ASP Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 165 ASP Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 165 ASP Chi-restraints excluded: chain Ay residue 176 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 54 MET Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Az residue 165 ASP Chi-restraints excluded: chain Az residue 177 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 54 MET Chi-restraints excluded: chain Bl residue 88 SER Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 153 LYS Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bn residue 267 MET Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bp residue 177 LYS Chi-restraints excluded: chain Bp residue 211 VAL Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 153 LYS Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 390 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 450 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 98 GLN Ad 98 GLN Ah 77 GLN Ai 98 GLN Ay 229 GLN Ba 76 GLN Bq 98 GLN Br 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 51894 Z= 0.356 Angle : 0.587 6.565 70740 Z= 0.312 Chirality : 0.046 0.184 7992 Planarity : 0.005 0.047 8748 Dihedral : 14.662 177.350 8721 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.54 % Allowed : 14.41 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.74 (0.10), residues: 5994 helix: 1.30 (0.11), residues: 2484 sheet: 0.55 (0.31), residues: 270 loop : -0.09 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAy 132 HIS 0.006 0.001 HISAd 217 PHE 0.016 0.003 PHEAg 200 TYR 0.018 0.002 TYRAs 94 ARG 0.006 0.001 ARGAg 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 951 time to evaluate : 4.244 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8669 (tmm) cc_final: 0.8303 (tmm) REVERT: Aa 176 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7811 (mttp) cc_final: 0.7514 (mtpt) REVERT: Aa 258 MET cc_start: 0.8820 (mmm) cc_final: 0.8511 (mmt) REVERT: Ab 54 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7160 (ttp) REVERT: Ab 136 CYS cc_start: 0.7920 (t) cc_final: 0.7516 (m) REVERT: Ab 176 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8050 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7774 (mmtt) REVERT: Ac 135 MET cc_start: 0.8901 (mmm) cc_final: 0.8464 (mmm) REVERT: Ac 136 CYS cc_start: 0.7576 (t) cc_final: 0.7318 (m) REVERT: Ac 165 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: Ad 56 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: Ad 134 MET cc_start: 0.9153 (mtp) cc_final: 0.8840 (ttt) REVERT: Ad 178 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: Ad 208 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8234 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8246 (tp) cc_final: 0.7969 (tp) REVERT: Ae 176 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7985 (mtmt) REVERT: Af 54 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7200 (ttp) REVERT: Af 176 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8097 (mtmt) REVERT: Af 265 LYS cc_start: 0.8160 (mptm) cc_final: 0.7933 (mptt) REVERT: Ag 58 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (mtpm) REVERT: Ag 136 CYS cc_start: 0.7880 (t) cc_final: 0.7270 (m) REVERT: Ag 178 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: Ag 244 GLU cc_start: 0.8287 (tt0) cc_final: 0.7970 (tt0) REVERT: Ag 265 LYS cc_start: 0.8320 (mptm) cc_final: 0.7897 (mmtm) REVERT: Ah 54 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7078 (ptp) REVERT: Ah 107 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6874 (mm-30) REVERT: Ah 136 CYS cc_start: 0.7865 (t) cc_final: 0.7322 (m) REVERT: Ah 146 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8505 (ttmt) REVERT: Ah 178 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: Ai 56 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7876 (mpt) REVERT: Ai 136 CYS cc_start: 0.7957 (t) cc_final: 0.7449 (m) REVERT: Ai 244 GLU cc_start: 0.8367 (tt0) cc_final: 0.8097 (tt0) REVERT: Ai 258 MET cc_start: 0.8849 (mmt) cc_final: 0.8598 (mmm) REVERT: At 58 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7674 (mmmm) REVERT: At 265 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7882 (mmtt) REVERT: Au 54 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7400 (ptm) REVERT: Av 107 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6656 (mm-30) REVERT: Aw 56 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8172 (mmm) REVERT: Aw 134 MET cc_start: 0.9188 (mtp) cc_final: 0.8969 (ttt) REVERT: Aw 244 GLU cc_start: 0.8340 (tt0) cc_final: 0.8119 (tt0) REVERT: Ax 56 MET cc_start: 0.8543 (mmm) cc_final: 0.8157 (mmm) REVERT: Ax 136 CYS cc_start: 0.7749 (t) cc_final: 0.7239 (p) REVERT: Ay 136 CYS cc_start: 0.7994 (t) cc_final: 0.7277 (m) REVERT: Ay 177 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7787 (mttp) REVERT: Ay 178 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: Az 54 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7370 (ptm) REVERT: Az 134 MET cc_start: 0.9191 (mtp) cc_final: 0.8856 (ttt) REVERT: Az 136 CYS cc_start: 0.7854 (t) cc_final: 0.7206 (m) REVERT: Az 177 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7525 (mttm) REVERT: Ba 91 ASP cc_start: 0.8808 (m-30) cc_final: 0.8483 (m-30) REVERT: Ba 176 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8166 (mtmt) REVERT: Bk 176 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7940 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7869 (t0) cc_final: 0.7634 (t70) REVERT: Bl 134 MET cc_start: 0.9130 (ttt) cc_final: 0.8861 (ttt) REVERT: Bl 136 CYS cc_start: 0.8047 (t) cc_final: 0.7433 (m) REVERT: Bm 134 MET cc_start: 0.9220 (mtp) cc_final: 0.8921 (ttt) REVERT: Bm 176 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8052 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8207 (mptm) cc_final: 0.7901 (mmtm) REVERT: Bn 63 THR cc_start: 0.8793 (p) cc_final: 0.8478 (t) REVERT: Bn 160 MET cc_start: 0.9325 (mmm) cc_final: 0.8993 (mmm) REVERT: Bo 79 ASP cc_start: 0.8840 (m-30) cc_final: 0.8548 (m-30) REVERT: Bo 136 CYS cc_start: 0.7758 (t) cc_final: 0.7423 (m) REVERT: Bo 139 GLU cc_start: 0.7669 (tp30) cc_final: 0.7309 (tt0) REVERT: Bo 173 MET cc_start: 0.8658 (tmm) cc_final: 0.8399 (tmm) REVERT: Bo 220 MET cc_start: 0.9444 (mtm) cc_final: 0.9042 (mtp) REVERT: Bp 56 MET cc_start: 0.8403 (mmm) cc_final: 0.7909 (mmm) REVERT: Bp 176 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8158 (mtmt) REVERT: Bq 54 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7391 (ptp) REVERT: Bq 265 LYS cc_start: 0.8204 (mptm) cc_final: 0.7944 (mmpt) REVERT: Br 176 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7955 (mtmt) REVERT: Bs 56 MET cc_start: 0.8360 (mmm) cc_final: 0.7845 (mmm) REVERT: Bs 136 CYS cc_start: 0.7688 (t) cc_final: 0.7406 (m) REVERT: Bs 139 GLU cc_start: 0.7724 (tp30) cc_final: 0.7507 (tp30) REVERT: Bs 220 MET cc_start: 0.9475 (mtm) cc_final: 0.9193 (mtp) outliers start: 133 outliers final: 86 residues processed: 1016 average time/residue: 1.6153 time to fit residues: 1975.2531 Evaluate side-chains 1055 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 942 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 165 ASP Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 165 ASP Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 56 MET Chi-restraints excluded: chain Ad residue 165 ASP Chi-restraints excluded: chain Ad residue 178 GLU Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 165 ASP Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Af residue 211 VAL Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 58 LYS Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ah residue 44 VAL Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 178 GLU Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 54 MET Chi-restraints excluded: chain Ai residue 56 MET Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 165 ASP Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 54 MET Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Au residue 165 ASP Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 56 MET Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 165 ASP Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 165 ASP Chi-restraints excluded: chain Ay residue 176 LYS Chi-restraints excluded: chain Ay residue 177 LYS Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 54 MET Chi-restraints excluded: chain Az residue 88 SER Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Az residue 165 ASP Chi-restraints excluded: chain Az residue 176 LYS Chi-restraints excluded: chain Az residue 177 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 54 MET Chi-restraints excluded: chain Bl residue 88 SER Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bl residue 260 THR Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 153 LYS Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bp residue 177 LYS Chi-restraints excluded: chain Bp residue 211 VAL Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 165 ASP Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 54 MET Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 9.9990 chunk 548 optimal weight: 0.8980 chunk 500 optimal weight: 0.0050 chunk 533 optimal weight: 4.9990 chunk 321 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 418 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 482 optimal weight: 9.9990 chunk 504 optimal weight: 5.9990 chunk 531 optimal weight: 6.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 98 GLN Ah 77 GLN Ai 98 GLN Ay 229 GLN Ba 76 GLN Bq 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 51894 Z= 0.150 Angle : 0.463 5.885 70740 Z= 0.246 Chirality : 0.039 0.152 7992 Planarity : 0.004 0.045 8748 Dihedral : 14.360 176.146 8721 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.93 % Allowed : 15.08 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.97 (0.11), residues: 5994 helix: 1.18 (0.10), residues: 2700 sheet: 0.94 (0.31), residues: 270 loop : 0.25 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAx 132 HIS 0.002 0.001 HISBk 69 PHE 0.014 0.002 PHEBp 200 TYR 0.018 0.001 TYRAs 94 ARG 0.005 0.000 ARGAg 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 984 time to evaluate : 4.222 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8621 (tmm) cc_final: 0.8270 (tmm) REVERT: Aa 176 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8031 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7659 (mttp) cc_final: 0.7338 (mtpt) REVERT: Aa 258 MET cc_start: 0.8757 (mmm) cc_final: 0.8499 (mmt) REVERT: Ab 54 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7125 (ttp) REVERT: Ab 136 CYS cc_start: 0.7748 (t) cc_final: 0.7425 (m) REVERT: Ab 176 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7728 (mmtt) REVERT: Ac 135 MET cc_start: 0.8903 (mmm) cc_final: 0.8511 (mmm) REVERT: Ac 136 CYS cc_start: 0.7597 (t) cc_final: 0.7188 (m) REVERT: Ad 56 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: Ad 134 MET cc_start: 0.9114 (mtp) cc_final: 0.8786 (ttt) REVERT: Ad 208 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8279 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8191 (tp) cc_final: 0.7989 (tp) REVERT: Ae 176 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7833 (mtmt) REVERT: Ae 220 MET cc_start: 0.9397 (mtm) cc_final: 0.9002 (mtp) REVERT: Af 136 CYS cc_start: 0.7932 (t) cc_final: 0.7533 (m) REVERT: Af 139 GLU cc_start: 0.7852 (tp30) cc_final: 0.7439 (tt0) REVERT: Af 165 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: Af 176 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7999 (mtmt) REVERT: Ag 54 MET cc_start: 0.7467 (ptm) cc_final: 0.6962 (tmm) REVERT: Ag 58 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7939 (mtpm) REVERT: Ag 136 CYS cc_start: 0.7782 (t) cc_final: 0.7212 (m) REVERT: Ag 178 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: Ag 244 GLU cc_start: 0.8211 (tt0) cc_final: 0.7911 (tt0) REVERT: Ag 265 LYS cc_start: 0.8265 (mptm) cc_final: 0.7812 (mmtm) REVERT: Ah 54 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7018 (ptp) REVERT: Ah 107 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6639 (mm-30) REVERT: Ah 135 MET cc_start: 0.8818 (mmm) cc_final: 0.8359 (mmm) REVERT: Ah 136 CYS cc_start: 0.7791 (t) cc_final: 0.7286 (m) REVERT: Ah 146 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8471 (ttmt) REVERT: Ah 178 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6885 (pt0) REVERT: Ai 56 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7831 (mpt) REVERT: Ai 136 CYS cc_start: 0.7866 (t) cc_final: 0.7429 (m) REVERT: Ai 146 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: Ai 244 GLU cc_start: 0.8354 (tt0) cc_final: 0.8068 (tt0) REVERT: Ai 258 MET cc_start: 0.8823 (mmt) cc_final: 0.8529 (mmm) REVERT: As 108 MET cc_start: 0.8653 (tpt) cc_final: 0.8345 (mmp) REVERT: As 136 CYS cc_start: 0.7845 (t) cc_final: 0.7433 (m) REVERT: At 265 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7752 (mmtt) REVERT: Av 72 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7132 (pt0) REVERT: Av 107 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6556 (mm-30) REVERT: Aw 56 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: Aw 244 GLU cc_start: 0.8333 (tt0) cc_final: 0.8133 (tt0) REVERT: Ax 56 MET cc_start: 0.8406 (mmm) cc_final: 0.7969 (mmm) REVERT: Ax 136 CYS cc_start: 0.7755 (t) cc_final: 0.7216 (m) REVERT: Ax 176 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8034 (mtmt) REVERT: Ay 136 CYS cc_start: 0.7940 (t) cc_final: 0.7473 (m) REVERT: Ay 178 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6850 (pt0) REVERT: Az 63 THR cc_start: 0.8729 (p) cc_final: 0.8499 (t) REVERT: Az 72 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7378 (pt0) REVERT: Az 134 MET cc_start: 0.9185 (mtp) cc_final: 0.8869 (ttt) REVERT: Az 136 CYS cc_start: 0.7749 (t) cc_final: 0.7141 (m) REVERT: Ba 91 ASP cc_start: 0.8803 (m-30) cc_final: 0.8495 (m-30) REVERT: Ba 176 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7948 (mtmt) REVERT: Bk 173 MET cc_start: 0.8465 (tmm) cc_final: 0.8132 (tmm) REVERT: Bk 176 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7865 (t0) cc_final: 0.7632 (t70) REVERT: Bl 108 MET cc_start: 0.8586 (tpt) cc_final: 0.8200 (mmt) REVERT: Bl 136 CYS cc_start: 0.7783 (t) cc_final: 0.7396 (m) REVERT: Bl 176 LYS cc_start: 0.8161 (mttp) cc_final: 0.7833 (mtmt) REVERT: Bm 134 MET cc_start: 0.9184 (mtp) cc_final: 0.8885 (ttt) REVERT: Bm 176 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7952 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8128 (mptm) cc_final: 0.7725 (mmtm) REVERT: Bn 63 THR cc_start: 0.8758 (p) cc_final: 0.8473 (t) REVERT: Bn 160 MET cc_start: 0.9263 (mmm) cc_final: 0.8629 (mmm) REVERT: Bo 79 ASP cc_start: 0.8811 (m-30) cc_final: 0.8527 (m-30) REVERT: Bo 136 CYS cc_start: 0.7736 (t) cc_final: 0.7492 (m) REVERT: Bo 139 GLU cc_start: 0.7705 (tp30) cc_final: 0.7304 (tt0) REVERT: Bo 173 MET cc_start: 0.8597 (tmm) cc_final: 0.8352 (tmm) REVERT: Bo 220 MET cc_start: 0.9433 (mtm) cc_final: 0.9022 (mtp) REVERT: Bp 176 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8042 (mtmt) REVERT: Bq 54 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7312 (ptp) REVERT: Bq 99 LEU cc_start: 0.8670 (tp) cc_final: 0.8431 (tp) REVERT: Br 72 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7398 (pt0) REVERT: Br 176 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7811 (mtmt) REVERT: Br 220 MET cc_start: 0.9450 (mtm) cc_final: 0.9176 (mtm) REVERT: Bs 56 MET cc_start: 0.8249 (mmm) cc_final: 0.7845 (mmm) REVERT: Bs 72 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7117 (pt0) REVERT: Bs 107 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6843 (mm-30) REVERT: Bs 139 GLU cc_start: 0.7740 (tp30) cc_final: 0.7532 (tp30) REVERT: Bs 220 MET cc_start: 0.9449 (mtm) cc_final: 0.9130 (mtp) outliers start: 101 outliers final: 63 residues processed: 1037 average time/residue: 1.6131 time to fit residues: 2014.8430 Evaluate side-chains 1040 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 955 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 56 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 165 ASP Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 178 GLU Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 56 MET Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Au residue 165 ASP Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 56 MET Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 165 ASP Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Az residue 165 ASP Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 231 ARG Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bl residue 260 THR Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 153 LYS Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 350 optimal weight: 8.9990 chunk 564 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 591 optimal weight: 3.9990 chunk 544 optimal weight: 2.9990 chunk 471 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 98 GLN Ah 77 GLN Ai 98 GLN Au 98 GLN Aw 87 GLN Ax 87 GLN Ax 113 ASN Ay 229 GLN Ba 76 GLN Bp 245 ASN Bq 98 GLN Br 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 51894 Z= 0.189 Angle : 0.493 6.454 70740 Z= 0.261 Chirality : 0.040 0.160 7992 Planarity : 0.005 0.045 8748 Dihedral : 14.473 176.999 8721 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.66 % Allowed : 15.52 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.02 (0.11), residues: 5994 helix: 1.32 (0.10), residues: 2646 sheet: 0.99 (0.31), residues: 270 loop : 0.17 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAf 132 HIS 0.003 0.001 HISAd 217 PHE 0.013 0.002 PHEBr 202 TYR 0.018 0.001 TYRAs 94 ARG 0.006 0.000 ARGAg 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 946 time to evaluate : 4.232 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8646 (tmm) cc_final: 0.8281 (tmm) REVERT: Aa 176 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8075 (mtmt) REVERT: Aa 177 LYS cc_start: 0.7669 (mttp) cc_final: 0.7374 (mtpt) REVERT: Aa 258 MET cc_start: 0.8778 (mmm) cc_final: 0.8508 (mmt) REVERT: Ab 54 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7190 (ttp) REVERT: Ab 136 CYS cc_start: 0.7711 (t) cc_final: 0.7460 (m) REVERT: Ab 176 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7883 (mtmt) REVERT: Ac 60 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7733 (mmtt) REVERT: Ac 135 MET cc_start: 0.8891 (mmm) cc_final: 0.8487 (mmm) REVERT: Ac 136 CYS cc_start: 0.7608 (t) cc_final: 0.7204 (m) REVERT: Ad 56 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: Ad 134 MET cc_start: 0.9123 (mtp) cc_final: 0.8797 (ttt) REVERT: Ad 208 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: Ae 67 LEU cc_start: 0.8188 (tp) cc_final: 0.7980 (tp) REVERT: Ae 176 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7837 (mtmt) REVERT: Af 136 CYS cc_start: 0.7912 (t) cc_final: 0.7519 (m) REVERT: Af 139 GLU cc_start: 0.7775 (tp30) cc_final: 0.7373 (tt0) REVERT: Af 176 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8031 (mtmt) REVERT: Ag 54 MET cc_start: 0.7494 (ptm) cc_final: 0.7032 (tmm) REVERT: Ag 136 CYS cc_start: 0.7790 (t) cc_final: 0.7217 (m) REVERT: Ag 178 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: Ag 244 GLU cc_start: 0.8258 (tt0) cc_final: 0.7954 (tt0) REVERT: Ag 265 LYS cc_start: 0.8263 (mptm) cc_final: 0.7825 (mmtm) REVERT: Ah 54 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7021 (ptp) REVERT: Ah 135 MET cc_start: 0.8867 (mmm) cc_final: 0.8403 (mmm) REVERT: Ah 136 CYS cc_start: 0.7704 (t) cc_final: 0.7191 (m) REVERT: Ah 146 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8514 (ttmt) REVERT: Ah 178 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: Ai 56 MET cc_start: 0.8482 (mmm) cc_final: 0.7800 (mpt) REVERT: Ai 136 CYS cc_start: 0.7871 (t) cc_final: 0.7438 (m) REVERT: Ai 146 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8084 (ttmt) REVERT: Ai 244 GLU cc_start: 0.8337 (tt0) cc_final: 0.8055 (tt0) REVERT: Ai 258 MET cc_start: 0.8859 (mmt) cc_final: 0.8504 (mmm) REVERT: As 136 CYS cc_start: 0.7785 (t) cc_final: 0.7409 (m) REVERT: Au 54 MET cc_start: 0.7560 (ptm) cc_final: 0.7035 (ptp) REVERT: Av 72 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7147 (pt0) REVERT: Av 107 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6585 (mm-30) REVERT: Aw 56 MET cc_start: 0.8451 (mmm) cc_final: 0.7955 (mmm) REVERT: Aw 244 GLU cc_start: 0.8362 (tt0) cc_final: 0.8135 (tt0) REVERT: Ax 56 MET cc_start: 0.8413 (mmm) cc_final: 0.8085 (mmm) REVERT: Ax 136 CYS cc_start: 0.7767 (t) cc_final: 0.7234 (m) REVERT: Ax 176 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8088 (mtmt) REVERT: Ay 136 CYS cc_start: 0.7937 (t) cc_final: 0.7471 (m) REVERT: Ay 178 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6881 (pt0) REVERT: Az 63 THR cc_start: 0.8731 (p) cc_final: 0.8496 (t) REVERT: Az 72 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7386 (pt0) REVERT: Az 134 MET cc_start: 0.9176 (mtp) cc_final: 0.8877 (ttt) REVERT: Az 136 CYS cc_start: 0.7750 (t) cc_final: 0.7148 (m) REVERT: Ba 91 ASP cc_start: 0.8810 (m-30) cc_final: 0.8491 (m-30) REVERT: Ba 176 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8067 (mtmt) REVERT: Ba 177 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7554 (mttm) REVERT: Bk 176 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7927 (mtmt) REVERT: Bl 102 ASP cc_start: 0.7884 (t0) cc_final: 0.7668 (t70) REVERT: Bl 108 MET cc_start: 0.8573 (tpt) cc_final: 0.8223 (mmt) REVERT: Bl 136 CYS cc_start: 0.7764 (t) cc_final: 0.7357 (m) REVERT: Bl 176 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7920 (mtmt) REVERT: Bm 134 MET cc_start: 0.9185 (mtp) cc_final: 0.8874 (ttt) REVERT: Bm 176 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7982 (mtmt) REVERT: Bm 265 LYS cc_start: 0.8119 (mptm) cc_final: 0.7716 (mmtm) REVERT: Bn 63 THR cc_start: 0.8765 (p) cc_final: 0.8475 (t) REVERT: Bn 160 MET cc_start: 0.9291 (mmm) cc_final: 0.8685 (mmm) REVERT: Bo 79 ASP cc_start: 0.8825 (m-30) cc_final: 0.8525 (m-30) REVERT: Bo 136 CYS cc_start: 0.7708 (t) cc_final: 0.7469 (m) REVERT: Bo 139 GLU cc_start: 0.7655 (tp30) cc_final: 0.7298 (tt0) REVERT: Bo 173 MET cc_start: 0.8637 (tmm) cc_final: 0.8356 (tmm) REVERT: Bo 220 MET cc_start: 0.9435 (mtm) cc_final: 0.9035 (mtp) REVERT: Bp 176 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8118 (mtmt) REVERT: Bq 54 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7303 (ptp) REVERT: Br 176 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7810 (mtmt) REVERT: Br 220 MET cc_start: 0.9460 (mtm) cc_final: 0.9187 (mtm) REVERT: Bs 56 MET cc_start: 0.8349 (mmm) cc_final: 0.7944 (mmm) REVERT: Bs 72 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7112 (pt0) REVERT: Bs 107 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6866 (mm-30) REVERT: Bs 139 GLU cc_start: 0.7737 (tp30) cc_final: 0.7534 (tp30) REVERT: Bs 220 MET cc_start: 0.9459 (mtm) cc_final: 0.9161 (mtp) outliers start: 87 outliers final: 63 residues processed: 999 average time/residue: 1.6409 time to fit residues: 1974.3790 Evaluate side-chains 1024 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 940 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 VAL Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 176 LYS Chi-restraints excluded: chain Ab residue 44 VAL Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 176 LYS Chi-restraints excluded: chain Ab residue 211 VAL Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 146 LYS Chi-restraints excluded: chain Ac residue 176 LYS Chi-restraints excluded: chain Ad residue 44 VAL Chi-restraints excluded: chain Ad residue 56 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 44 VAL Chi-restraints excluded: chain Ae residue 176 LYS Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Ag residue 44 VAL Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 146 LYS Chi-restraints excluded: chain Ah residue 165 ASP Chi-restraints excluded: chain Ah residue 178 GLU Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 146 LYS Chi-restraints excluded: chain Ai residue 165 ASP Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain At residue 44 VAL Chi-restraints excluded: chain At residue 165 ASP Chi-restraints excluded: chain At residue 211 VAL Chi-restraints excluded: chain Au residue 44 VAL Chi-restraints excluded: chain Au residue 153 LYS Chi-restraints excluded: chain Au residue 165 ASP Chi-restraints excluded: chain Av residue 44 VAL Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 211 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 172 GLU Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ax residue 44 VAL Chi-restraints excluded: chain Ax residue 176 LYS Chi-restraints excluded: chain Ax residue 211 VAL Chi-restraints excluded: chain Ay residue 44 VAL Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 178 GLU Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Az residue 44 VAL Chi-restraints excluded: chain Az residue 153 LYS Chi-restraints excluded: chain Ba residue 44 VAL Chi-restraints excluded: chain Ba residue 165 ASP Chi-restraints excluded: chain Ba residue 176 LYS Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bk residue 44 VAL Chi-restraints excluded: chain Bk residue 176 LYS Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bl residue 44 VAL Chi-restraints excluded: chain Bl residue 176 LYS Chi-restraints excluded: chain Bl residue 211 VAL Chi-restraints excluded: chain Bl residue 260 THR Chi-restraints excluded: chain Bm residue 44 VAL Chi-restraints excluded: chain Bm residue 153 LYS Chi-restraints excluded: chain Bm residue 176 LYS Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bn residue 44 VAL Chi-restraints excluded: chain Bn residue 211 VAL Chi-restraints excluded: chain Bo residue 44 VAL Chi-restraints excluded: chain Bp residue 44 VAL Chi-restraints excluded: chain Bp residue 54 MET Chi-restraints excluded: chain Bp residue 176 LYS Chi-restraints excluded: chain Bq residue 44 VAL Chi-restraints excluded: chain Bq residue 54 MET Chi-restraints excluded: chain Bq residue 165 ASP Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Br residue 44 VAL Chi-restraints excluded: chain Br residue 153 LYS Chi-restraints excluded: chain Br residue 176 LYS Chi-restraints excluded: chain Br residue 211 VAL Chi-restraints excluded: chain Bs residue 44 VAL Chi-restraints excluded: chain Bs residue 108 MET Chi-restraints excluded: chain Bs residue 197 ARG Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 212 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 2.9990 chunk 501 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 434 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 471 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 484 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 98 GLN Ah 77 GLN Ai 98 GLN Ba 76 GLN Bq 98 GLN Br 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103063 restraints weight = 47158.261| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.55 r_work: 0.2981 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 51894 Z= 0.199 Angle : 0.498 6.686 70740 Z= 0.264 Chirality : 0.041 0.163 7992 Planarity : 0.005 0.045 8748 Dihedral : 14.472 176.800 8721 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.99 % Allowed : 15.18 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.01 (0.11), residues: 5994 helix: 1.31 (0.10), residues: 2646 sheet: 1.01 (0.31), residues: 270 loop : 0.17 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAf 132 HIS 0.003 0.001 HISAd 217 PHE 0.014 0.002 PHEBr 202 TYR 0.018 0.001 TYRAs 94 ARG 0.007 0.000 ARGAg 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25625.29 seconds wall clock time: 435 minutes 19.20 seconds (26119.20 seconds total)