Starting phenix.real_space_refine on Thu Jan 16 05:50:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.map" model { file = "/net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opc_17048/01_2025/8opc_17048.cif" } resolution = 2.99 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= 0.022 sd= 0.275 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 140 5.49 5 S 392 5.16 5 C 32760 2.51 5 N 9100 2.21 5 O 10696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 53088 Number of models: 1 Model: "" Number of chains: 2 Chain: "Be" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Cd" 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: Bg, Ba, Bc, Bm, Bo, Bi, Bk, Bu, Bw, Bq, Bs, By, Aa, Cc, Ac, Ae, Ag, Ai, Ak, Am, Ao, Aq, As, Au, Aw, Ay, Ca, Bd, Bf, Bb, Bl, Bn, Bh, Bj, Bt, Bv, Bp, Br, Bx, Bz, Ab, Ad, Af, Ah, Aj, Al, An, Ap, Ar, At, Av, Ax, Az, Cb Time building chain proxies: 8.73, per 1000 atoms: 0.16 Number of scatterers: 53088 At special positions: 0 Unit cell: (145.35, 144.4, 234.65, 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 392 16.00 P 140 15.00 O 10696 8.00 N 9100 7.00 C 32760 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: 10.31 Conformation dependent library (CDL) restraints added in 5.1 seconds 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11984 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 56 sheets defined 46.0% alpha, 5.3% beta 0 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 12.62 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAa 72 " --> pdb=" O GLUAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 76 through 81 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 226 Processing helix chain 'Ac' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAc 72 " --> pdb=" O GLUAc 68 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 76 through 81 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 226 Processing helix chain 'Ae' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 226 Processing helix chain 'Ag' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 226 Processing helix chain 'Ai' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAi 72 " --> pdb=" O GLUAi 68 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 76 through 81 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 226 Processing helix chain 'Ak' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAk 72 " --> pdb=" O GLUAk 68 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 76 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAk 151 " --> pdb=" O PROAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 175 Processing helix chain 'Ak' and resid 182 through 188 Processing helix chain 'Ak' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 226 Processing helix chain 'Am' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 76 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAm 151 " --> pdb=" O PROAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 175 Processing helix chain 'Am' and resid 182 through 188 Processing helix chain 'Am' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 226 Processing helix chain 'Ao' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 76 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 removed outlier: 3.572A pdb=" N ASNAo 151 " --> pdb=" O PROAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 175 Processing helix chain 'Ao' and resid 182 through 188 Processing helix chain 'Ao' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 226 Processing helix chain 'Aq' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAq 72 " --> pdb=" O GLUAq 68 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 76 through 81 Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAq 151 " --> pdb=" O PROAq 147 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 175 Processing helix chain 'Aq' and resid 182 through 188 Processing helix chain 'Aq' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAq 197 " --> pdb=" O SERAq 194 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 226 Processing helix chain 'As' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAs 72 " --> pdb=" O GLUAs 68 " (cutoff:3.500A) Processing helix chain 'As' and resid 76 through 81 Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 226 Processing helix chain 'Au' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAu 72 " --> pdb=" O GLUAu 68 " (cutoff:3.500A) Processing helix chain 'Au' and resid 76 through 81 Processing helix chain 'Au' and resid 86 through 102 Processing helix chain 'Au' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 226 Processing helix chain 'Aw' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAw 72 " --> pdb=" O GLUAw 68 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 76 through 81 Processing helix chain 'Aw' and resid 86 through 102 Processing helix chain 'Aw' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 removed outlier: 3.574A 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 175 Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 226 Processing helix chain 'Ay' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAy 72 " --> pdb=" O GLUAy 68 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 76 through 81 Processing helix chain 'Ay' and resid 86 through 102 Processing helix chain 'Ay' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAy 111 " --> pdb=" O GLUAy 107 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAy 197 " --> pdb=" O SERAy 194 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 210 through 226 Processing helix chain 'Ba' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBa 72 " --> pdb=" O GLUBa 68 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 76 through 81 Processing helix chain 'Ba' and resid 86 through 102 Processing helix chain 'Ba' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBa 111 " --> pdb=" O GLUBa 107 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBa 197 " --> pdb=" O SERBa 194 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 210 through 226 Processing helix chain 'Bc' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBc 72 " --> pdb=" O GLUBc 68 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 76 through 81 Processing helix chain 'Bc' and resid 86 through 102 Processing helix chain 'Bc' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBc 111 " --> pdb=" O GLUBc 107 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBc 151 " --> pdb=" O PROBc 147 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 155 through 161 Processing helix chain 'Bc' and resid 163 through 175 Processing helix chain 'Bc' and resid 182 through 188 Processing helix chain 'Bc' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBc 197 " --> pdb=" O SERBc 194 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 210 through 226 Processing helix chain 'Be' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBe 72 " --> pdb=" O GLUBe 68 " (cutoff:3.500A) Processing helix chain 'Be' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEBe 80 " --> pdb=" O GLNBe 76 " (cutoff:3.500A) Processing helix chain 'Be' and resid 86 through 102 Processing helix chain 'Be' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBe 111 " --> pdb=" O GLUBe 107 " (cutoff:3.500A) Processing helix chain 'Be' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBe 151 " --> pdb=" O PROBe 147 " (cutoff:3.500A) Processing helix chain 'Be' and resid 155 through 161 Processing helix chain 'Be' and resid 163 through 175 Processing helix chain 'Be' and resid 182 through 188 Processing helix chain 'Be' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBe 197 " --> pdb=" O SERBe 194 " (cutoff:3.500A) Processing helix chain 'Be' and resid 210 through 226 Processing helix chain 'Bg' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBg 72 " --> pdb=" O GLUBg 68 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 76 through 81 Processing helix chain 'Bg' and resid 86 through 102 Processing helix chain 'Bg' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBg 111 " --> pdb=" O GLUBg 107 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBg 151 " --> pdb=" O PROBg 147 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 155 through 161 Processing helix chain 'Bg' and resid 163 through 175 Processing helix chain 'Bg' and resid 182 through 188 Processing helix chain 'Bg' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBg 197 " --> pdb=" O SERBg 194 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 210 through 226 Processing helix chain 'Bi' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBi 72 " --> pdb=" O GLUBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 76 through 81 Processing helix chain 'Bi' and resid 86 through 102 Processing helix chain 'Bi' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBi 111 " --> pdb=" O GLUBi 107 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBi 151 " --> pdb=" O PROBi 147 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 155 through 161 Processing helix chain 'Bi' and resid 163 through 175 Processing helix chain 'Bi' and resid 182 through 188 Processing helix chain 'Bi' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBi 197 " --> pdb=" O SERBi 194 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 210 through 226 Processing helix chain 'Bk' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBk 72 " --> pdb=" O GLUBk 68 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 76 through 81 Processing helix chain 'Bk' and resid 86 through 102 Processing helix chain 'Bk' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBk 111 " --> pdb=" O GLUBk 107 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Bk' and resid 182 through 188 Processing helix chain 'Bk' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBk 197 " --> pdb=" O SERBk 194 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 210 through 226 Processing helix chain 'Bm' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBm 72 " --> pdb=" O GLUBm 68 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 76 through 81 Processing helix chain 'Bm' and resid 86 through 102 Processing helix chain 'Bm' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBm 111 " --> pdb=" O GLUBm 107 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Bm' and resid 182 through 188 Processing helix chain 'Bm' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBm 197 " --> pdb=" O SERBm 194 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 210 through 226 Processing helix chain 'Bo' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBo 72 " --> pdb=" O GLUBo 68 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 76 through 81 Processing helix chain 'Bo' and resid 86 through 102 Processing helix chain 'Bo' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBo 111 " --> pdb=" O GLUBo 107 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Bo' and resid 182 through 188 Processing helix chain 'Bo' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBo 197 " --> pdb=" O SERBo 194 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 210 through 226 Processing helix chain 'Bq' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBq 72 " --> pdb=" O GLUBq 68 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 76 through 81 removed outlier: 3.501A pdb=" N ILEBq 80 " --> pdb=" O GLNBq 76 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 86 through 102 Processing helix chain 'Bq' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBq 111 " --> pdb=" O GLUBq 107 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Bq' and resid 182 through 188 Processing helix chain 'Bq' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBq 197 " --> pdb=" O SERBq 194 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 210 through 226 Processing helix chain 'Bs' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBs 72 " --> pdb=" O GLUBs 68 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 76 through 81 Processing helix chain 'Bs' and resid 86 through 102 Processing helix chain 'Bs' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBs 111 " --> pdb=" O GLUBs 107 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 145 through 151 removed outlier: 3.573A 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 175 Processing helix chain 'Bs' and resid 182 through 188 Processing helix chain 'Bs' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBs 197 " --> pdb=" O SERBs 194 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 210 through 226 Processing helix chain 'Bu' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBu 72 " --> pdb=" O GLUBu 68 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEBu 80 " --> pdb=" O GLNBu 76 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 86 through 102 Processing helix chain 'Bu' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBu 111 " --> pdb=" O GLUBu 107 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBu 151 " --> pdb=" O PROBu 147 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 155 through 161 Processing helix chain 'Bu' and resid 163 through 175 Processing helix chain 'Bu' and resid 182 through 188 Processing helix chain 'Bu' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBu 197 " --> pdb=" O SERBu 194 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 210 through 226 Processing helix chain 'Bw' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBw 72 " --> pdb=" O GLUBw 68 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 76 through 81 Processing helix chain 'Bw' and resid 86 through 102 Processing helix chain 'Bw' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBw 111 " --> pdb=" O GLUBw 107 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBw 151 " --> pdb=" O PROBw 147 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 155 through 161 Processing helix chain 'Bw' and resid 163 through 175 Processing helix chain 'Bw' and resid 182 through 188 Processing helix chain 'Bw' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBw 197 " --> pdb=" O SERBw 194 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 210 through 226 Processing helix chain 'By' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBy 72 " --> pdb=" O GLUBy 68 " (cutoff:3.500A) Processing helix chain 'By' and resid 76 through 81 Processing helix chain 'By' and resid 86 through 102 Processing helix chain 'By' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBy 111 " --> pdb=" O GLUBy 107 " (cutoff:3.500A) Processing helix chain 'By' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBy 151 " --> pdb=" O PROBy 147 " (cutoff:3.500A) Processing helix chain 'By' and resid 155 through 161 Processing helix chain 'By' and resid 163 through 175 Processing helix chain 'By' and resid 182 through 188 Processing helix chain 'By' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBy 197 " --> pdb=" O SERBy 194 " (cutoff:3.500A) Processing helix chain 'By' and resid 210 through 226 Processing helix chain 'Ca' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUCa 72 " --> pdb=" O GLUCa 68 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 76 through 81 Processing helix chain 'Ca' and resid 86 through 102 Processing helix chain 'Ca' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALCa 111 " --> pdb=" O GLUCa 107 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNCa 151 " --> pdb=" O PROCa 147 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 155 through 161 Processing helix chain 'Ca' and resid 163 through 175 Processing helix chain 'Ca' and resid 182 through 188 Processing helix chain 'Ca' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGCa 197 " --> pdb=" O SERCa 194 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 210 through 226 Processing helix chain 'Cc' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUCc 72 " --> pdb=" O GLUCc 68 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 76 through 81 Processing helix chain 'Cc' and resid 86 through 102 Processing helix chain 'Cc' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALCc 111 " --> pdb=" O GLUCc 107 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNCc 151 " --> pdb=" O PROCc 147 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 155 through 161 Processing helix chain 'Cc' and resid 163 through 175 Processing helix chain 'Cc' and resid 182 through 188 Processing helix chain 'Cc' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGCc 197 " --> pdb=" O SERCc 194 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 210 through 226 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ac' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ae' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ag' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ai' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Ak' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Am' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ao' and resid 131 through 136 Processing sheet with id=AB8, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Aq' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'As' and resid 131 through 136 Processing sheet with id=AC3, first strand: chain 'Au' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Au' and resid 131 through 136 Processing sheet with id=AC5, first strand: chain 'Aw' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Aw' and resid 131 through 136 Processing sheet with id=AC7, first strand: chain 'Ay' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Ay' and resid 131 through 136 Processing sheet with id=AC9, first strand: chain 'Ba' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'Ba' and resid 131 through 136 Processing sheet with id=AD2, first strand: chain 'Bc' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Bc' and resid 131 through 136 Processing sheet with id=AD4, first strand: chain 'Be' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Be' and resid 131 through 136 Processing sheet with id=AD6, first strand: chain 'Bg' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Bg' and resid 131 through 136 Processing sheet with id=AD8, first strand: chain 'Bi' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Bi' and resid 131 through 136 Processing sheet with id=AE1, first strand: chain 'Bk' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'Bk' and resid 131 through 136 Processing sheet with id=AE3, first strand: chain 'Bm' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'Bm' and resid 131 through 136 Processing sheet with id=AE5, first strand: chain 'Bo' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'Bo' and resid 131 through 136 Processing sheet with id=AE7, first strand: chain 'Bq' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'Bq' and resid 131 through 136 Processing sheet with id=AE9, first strand: chain 'Bs' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'Bs' and resid 131 through 136 Processing sheet with id=AF2, first strand: chain 'Bu' and resid 58 through 59 Processing sheet with id=AF3, first strand: chain 'Bu' and resid 131 through 136 Processing sheet with id=AF4, first strand: chain 'Bw' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'Bw' and resid 131 through 136 Processing sheet with id=AF6, first strand: chain 'By' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'By' and resid 131 through 136 Processing sheet with id=AF8, first strand: chain 'Ca' and resid 58 through 59 Processing sheet with id=AF9, first strand: chain 'Ca' and resid 131 through 136 Processing sheet with id=AG1, first strand: chain 'Cc' and resid 58 through 59 Processing sheet with id=AG2, first strand: chain 'Cc' and resid 131 through 136 1926 hydrogen bonds defined for protein. 5442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 15.87 Time building geometry restraints manager: 12.22 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: 11431 1.33 - 1.45: 12107 1.45 - 1.57: 29830 1.57 - 1.69: 252 1.69 - 1.81: 756 Bond restraints: 54376 Sorted by residual: bond pdb=" C ASNAi 113 " pdb=" N GLYAi 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.54e+01 bond pdb=" C ASNBa 113 " pdb=" N GLYBa 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNCc 113 " pdb=" N GLYCc 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNBs 113 " pdb=" N GLYBs 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNBm 113 " pdb=" N GLYBm 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.52e+01 ... (remaining 54371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 71354 1.72 - 3.45: 2146 3.45 - 5.17: 420 5.17 - 6.90: 140 6.90 - 8.62: 84 Bond angle restraints: 74144 Sorted by residual: angle pdb=" N ASNAo 122 " pdb=" CA ASNAo 122 " pdb=" C ASNAo 122 " ideal model delta sigma weight residual 112.97 119.77 -6.80 1.06e+00 8.90e-01 4.11e+01 angle pdb=" N ASNAg 122 " pdb=" CA ASNAg 122 " pdb=" C ASNAg 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.11e+01 angle pdb=" N ASNAy 122 " pdb=" CA ASNAy 122 " pdb=" C ASNAy 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" N ASNAe 122 " pdb=" CA ASNAe 122 " pdb=" C ASNAe 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" N ASNBu 122 " pdb=" CA ASNBu 122 " pdb=" C ASNBu 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 ... (remaining 74139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 27687 15.57 - 31.14: 4009 31.14 - 46.70: 1288 46.70 - 62.27: 588 62.27 - 77.84: 84 Dihedral angle restraints: 33656 sinusoidal: 15120 harmonic: 18536 Sorted by residual: dihedral pdb=" CA LEUCa 261 " pdb=" C LEUCa 261 " pdb=" N LEUCa 262 " pdb=" CA LEUCa 262 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEUBi 261 " pdb=" C LEUBi 261 " pdb=" N LEUBi 262 " pdb=" CA LEUBi 262 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEUAu 261 " pdb=" C LEUAu 261 " pdb=" N LEUAu 262 " pdb=" CA LEUAu 262 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 33653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5077 0.030 - 0.061: 2415 0.061 - 0.091: 507 0.091 - 0.122: 252 0.122 - 0.152: 121 Chirality restraints: 8372 Sorted by residual: chirality pdb=" CA GLUAs 107 " pdb=" N GLUAs 107 " pdb=" C GLUAs 107 " pdb=" CB GLUAs 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLUBu 107 " pdb=" N GLUBu 107 " pdb=" C GLUBu 107 " pdb=" CB GLUBu 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLUCc 107 " pdb=" N GLUCc 107 " pdb=" C GLUCc 107 " pdb=" CB GLUCc 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 8369 not shown) Planarity restraints: 9184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METBc 54 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C METBc 54 " 0.033 2.00e-02 2.50e+03 pdb=" O METBc 54 " -0.012 2.00e-02 2.50e+03 pdb=" N ARGBc 55 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METBi 54 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C METBi 54 " -0.033 2.00e-02 2.50e+03 pdb=" O METBi 54 " 0.012 2.00e-02 2.50e+03 pdb=" N ARGBi 55 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAg 54 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C METAg 54 " -0.033 2.00e-02 2.50e+03 pdb=" O METAg 54 " 0.012 2.00e-02 2.50e+03 pdb=" N ARGAg 55 " 0.011 2.00e-02 2.50e+03 ... (remaining 9181 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5307 2.74 - 3.28: 50671 3.28 - 3.82: 90924 3.82 - 4.36: 109658 4.36 - 4.90: 185749 Nonbonded interactions: 442309 Sorted by model distance: nonbonded pdb=" OH TYRAa 184 " pdb=" O2 UAb 4 " model vdw 2.198 3.040 nonbonded pdb=" OH TYRBk 184 " pdb=" O2 UBl 4 " model vdw 2.198 3.040 nonbonded pdb=" OH TYRBc 184 " pdb=" O2 UBd 4 " model vdw 2.198 3.040 nonbonded pdb=" OH TYRAo 184 " pdb=" O2 UAp 4 " model vdw 2.198 3.040 nonbonded pdb=" OH TYRAc 184 " pdb=" O2 UAd 4 " model vdw 2.198 3.040 ... (remaining 442304 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: 0.35 Found NCS groups: ncs_group { reference = chain 'Be' selection = chain 'Bg' selection = chain 'Ba' selection = chain 'Bc' selection = chain 'Bm' selection = chain 'Bo' selection = chain 'Bi' selection = chain 'Bk' selection = chain 'Bu' selection = chain 'Bw' selection = chain 'Bq' selection = chain 'Bs' selection = chain 'By' selection = chain 'Aa' selection = chain 'Cc' selection = chain 'Ac' selection = chain 'Ae' selection = chain 'Ag' selection = chain 'Ai' selection = chain 'Ak' selection = chain 'Am' selection = chain 'Ao' selection = chain 'Aq' selection = chain 'As' selection = chain 'Au' selection = chain 'Aw' selection = chain 'Ay' selection = chain 'Ca' } ncs_group { reference = chain 'Cd' selection = chain 'Bd' selection = chain 'Bf' selection = chain 'Bb' selection = chain 'Bl' selection = chain 'Bn' selection = chain 'Bh' selection = chain 'Bj' selection = chain 'Bt' selection = chain 'Bv' selection = chain 'Bp' selection = chain 'Br' selection = chain 'Bx' selection = chain 'Bz' selection = chain 'Ab' selection = chain 'Ad' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Aj' selection = chain 'Al' selection = chain 'An' selection = chain 'Ap' selection = chain 'Ar' selection = chain 'At' selection = chain 'Av' selection = chain 'Ax' selection = chain 'Az' 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: 1.050 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: 0.050 Extract box with map and model: 2.000 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 80.140 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.500 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:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.005 0.061 54376 Z= 0.320 Angle : 0.769 8.624 74144 Z= 0.482 Chirality : 0.041 0.152 8372 Planarity : 0.005 0.038 9184 Dihedral : 17.781 77.838 21672 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.08 % Allowed : 28.01 % Favored : 70.92 % 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: -0.67 (0.10), residues: 6272 helix: 0.50 (0.11), residues: 2660 sheet: 1.04 (0.25), residues: 280 loop : -1.40 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPBg 132 HIS 0.002 0.001 HISBu 217 PHE 0.021 0.003 PHEBq 202 TYR 0.008 0.001 TYRAi 184 ARG 0.002 0.000 ARGBq 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1326 time to evaluate : 4.450 Fit side-chains REVERT: Aa 231 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8128 (mmm160) REVERT: Ac 134 MET cc_start: 0.8692 (ttt) cc_final: 0.8389 (ttt) REVERT: Ac 258 MET cc_start: 0.7282 (mtt) cc_final: 0.6985 (mtt) REVERT: Ae 160 MET cc_start: 0.9521 (mmm) cc_final: 0.9283 (mmm) REVERT: Ae 267 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4502 (pp-130) REVERT: Ag 53 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7776 (mtmt) REVERT: Ag 77 GLN cc_start: 0.8575 (mt0) cc_final: 0.8335 (mt0) REVERT: Ag 134 MET cc_start: 0.8774 (ttt) cc_final: 0.8494 (ttt) REVERT: Ag 245 ASN cc_start: 0.9161 (t0) cc_final: 0.8879 (t0) REVERT: Ai 53 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7730 (mtmt) REVERT: Ai 245 ASN cc_start: 0.9144 (t0) cc_final: 0.8922 (t0) REVERT: Ai 267 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4583 (tmm) REVERT: Ak 134 MET cc_start: 0.8714 (ttt) cc_final: 0.8423 (ttt) REVERT: Ak 153 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8604 (mptt) REVERT: Ao 53 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7931 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8633 (m-30) cc_final: 0.8412 (m-30) REVERT: Ao 98 GLN cc_start: 0.8742 (tt0) cc_final: 0.8518 (tt0) REVERT: Ao 134 MET cc_start: 0.8719 (ttt) cc_final: 0.8378 (ttt) REVERT: Ao 153 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8664 (mptt) REVERT: Aq 53 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8053 (mttm) REVERT: Aq 91 ASP cc_start: 0.8695 (m-30) cc_final: 0.8360 (m-30) REVERT: Aq 160 MET cc_start: 0.9488 (mmm) cc_final: 0.9275 (mmm) REVERT: As 53 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8045 (mttp) REVERT: As 108 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: As 267 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4806 (tmm) REVERT: Au 77 GLN cc_start: 0.8518 (mt0) cc_final: 0.8297 (mt0) REVERT: Aw 134 MET cc_start: 0.8696 (ttt) cc_final: 0.8291 (ttm) REVERT: Aw 153 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8639 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8251 (mmt180) REVERT: Aw 267 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.4492 (tmm) REVERT: Ay 160 MET cc_start: 0.9508 (mmm) cc_final: 0.9270 (mmp) REVERT: Ba 113 ASN cc_start: 0.9019 (m-40) cc_final: 0.8763 (m-40) REVERT: Ba 153 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8702 (mptt) REVERT: Ba 160 MET cc_start: 0.9495 (mmm) cc_final: 0.9248 (mmm) REVERT: Ba 212 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8191 (ttp80) REVERT: Ba 267 MET cc_start: 0.4895 (OUTLIER) cc_final: 0.4441 (pp-130) REVERT: Bc 53 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7926 (mttm) REVERT: Bc 267 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.4421 (pp-130) REVERT: Be 153 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8579 (mptt) REVERT: Be 267 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4292 (tmm) REVERT: Bg 113 ASN cc_start: 0.9122 (m-40) cc_final: 0.8798 (m-40) REVERT: Bg 153 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8416 (mptt) REVERT: Bg 231 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8249 (mmt180) REVERT: Bi 116 MET cc_start: 0.9225 (ttp) cc_final: 0.9024 (ttt) REVERT: Bi 153 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8488 (mptt) REVERT: Bk 134 MET cc_start: 0.8725 (ttt) cc_final: 0.8494 (ttt) REVERT: Bk 153 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8483 (mttt) REVERT: Bm 53 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8005 (mttp) REVERT: Bm 153 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8390 (mptt) REVERT: Bm 258 MET cc_start: 0.7170 (mtt) cc_final: 0.6953 (mtt) REVERT: Bo 54 MET cc_start: 0.8857 (ptm) cc_final: 0.8515 (ptm) REVERT: Bo 153 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8364 (mttt) REVERT: Bo 267 MET cc_start: 0.5085 (OUTLIER) cc_final: 0.4785 (tmm) REVERT: Bq 134 MET cc_start: 0.8734 (ttt) cc_final: 0.8370 (ttt) REVERT: Bq 153 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8468 (mptt) REVERT: Bq 267 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4542 (tmm) REVERT: Bs 98 GLN cc_start: 0.8733 (tt0) cc_final: 0.8521 (tt0) REVERT: Bs 153 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8263 (mttt) REVERT: Bu 53 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8086 (mttm) REVERT: Bu 153 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8214 (mttt) REVERT: Bu 267 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4317 (tmm) REVERT: Bw 53 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7840 (mtmt) REVERT: Bw 91 ASP cc_start: 0.8687 (m-30) cc_final: 0.8425 (m-30) REVERT: Bw 134 MET cc_start: 0.8646 (ttt) cc_final: 0.8379 (ttt) REVERT: Bw 160 MET cc_start: 0.9494 (mmm) cc_final: 0.9279 (mmm) REVERT: Bw 212 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8144 (ttt-90) REVERT: By 53 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7888 (mtmt) REVERT: By 153 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8693 (mptt) REVERT: Ca 53 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7807 (mtmt) REVERT: Ca 134 MET cc_start: 0.8683 (ttt) cc_final: 0.8400 (ttm) REVERT: Ca 267 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4425 (tmm) REVERT: Cc 53 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7881 (mtmt) REVERT: Cc 134 MET cc_start: 0.8658 (ttt) cc_final: 0.8352 (ttt) REVERT: Cc 153 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8704 (mptt) outliers start: 59 outliers final: 10 residues processed: 1326 average time/residue: 1.4426 time to fit residues: 2359.7741 Evaluate side-chains 988 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 966 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 267 MET Chi-restraints excluded: chain Ae residue 267 MET Chi-restraints excluded: chain Ag residue 267 MET Chi-restraints excluded: chain Ai residue 267 MET Chi-restraints excluded: chain Ak residue 267 MET Chi-restraints excluded: chain Am residue 267 MET Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 267 MET Chi-restraints excluded: chain As residue 108 MET Chi-restraints excluded: chain As residue 267 MET Chi-restraints excluded: chain Aw residue 267 MET Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 267 MET Chi-restraints excluded: chain Bc residue 267 MET Chi-restraints excluded: chain Be residue 267 MET Chi-restraints excluded: chain Bo residue 267 MET Chi-restraints excluded: chain Bq residue 267 MET Chi-restraints excluded: chain Bs residue 267 MET Chi-restraints excluded: chain Bu residue 267 MET Chi-restraints excluded: chain Bw residue 267 MET Chi-restraints excluded: chain By residue 267 MET Chi-restraints excluded: chain Ca residue 267 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 3.9990 chunk 466 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 482 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 chunk 359 optimal weight: 2.9990 chunk 559 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 82 ASN ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 245 ASN Ae 77 GLN Ae 82 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 82 ASN Ag 245 ASN Ai 77 GLN Ai 82 ASN Ai 245 ASN Ak 77 GLN Ak 82 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 82 ASN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN Ao 82 ASN Ao 98 GLN Aq 77 GLN Aq 82 ASN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 82 ASN Au 82 ASN ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 77 GLN Aw 82 ASN ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 82 ASN ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 82 ASN Ba 245 ASN ** Bc 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 82 ASN Bc 245 ASN Be 77 GLN Be 82 ASN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 245 ASN Bg 82 ASN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 245 ASN Bi 82 ASN Bi 113 ASN ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 245 ASN Bk 77 GLN Bk 82 ASN Bm 77 GLN Bm 82 ASN Bm 245 ASN Bo 77 GLN Bo 82 ASN Bq 77 GLN Bq 82 ASN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 245 ASN Bs 77 GLN Bs 82 ASN Bs 98 GLN ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 245 ASN Bu 77 GLN Bu 82 ASN Bu 245 ASN ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 245 ASN ** By 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** By 77 GLN By 82 ASN Ca 77 GLN Ca 82 ASN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.090803 restraints weight = 68318.354| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.01 r_work: 0.2775 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 54376 Z= 0.292 Angle : 0.538 6.861 74144 Z= 0.274 Chirality : 0.041 0.153 8372 Planarity : 0.005 0.043 9184 Dihedral : 11.065 59.982 9166 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.63 % Allowed : 28.12 % Favored : 68.26 % 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: 6272 helix: 0.75 (0.11), residues: 2660 sheet: 1.66 (0.27), residues: 280 loop : -1.02 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPBs 132 HIS 0.002 0.000 HISBu 259 PHE 0.014 0.002 PHEBe 202 TYR 0.016 0.001 TYRBs 198 ARG 0.002 0.000 ARGBk 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 996 time to evaluate : 4.541 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8026 (mtt-85) REVERT: Ac 113 ASN cc_start: 0.9011 (m110) cc_final: 0.8781 (m-40) REVERT: Ac 134 MET cc_start: 0.8794 (ttt) cc_final: 0.8488 (ttt) REVERT: Ae 160 MET cc_start: 0.9482 (mmm) cc_final: 0.9244 (mmm) REVERT: Ae 212 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8089 (ttt90) REVERT: Ag 53 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: Ag 102 ASP cc_start: 0.8497 (t0) cc_final: 0.8222 (t0) REVERT: Ag 134 MET cc_start: 0.8885 (ttt) cc_final: 0.8627 (ttt) REVERT: Ag 153 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8084 (mptt) REVERT: Ag 177 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8255 (mttp) REVERT: Ag 191 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: Ag 245 ASN cc_start: 0.9048 (t0) cc_final: 0.8731 (t0) REVERT: Ai 91 ASP cc_start: 0.8632 (m-30) cc_final: 0.8404 (m-30) REVERT: Ai 134 MET cc_start: 0.8913 (ttt) cc_final: 0.8702 (ttt) REVERT: Ai 191 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8410 (mtt180) REVERT: Am 91 ASP cc_start: 0.8665 (m-30) cc_final: 0.8369 (m-30) REVERT: Am 191 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7913 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7702 (mtmt) REVERT: Ao 98 GLN cc_start: 0.8659 (tt0) cc_final: 0.8458 (tt0) REVERT: Ao 113 ASN cc_start: 0.8844 (m110) cc_final: 0.8486 (m-40) REVERT: Aq 91 ASP cc_start: 0.8676 (m-30) cc_final: 0.8296 (m-30) REVERT: Aq 160 MET cc_start: 0.9454 (mmm) cc_final: 0.9142 (mmt) REVERT: Aq 191 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7892 (mtt-85) REVERT: As 53 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7884 (mttm) REVERT: As 113 ASN cc_start: 0.8846 (m-40) cc_final: 0.8547 (m-40) REVERT: As 191 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7761 (mtt180) REVERT: Au 191 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8024 (mtt180) REVERT: Aw 134 MET cc_start: 0.8757 (ttt) cc_final: 0.8551 (ttt) REVERT: Aw 153 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8579 (mmtt) REVERT: Aw 191 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7528 (mtt180) REVERT: Ay 91 ASP cc_start: 0.8805 (m-30) cc_final: 0.8473 (m-30) REVERT: Ay 113 ASN cc_start: 0.8813 (m-40) cc_final: 0.8322 (m110) REVERT: Ay 160 MET cc_start: 0.9456 (mmm) cc_final: 0.9234 (mmp) REVERT: Ay 191 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7825 (mtt180) REVERT: Ay 212 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8185 (ttp80) REVERT: Ba 160 MET cc_start: 0.9465 (mmm) cc_final: 0.9203 (mmm) REVERT: Ba 212 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7962 (ttt90) REVERT: Ba 245 ASN cc_start: 0.8978 (t0) cc_final: 0.8736 (t0) REVERT: Bc 53 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7940 (mttm) REVERT: Bc 191 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: Bg 113 ASN cc_start: 0.8971 (m-40) cc_final: 0.8660 (m110) REVERT: Bg 153 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8364 (mttt) REVERT: Bg 191 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7846 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8089 (mtt180) REVERT: Bi 212 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8192 (ttp80) REVERT: Bi 231 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8207 (mmt180) REVERT: Bk 108 MET cc_start: 0.8875 (tpt) cc_final: 0.8602 (tpp) REVERT: Bk 191 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: Bm 153 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8387 (mptt) REVERT: Bo 54 MET cc_start: 0.8860 (ptm) cc_final: 0.8606 (ptm) REVERT: Bo 95 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8193 (mt-10) REVERT: Bo 153 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8408 (mptt) REVERT: Bo 191 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7675 (mtt180) REVERT: Bq 91 ASP cc_start: 0.8522 (m-30) cc_final: 0.8285 (m-30) REVERT: Bq 113 ASN cc_start: 0.8885 (m110) cc_final: 0.8587 (m-40) REVERT: Bq 153 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8386 (mptt) REVERT: Bs 153 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8209 (mttt) REVERT: Bs 191 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7723 (mtt180) REVERT: Bw 53 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7778 (mtmt) REVERT: Bw 91 ASP cc_start: 0.8637 (m-30) cc_final: 0.8178 (m-30) REVERT: Bw 160 MET cc_start: 0.9407 (mmm) cc_final: 0.9145 (mmm) REVERT: By 53 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7743 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7639 (mtmt) REVERT: Ca 108 MET cc_start: 0.8761 (tpt) cc_final: 0.8534 (tpp) REVERT: Ca 191 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8205 (mtt-85) REVERT: Cc 53 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7742 (mtmt) REVERT: Cc 91 ASP cc_start: 0.8643 (m-30) cc_final: 0.8371 (m-30) REVERT: Cc 134 MET cc_start: 0.8770 (ttt) cc_final: 0.8312 (ttt) outliers start: 199 outliers final: 89 residues processed: 1118 average time/residue: 1.4232 time to fit residues: 1976.2003 Evaluate side-chains 1012 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 903 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 177 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 191 ARG Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 267 MET Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 267 MET Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 191 ARG Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 103 ILE Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 231 ARG Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 267 MET Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 141 VAL Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 211 VAL Chi-restraints excluded: chain Cc residue 267 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 91 optimal weight: 0.8980 chunk 521 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 552 optimal weight: 4.9990 chunk 477 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 361 optimal weight: 6.9990 chunk 505 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 82 ASN Ac 82 ASN Ac 245 ASN Ae 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 82 ASN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN Aq 245 ASN ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 113 ASN Bi 245 ASN Bk 113 ASN Bk 158 GLN Bm 245 ASN Bo 82 ASN ** Bo 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 82 ASN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 245 ASN Bs 245 ASN ** Bu 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 245 ASN Bw 158 GLN By 113 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 82 ASN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.090968 restraints weight = 68928.002| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.02 r_work: 0.2768 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 54376 Z= 0.287 Angle : 0.527 7.389 74144 Z= 0.266 Chirality : 0.040 0.155 8372 Planarity : 0.004 0.046 9184 Dihedral : 10.855 59.937 9115 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.32 % Allowed : 27.22 % Favored : 68.46 % 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: 0.01 (0.11), residues: 6272 helix: 0.87 (0.11), residues: 2660 sheet: 1.89 (0.28), residues: 280 loop : -0.88 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPCc 132 HIS 0.002 0.000 HISBy 259 PHE 0.014 0.002 PHEBa 202 TYR 0.012 0.001 TYRBa 198 ARG 0.002 0.000 ARGAu 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 949 time to evaluate : 4.474 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8097 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8982 (m110) cc_final: 0.8727 (m-40) REVERT: Ac 122 ASN cc_start: 0.9292 (m-40) cc_final: 0.8941 (m-40) REVERT: Ae 53 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7964 (mmtt) REVERT: Ae 160 MET cc_start: 0.9475 (mmm) cc_final: 0.9195 (mmm) REVERT: Ae 212 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8112 (ttt90) REVERT: Ag 53 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7758 (mtmt) REVERT: Ag 134 MET cc_start: 0.8918 (ttt) cc_final: 0.8667 (ttt) REVERT: Ag 191 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: Ag 245 ASN cc_start: 0.9034 (t0) cc_final: 0.8674 (t0) REVERT: Ai 53 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7715 (mtmt) REVERT: Ai 134 MET cc_start: 0.8956 (ttt) cc_final: 0.8695 (ttt) REVERT: Ai 191 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (mtt180) REVERT: Ak 108 MET cc_start: 0.8871 (tpt) cc_final: 0.8503 (tpp) REVERT: Am 191 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7971 (mtt180) REVERT: Am 245 ASN cc_start: 0.9142 (t0) cc_final: 0.8925 (t0) REVERT: Ao 53 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7696 (mtmt) REVERT: Ao 113 ASN cc_start: 0.8912 (m110) cc_final: 0.8620 (m-40) REVERT: Ao 153 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8701 (mptt) REVERT: Ao 191 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8201 (mtt180) REVERT: Ao 212 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8078 (ttt90) REVERT: Aq 91 ASP cc_start: 0.8654 (m-30) cc_final: 0.8316 (m-30) REVERT: Aq 160 MET cc_start: 0.9480 (mmm) cc_final: 0.9250 (mmm) REVERT: Aq 191 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8015 (mtt-85) REVERT: As 53 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8019 (mttp) REVERT: As 191 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7801 (mtt180) REVERT: Au 191 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8073 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8636 (mmtt) REVERT: Aw 191 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7522 (mtt180) REVERT: Aw 231 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7982 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8765 (m-30) cc_final: 0.8514 (m-30) REVERT: Ay 95 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8263 (mt-10) REVERT: Ay 191 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7843 (mtt180) REVERT: Ba 160 MET cc_start: 0.9453 (mmm) cc_final: 0.9137 (mmm) REVERT: Ba 212 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7976 (ttt90) REVERT: Bc 53 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7929 (mttm) REVERT: Bc 191 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7949 (mtt180) REVERT: Bg 113 ASN cc_start: 0.8929 (m-40) cc_final: 0.8707 (m110) REVERT: Bg 153 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8410 (mttt) REVERT: Bg 191 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7904 (mtt-85) REVERT: Bg 212 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8252 (ttp80) REVERT: Bi 191 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8112 (mtt180) REVERT: Bi 212 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8187 (ttp80) REVERT: Bk 108 MET cc_start: 0.8962 (tpt) cc_final: 0.8690 (tpp) REVERT: Bk 191 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8064 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8219 (mtt-85) REVERT: Bo 95 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8174 (mt-10) REVERT: Bo 191 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7671 (mtt180) REVERT: Bq 95 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8259 (mt-10) REVERT: Bq 113 ASN cc_start: 0.8863 (m110) cc_final: 0.8571 (m110) REVERT: Bq 153 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8391 (mptt) REVERT: Bs 108 MET cc_start: 0.9048 (tpt) cc_final: 0.8625 (tpt) REVERT: Bs 134 MET cc_start: 0.8895 (ttt) cc_final: 0.8623 (ttt) REVERT: Bs 153 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8366 (mttt) REVERT: Bs 191 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7774 (mtt180) REVERT: Bu 113 ASN cc_start: 0.8735 (m110) cc_final: 0.8302 (m-40) REVERT: Bw 53 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7779 (mtmt) REVERT: Bw 160 MET cc_start: 0.9422 (mmm) cc_final: 0.9159 (mmm) REVERT: Bw 197 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7877 (ptm160) REVERT: By 53 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7717 (mtmt) REVERT: By 134 MET cc_start: 0.8849 (ttt) cc_final: 0.8636 (ttt) REVERT: Ca 53 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7727 (mtmt) REVERT: Ca 191 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8227 (mtt-85) REVERT: Cc 53 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7754 (mtmt) REVERT: Cc 91 ASP cc_start: 0.8624 (m-30) cc_final: 0.8341 (m-30) REVERT: Cc 134 MET cc_start: 0.8837 (ttt) cc_final: 0.8419 (ttt) outliers start: 237 outliers final: 108 residues processed: 1100 average time/residue: 1.4806 time to fit residues: 2009.6003 Evaluate side-chains 991 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 859 time to evaluate : 4.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 191 ARG Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 267 MET Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 267 MET Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 80 ILE Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 191 ARG Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 149 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 173 MET Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bu residue 246 THR Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 267 MET Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 149 VAL Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain By residue 267 MET Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 204 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 427 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 518 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 576 optimal weight: 5.9990 chunk 592 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 229 GLN Ac 245 ASN Ae 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 229 GLN ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 229 GLN Ba 245 ASN Bc 77 GLN Bc 229 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 229 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 229 GLN Bo 229 GLN Bq 77 GLN Bq 122 ASN Bs 229 GLN ** Bu 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 82 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.089243 restraints weight = 69052.044| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.01 r_work: 0.2764 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 54376 Z= 0.378 Angle : 0.561 9.024 74144 Z= 0.283 Chirality : 0.042 0.169 8372 Planarity : 0.005 0.050 9184 Dihedral : 10.966 60.184 9115 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.68 % Allowed : 27.73 % Favored : 67.58 % 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: -0.07 (0.11), residues: 6272 helix: 0.76 (0.10), residues: 2660 sheet: 1.86 (0.27), residues: 280 loop : -0.88 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAu 132 HIS 0.003 0.001 HISBy 259 PHE 0.016 0.003 PHEBa 202 TYR 0.015 0.001 TYRCc 180 ARG 0.002 0.000 ARGAe 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 906 time to evaluate : 4.476 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8062 (mtt180) REVERT: Ae 53 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7971 (mmtt) REVERT: Ae 160 MET cc_start: 0.9484 (mmm) cc_final: 0.9207 (mmm) REVERT: Ae 197 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7954 (ptm160) REVERT: Ae 212 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8105 (ttt90) REVERT: Ag 53 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7763 (mtmt) REVERT: Ag 134 MET cc_start: 0.8947 (ttt) cc_final: 0.8730 (ttt) REVERT: Ag 191 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7838 (mtt-85) REVERT: Ai 53 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7649 (mtmt) REVERT: Ai 102 ASP cc_start: 0.8596 (t0) cc_final: 0.8371 (t0) REVERT: Ai 134 MET cc_start: 0.8968 (ttt) cc_final: 0.8649 (ttt) REVERT: Ai 191 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8511 (mtt180) REVERT: Am 53 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: Am 191 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7704 (mtmt) REVERT: Ao 153 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8805 (mptt) REVERT: Ao 212 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8093 (ttt90) REVERT: Aq 91 ASP cc_start: 0.8641 (m-30) cc_final: 0.8302 (m-30) REVERT: Aq 160 MET cc_start: 0.9495 (mmm) cc_final: 0.9244 (mmm) REVERT: Aq 191 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8040 (mtt180) REVERT: As 53 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7914 (mttp) REVERT: As 191 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7908 (mtt180) REVERT: As 231 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8321 (mmm160) REVERT: Au 53 LYS cc_start: 0.8242 (mttt) cc_final: 0.8017 (mttm) REVERT: Au 191 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8738 (mmtt) REVERT: Aw 197 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8189 (ptm160) REVERT: Ay 91 ASP cc_start: 0.8788 (m-30) cc_final: 0.8551 (m-30) REVERT: Ay 95 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8280 (mt-10) REVERT: Ay 191 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7864 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7443 (mmtt) REVERT: Ba 122 ASN cc_start: 0.9016 (m-40) cc_final: 0.8793 (m-40) REVERT: Ba 160 MET cc_start: 0.9454 (mmm) cc_final: 0.9221 (mmm) REVERT: Ba 212 ARG cc_start: 0.8413 (ttp80) cc_final: 0.7984 (ttt90) REVERT: Ba 245 ASN cc_start: 0.9014 (t0) cc_final: 0.8730 (t0) REVERT: Bc 77 GLN cc_start: 0.8339 (mt0) cc_final: 0.8114 (mt0) REVERT: Bc 191 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7995 (mtt-85) REVERT: Be 191 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7909 (mtt-85) REVERT: Bg 113 ASN cc_start: 0.8965 (m-40) cc_final: 0.8723 (m-40) REVERT: Bg 191 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: Bg 212 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8264 (ttp80) REVERT: Bi 53 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8048 (mttt) REVERT: Bi 191 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (mtt180) REVERT: Bi 212 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8196 (ttp80) REVERT: Bk 191 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8055 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8300 (mtt-85) REVERT: Bm 267 MET cc_start: 0.4329 (mtp) cc_final: 0.3894 (mtp) REVERT: Bo 95 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8210 (mt-10) REVERT: Bo 122 ASN cc_start: 0.8966 (m-40) cc_final: 0.8728 (m-40) REVERT: Bo 191 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7880 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8200 (mmm160) REVERT: Bq 95 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8189 (mt-10) REVERT: Bq 134 MET cc_start: 0.8978 (ttt) cc_final: 0.8624 (ttt) REVERT: Bq 153 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8456 (mptt) REVERT: Bs 153 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8360 (mttt) REVERT: Bs 191 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7837 (mtt180) REVERT: Bw 53 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7747 (mtmt) REVERT: Bw 160 MET cc_start: 0.9428 (mmm) cc_final: 0.9168 (mmm) REVERT: Bw 197 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7929 (ptm160) REVERT: By 53 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7663 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7729 (mtmt) REVERT: Ca 191 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8233 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6309 (mmt) REVERT: Cc 53 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7721 (mtmt) REVERT: Cc 91 ASP cc_start: 0.8637 (m-30) cc_final: 0.8384 (m-30) REVERT: Cc 134 MET cc_start: 0.8888 (ttt) cc_final: 0.8490 (ttt) REVERT: Cc 191 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8228 (mtt-85) outliers start: 257 outliers final: 142 residues processed: 1070 average time/residue: 1.4451 time to fit residues: 1911.5664 Evaluate side-chains 1012 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 837 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 103 ILE Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 197 ARG Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 53 LYS Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 267 MET Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 135 MET Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 80 ILE Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 191 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 246 THR Chi-restraints excluded: chain Bi residue 53 LYS Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 81 SER Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 103 ILE Chi-restraints excluded: chain Bq residue 106 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 236 ASP Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 231 ARG Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 78 ILE Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bu residue 246 THR Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 267 MET Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 53 LYS Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 208 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 439 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 480 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 431 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Am 77 GLN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN Bq 122 ASN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 245 ASN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094035 restraints weight = 68226.353| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.02 r_work: 0.2816 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 54376 Z= 0.153 Angle : 0.481 9.302 74144 Z= 0.242 Chirality : 0.038 0.144 8372 Planarity : 0.004 0.047 9184 Dihedral : 10.505 59.503 9112 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.81 % Allowed : 29.43 % Favored : 67.77 % 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: 0.12 (0.11), residues: 6272 helix: 1.24 (0.11), residues: 2492 sheet: 0.44 (0.29), residues: 336 loop : -0.83 (0.11), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBy 132 HIS 0.002 0.000 HISAu 259 PHE 0.012 0.002 PHEBg 202 TYR 0.014 0.001 TYRAw 198 ARG 0.002 0.000 ARGAi 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 988 time to evaluate : 4.530 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7992 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8878 (m110) cc_final: 0.8599 (m-40) REVERT: Ae 160 MET cc_start: 0.9456 (mmm) cc_final: 0.9174 (mmm) REVERT: Ae 197 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7781 (ptm160) REVERT: Ae 212 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7975 (ttt90) REVERT: Ag 53 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7706 (mtmt) REVERT: Ag 153 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8392 (mptt) REVERT: Ag 191 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7802 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7734 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (mtt180) REVERT: Am 53 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: Am 95 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8165 (mt-10) REVERT: Am 191 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7995 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7689 (mtmt) REVERT: Ao 113 ASN cc_start: 0.8727 (m110) cc_final: 0.8366 (m110) REVERT: Ao 212 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8017 (ttt90) REVERT: Aq 91 ASP cc_start: 0.8603 (m-30) cc_final: 0.8298 (m-30) REVERT: Aq 160 MET cc_start: 0.9457 (mmm) cc_final: 0.9174 (mmm) REVERT: Aq 191 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: As 53 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7964 (mttp) REVERT: As 95 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8227 (mt-10) REVERT: As 191 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7814 (mtt180) REVERT: Au 53 LYS cc_start: 0.8295 (mttt) cc_final: 0.8083 (mttm) REVERT: Au 98 GLN cc_start: 0.8495 (tt0) cc_final: 0.8124 (tt0) REVERT: Au 181 MET cc_start: 0.9226 (tpp) cc_final: 0.8934 (tpp) REVERT: Au 191 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8066 (mtt180) REVERT: Aw 153 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8812 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7914 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8783 (m-30) cc_final: 0.8558 (m-30) REVERT: Ay 160 MET cc_start: 0.9428 (mmm) cc_final: 0.9129 (mmm) REVERT: Ay 191 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: Ba 122 ASN cc_start: 0.9000 (m-40) cc_final: 0.8778 (m-40) REVERT: Ba 160 MET cc_start: 0.9435 (mmm) cc_final: 0.9189 (mmm) REVERT: Ba 191 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8236 (mmt90) REVERT: Ba 212 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7993 (ttt90) REVERT: Bc 191 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7929 (mtt-85) REVERT: Be 134 MET cc_start: 0.8864 (ttt) cc_final: 0.8619 (ttt) REVERT: Be 191 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7835 (mtt-85) REVERT: Bg 113 ASN cc_start: 0.8640 (m-40) cc_final: 0.8313 (m110) REVERT: Bg 153 LYS cc_start: 0.8996 (mmpt) cc_final: 0.8323 (mttt) REVERT: Bg 231 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8076 (mmt180) REVERT: Bi 191 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8081 (mtt-85) REVERT: Bk 108 MET cc_start: 0.8911 (tpt) cc_final: 0.8541 (tpp) REVERT: Bm 191 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8168 (mtt-85) REVERT: Bm 267 MET cc_start: 0.3747 (mtp) cc_final: 0.3530 (mtp) REVERT: Bo 95 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8164 (mt-10) REVERT: Bo 122 ASN cc_start: 0.8958 (m-40) cc_final: 0.8750 (m-40) REVERT: Bo 191 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7859 (mtt180) REVERT: Bq 95 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8166 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8318 (tp30) cc_final: 0.8103 (mm-30) REVERT: Bq 134 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8556 (ttt) REVERT: Bq 153 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8354 (mptt) REVERT: Bs 108 MET cc_start: 0.8939 (tpt) cc_final: 0.8656 (tpt) REVERT: Bs 153 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8368 (mttt) REVERT: Bs 191 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7731 (mtt180) REVERT: Bu 113 ASN cc_start: 0.8540 (m110) cc_final: 0.8096 (m110) REVERT: Bw 91 ASP cc_start: 0.8576 (m-30) cc_final: 0.8213 (m-30) REVERT: Bw 160 MET cc_start: 0.9394 (mmm) cc_final: 0.9111 (mmm) REVERT: By 53 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7765 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8395 (mmtt) cc_final: 0.7737 (mtmt) REVERT: Ca 113 ASN cc_start: 0.8332 (m110) cc_final: 0.7914 (m110) REVERT: Ca 258 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6143 (mmt) REVERT: Cc 53 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7741 (mtmt) REVERT: Cc 91 ASP cc_start: 0.8598 (m-30) cc_final: 0.8373 (m-30) REVERT: Cc 95 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8208 (mt-10) REVERT: Cc 134 MET cc_start: 0.8818 (ttt) cc_final: 0.8522 (ttt) REVERT: Cc 191 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8030 (mtt-85) outliers start: 154 outliers final: 58 residues processed: 1076 average time/residue: 1.4871 time to fit residues: 1965.3767 Evaluate side-chains 968 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 886 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 191 ARG Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 80 ILE Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 54 MET Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 106 THR Chi-restraints excluded: chain Bq residue 134 MET Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 173 MET Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 364 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 555 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 568 optimal weight: 1.9990 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 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Am 77 GLN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 229 GLN Au 245 ASN ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 82 ASN Bq 69 HIS Bq 122 ASN ** Bu 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 77 GLN ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** By 69 HIS ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.088426 restraints weight = 69008.839| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.01 r_work: 0.2743 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 54376 Z= 0.433 Angle : 0.582 11.162 74144 Z= 0.293 Chirality : 0.044 0.174 8372 Planarity : 0.005 0.052 9184 Dihedral : 10.986 60.256 9103 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.41 % Allowed : 27.82 % Favored : 67.77 % 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: -0.14 (0.11), residues: 6272 helix: 0.93 (0.11), residues: 2492 sheet: -0.03 (0.25), residues: 392 loop : -0.88 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAy 132 HIS 0.004 0.001 HISBc 259 PHE 0.017 0.003 PHEBa 163 TYR 0.017 0.001 TYRBs 198 ARG 0.005 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 890 time to evaluate : 4.528 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8067 (mtt180) REVERT: Ae 53 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: Ae 197 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: Ae 212 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8045 (ttt90) REVERT: Ag 53 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: Ag 191 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7835 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7666 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8518 (mtt180) REVERT: Ak 91 ASP cc_start: 0.8688 (m-30) cc_final: 0.8460 (m-30) REVERT: Am 53 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7773 (mtmt) REVERT: Am 95 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8154 (mt-10) REVERT: Am 191 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8050 (mtt180) REVERT: Am 245 ASN cc_start: 0.9127 (t0) cc_final: 0.8907 (t0) REVERT: Ao 53 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7697 (mtmt) REVERT: Ao 212 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8025 (ttt90) REVERT: Aq 72 GLU cc_start: 0.7899 (pt0) cc_final: 0.7205 (pp20) REVERT: Aq 91 ASP cc_start: 0.8562 (m-30) cc_final: 0.8228 (m-30) REVERT: Aq 160 MET cc_start: 0.9470 (mmm) cc_final: 0.9231 (mmm) REVERT: Aq 191 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: As 53 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7920 (mttp) REVERT: As 191 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: As 231 ARG cc_start: 0.8604 (mmt180) cc_final: 0.8263 (mmm160) REVERT: Au 191 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8120 (mtt180) REVERT: Aw 95 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8308 (mt-10) REVERT: Aw 122 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8501 (m-40) REVERT: Aw 153 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8719 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8018 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8769 (m-30) cc_final: 0.8497 (m-30) REVERT: Ay 191 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7498 (mmtt) REVERT: Ba 122 ASN cc_start: 0.9203 (m-40) cc_final: 0.8961 (m-40) REVERT: Ba 160 MET cc_start: 0.9445 (mmm) cc_final: 0.9084 (mmm) REVERT: Bc 191 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7981 (mtt-85) REVERT: Be 95 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8203 (mt-10) REVERT: Be 191 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7945 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8109 (mtt180) REVERT: Bi 212 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8159 (ttp80) REVERT: Bk 191 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8064 (mtt-85) REVERT: Bk 267 MET cc_start: 0.3707 (OUTLIER) cc_final: 0.3505 (ptm) REVERT: Bm 191 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (mtt-85) REVERT: Bo 95 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8169 (mt-10) REVERT: Bo 122 ASN cc_start: 0.9148 (m-40) cc_final: 0.8899 (m-40) REVERT: Bo 191 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: Bq 95 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8162 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8353 (tp30) cc_final: 0.8122 (mm-30) REVERT: Bq 134 MET cc_start: 0.8967 (ttt) cc_final: 0.8619 (ttt) REVERT: Bs 153 LYS cc_start: 0.9072 (mmpt) cc_final: 0.8272 (mttt) REVERT: Bs 198 TYR cc_start: 0.9336 (m-80) cc_final: 0.8929 (m-80) REVERT: Bw 53 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: Bw 160 MET cc_start: 0.9424 (mmm) cc_final: 0.9168 (mmm) REVERT: Bw 197 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7931 (ptm160) REVERT: By 53 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7697 (mtmt) REVERT: By 191 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8397 (mtt180) REVERT: Ca 53 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: Ca 72 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: Ca 258 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6120 (mmt) REVERT: Cc 53 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7713 (mtmt) REVERT: Cc 91 ASP cc_start: 0.8610 (m-30) cc_final: 0.8393 (m-30) REVERT: Cc 95 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8218 (mt-10) REVERT: Cc 134 MET cc_start: 0.8900 (ttt) cc_final: 0.8541 (ttt) REVERT: Cc 191 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8096 (mtt-85) outliers start: 242 outliers final: 144 residues processed: 1060 average time/residue: 1.4735 time to fit residues: 1932.1206 Evaluate side-chains 1010 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 835 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 103 ILE Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Aa residue 255 SER Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 122 ASN Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 53 LYS Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 255 SER Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 80 ILE Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 81 SER Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bk residue 267 MET Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 149 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bo residue 267 MET Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 103 ILE Chi-restraints excluded: chain Bq residue 106 THR Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 236 ASP Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 149 VAL Chi-restraints excluded: chain Bs residue 173 MET Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 78 ILE Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 149 VAL Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 258 MET Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 191 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 72 GLU Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 53 LYS Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 122 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 423 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 598 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 GLN ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN Bg 113 ASN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 122 ASN Bs 98 GLN ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.091172 restraints weight = 68470.960| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.02 r_work: 0.2786 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 54376 Z= 0.231 Angle : 0.513 11.157 74144 Z= 0.257 Chirality : 0.040 0.152 8372 Planarity : 0.004 0.050 9184 Dihedral : 10.688 59.790 9100 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.75 % Allowed : 28.39 % Favored : 67.86 % 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: 0.01 (0.11), residues: 6272 helix: 1.10 (0.11), residues: 2492 sheet: -0.02 (0.25), residues: 392 loop : -0.83 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAy 132 HIS 0.001 0.000 HISBc 259 PHE 0.014 0.002 PHEBg 202 TYR 0.018 0.001 TYRAw 198 ARG 0.005 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 909 time to evaluate : 4.573 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: Ac 95 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8279 (mt-10) REVERT: Ae 197 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7808 (ptm160) REVERT: Ae 212 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8109 (ttp80) REVERT: Ag 53 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7709 (mtmt) REVERT: Ag 153 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8300 (mptt) REVERT: Ag 191 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7805 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7671 (mtmt) REVERT: Ai 79 ASP cc_start: 0.9072 (m-30) cc_final: 0.8768 (m-30) REVERT: Ai 191 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8478 (mtt180) REVERT: Ak 191 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8328 (mtt-85) REVERT: Am 53 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7775 (mtmt) REVERT: Am 95 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8215 (mt-10) REVERT: Am 191 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7999 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7695 (mtmt) REVERT: Ao 113 ASN cc_start: 0.8860 (m110) cc_final: 0.8590 (m-40) REVERT: Ao 212 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7987 (ttt90) REVERT: Aq 72 GLU cc_start: 0.7877 (pt0) cc_final: 0.7231 (pp20) REVERT: Aq 91 ASP cc_start: 0.8550 (m-30) cc_final: 0.8247 (m-30) REVERT: Aq 191 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7964 (mtt180) REVERT: As 53 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7901 (mttp) REVERT: As 191 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7779 (mtt180) REVERT: As 231 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (mmm160) REVERT: Au 53 LYS cc_start: 0.8338 (mttt) cc_final: 0.8110 (mttm) REVERT: Au 98 GLN cc_start: 0.8690 (tt0) cc_final: 0.8387 (tt0) REVERT: Au 191 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8095 (mtt180) REVERT: Aw 79 ASP cc_start: 0.9019 (m-30) cc_final: 0.8743 (m-30) REVERT: Aw 95 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8286 (mt-10) REVERT: Aw 231 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7978 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8754 (m-30) cc_final: 0.8512 (m-30) REVERT: Ay 160 MET cc_start: 0.9444 (mmm) cc_final: 0.9153 (mmm) REVERT: Ay 191 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7724 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7486 (mmtt) REVERT: Ba 122 ASN cc_start: 0.9129 (m-40) cc_final: 0.8909 (m110) REVERT: Ba 160 MET cc_start: 0.9440 (mmm) cc_final: 0.9181 (mmm) REVERT: Bc 191 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: Be 95 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8150 (mt-10) REVERT: Be 191 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7890 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: Bi 212 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8097 (ttp80) REVERT: Bk 108 MET cc_start: 0.8980 (tpt) cc_final: 0.8610 (tpp) REVERT: Bk 191 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8055 (mtt-85) REVERT: Bm 72 GLU cc_start: 0.7935 (pt0) cc_final: 0.7155 (pp20) REVERT: Bm 134 MET cc_start: 0.8850 (ttt) cc_final: 0.8618 (ttt) REVERT: Bm 191 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8213 (mtt-85) REVERT: Bo 79 ASP cc_start: 0.9098 (m-30) cc_final: 0.8874 (m-30) REVERT: Bo 95 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8124 (mt-10) REVERT: Bo 122 ASN cc_start: 0.9090 (m-40) cc_final: 0.8843 (m-40) REVERT: Bo 191 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7834 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8120 (mmm160) REVERT: Bq 95 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8104 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8332 (tp30) cc_final: 0.8072 (mm-30) REVERT: Bq 153 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8370 (mptt) REVERT: Bq 212 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8088 (ttt90) REVERT: Bs 108 MET cc_start: 0.8982 (tpt) cc_final: 0.8583 (tpt) REVERT: Bs 153 LYS cc_start: 0.9072 (mmpt) cc_final: 0.8442 (mptt) REVERT: Bu 113 ASN cc_start: 0.8713 (m110) cc_final: 0.8271 (m-40) REVERT: Bu 208 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8474 (mtt90) REVERT: Bw 53 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7728 (mtmt) REVERT: Bw 197 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: By 53 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7693 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7752 (mtmt) REVERT: Ca 72 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: Ca 258 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6071 (mmt) REVERT: Cc 91 ASP cc_start: 0.8556 (m-30) cc_final: 0.8354 (m-30) REVERT: Cc 95 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8146 (mt-10) REVERT: Cc 134 MET cc_start: 0.8869 (ttt) cc_final: 0.8546 (ttt) REVERT: Cc 191 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8063 (mtt-85) outliers start: 206 outliers final: 111 residues processed: 1062 average time/residue: 1.4663 time to fit residues: 1918.5450 Evaluate side-chains 1006 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 867 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 191 ARG Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 53 LYS Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 80 ILE Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 255 SER Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 258 MET Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 72 GLU Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 103 ILE Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 220 MET Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 436 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 604 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Am 77 GLN Am 113 ASN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 113 ASN Bw 158 GLN ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094243 restraints weight = 68039.932| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.02 r_work: 0.2831 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54376 Z= 0.149 Angle : 0.486 11.436 74144 Z= 0.243 Chirality : 0.038 0.143 8372 Planarity : 0.004 0.048 9184 Dihedral : 10.427 59.416 9100 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.37 % Allowed : 29.45 % Favored : 68.19 % 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: 0.22 (0.11), residues: 6272 helix: 1.37 (0.11), residues: 2492 sheet: 0.04 (0.25), residues: 392 loop : -0.77 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPCc 132 HIS 0.002 0.000 HISAk 69 PHE 0.012 0.002 PHEBg 202 TYR 0.015 0.001 TYRAw 198 ARG 0.005 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 950 time to evaluate : 4.550 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7969 (mtt180) REVERT: Ac 231 ARG cc_start: 0.8468 (mmt180) cc_final: 0.8172 (mmm160) REVERT: Ag 53 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7592 (mtmt) REVERT: Ag 153 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8362 (mptt) REVERT: Ag 191 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7717 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7698 (mtmt) REVERT: Ai 79 ASP cc_start: 0.9060 (m-30) cc_final: 0.8777 (m-30) REVERT: Ai 191 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8424 (mtt180) REVERT: Ak 191 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8274 (mtt-85) REVERT: Am 47 ILE cc_start: 0.9325 (pt) cc_final: 0.9120 (mp) REVERT: Am 95 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8192 (mt-10) REVERT: Am 191 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7926 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7723 (mtmt) REVERT: Ao 112 MET cc_start: 0.9035 (mmp) cc_final: 0.8779 (mmp) REVERT: Ao 113 ASN cc_start: 0.8615 (m110) cc_final: 0.8270 (m110) REVERT: Ao 212 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7975 (ttt90) REVERT: Aq 72 GLU cc_start: 0.7874 (pt0) cc_final: 0.7221 (pp20) REVERT: Aq 91 ASP cc_start: 0.8545 (m-30) cc_final: 0.8246 (m-30) REVERT: Aq 191 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7968 (mtt180) REVERT: As 53 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7938 (mttp) REVERT: As 113 ASN cc_start: 0.8246 (m-40) cc_final: 0.8027 (m110) REVERT: As 134 MET cc_start: 0.8652 (ttt) cc_final: 0.8317 (ttt) REVERT: As 191 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7718 (mtt180) REVERT: As 231 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8266 (mmm160) REVERT: Au 98 GLN cc_start: 0.8567 (tt0) cc_final: 0.8214 (tt0) REVERT: Au 191 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8040 (mtt180) REVERT: Aw 79 ASP cc_start: 0.8858 (m-30) cc_final: 0.8624 (m-30) REVERT: Aw 231 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7934 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8740 (m-30) cc_final: 0.8508 (m-30) REVERT: Ay 160 MET cc_start: 0.9411 (mmm) cc_final: 0.9116 (mmm) REVERT: Ay 191 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7685 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8057 (mttm) REVERT: Ba 122 ASN cc_start: 0.9110 (m-40) cc_final: 0.8886 (m-40) REVERT: Ba 160 MET cc_start: 0.9421 (mmm) cc_final: 0.9154 (mmm) REVERT: Bc 191 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7926 (mtt180) REVERT: Be 54 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8711 (ttp) REVERT: Be 95 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8125 (mt-10) REVERT: Be 191 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: Bg 231 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8061 (mmt180) REVERT: Bk 108 MET cc_start: 0.8911 (tpt) cc_final: 0.8472 (tpp) REVERT: Bk 191 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8022 (mtt-85) REVERT: Bm 53 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8017 (mttp) REVERT: Bm 72 GLU cc_start: 0.7962 (pt0) cc_final: 0.7251 (pp20) REVERT: Bm 153 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8309 (mptt) REVERT: Bm 191 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8167 (mtt-85) REVERT: Bm 208 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8511 (mtt90) REVERT: Bo 72 GLU cc_start: 0.7975 (pt0) cc_final: 0.7263 (pp20) REVERT: Bo 79 ASP cc_start: 0.8981 (m-30) cc_final: 0.8738 (m-30) REVERT: Bo 95 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8115 (mt-10) REVERT: Bo 122 ASN cc_start: 0.9058 (m-40) cc_final: 0.8840 (m-40) REVERT: Bo 191 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7841 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8401 (mmm160) cc_final: 0.8058 (mmm160) REVERT: Bq 95 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8111 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8199 (tp30) cc_final: 0.7987 (mm-30) REVERT: Bq 153 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8309 (mptt) REVERT: Bs 72 GLU cc_start: 0.7971 (pt0) cc_final: 0.7235 (pp20) REVERT: Bs 108 MET cc_start: 0.8915 (tpt) cc_final: 0.8620 (tpt) REVERT: Bs 153 LYS cc_start: 0.9021 (mmpt) cc_final: 0.8373 (mptt) REVERT: Bu 113 ASN cc_start: 0.8500 (m110) cc_final: 0.8052 (m110) REVERT: Bu 122 ASN cc_start: 0.8843 (m110) cc_final: 0.8634 (m-40) REVERT: Bw 53 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7728 (mtmt) REVERT: Bw 91 ASP cc_start: 0.8584 (m-30) cc_final: 0.8209 (m-30) REVERT: Bw 212 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8044 (ttt-90) REVERT: By 53 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7684 (mtmt) REVERT: By 72 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7846 (pp20) REVERT: By 113 ASN cc_start: 0.8756 (m110) cc_final: 0.8536 (m110) REVERT: By 191 ARG cc_start: 0.8806 (mtt90) cc_final: 0.8603 (mtt180) REVERT: Ca 53 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7753 (mtmt) REVERT: Ca 113 ASN cc_start: 0.8198 (m110) cc_final: 0.7921 (m110) REVERT: Ca 258 MET cc_start: 0.6367 (mtt) cc_final: 0.5838 (mmt) REVERT: Cc 91 ASP cc_start: 0.8595 (m-30) cc_final: 0.8391 (m-30) REVERT: Cc 95 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8142 (mt-10) REVERT: Cc 134 MET cc_start: 0.8811 (ttt) cc_final: 0.8556 (ttt) REVERT: Cc 191 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7984 (mtt-85) outliers start: 130 outliers final: 79 residues processed: 1043 average time/residue: 1.5012 time to fit residues: 1923.7230 Evaluate side-chains 990 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 892 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 191 ARG Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Be residue 54 MET Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 80 ILE Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 232 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 490 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 353 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 493 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 485 optimal weight: 0.0050 chunk 17 optimal weight: 10.0000 chunk 529 optimal weight: 0.6980 overall best weight: 2.1456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 98 GLN ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 69 HIS Be 77 GLN Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 77 GLN ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** By 189 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.093322 restraints weight = 68272.619| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.02 r_work: 0.2801 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54376 Z= 0.193 Angle : 0.508 12.578 74144 Z= 0.252 Chirality : 0.039 0.139 8372 Planarity : 0.004 0.049 9184 Dihedral : 10.545 59.550 9100 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 29.57 % Favored : 67.88 % 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: 0.25 (0.11), residues: 6272 helix: 1.40 (0.11), residues: 2492 sheet: 0.00 (0.25), residues: 392 loop : -0.76 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAw 132 HIS 0.001 0.000 HISAu 69 PHE 0.012 0.002 PHEBg 202 TYR 0.016 0.001 TYRBs 198 ARG 0.008 0.000 ARGAa 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 919 time to evaluate : 4.389 Fit side-chains revert: symmetry clash REVERT: Aa 98 GLN cc_start: 0.8651 (tt0) cc_final: 0.8423 (tt0) REVERT: Aa 191 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7980 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8838 (m110) cc_final: 0.8552 (m-40) REVERT: Ac 231 ARG cc_start: 0.8461 (mmt180) cc_final: 0.8156 (mmm160) REVERT: Ag 53 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7633 (mtmt) REVERT: Ag 150 GLU cc_start: 0.8386 (pt0) cc_final: 0.8146 (pt0) REVERT: Ag 153 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8328 (mptt) REVERT: Ag 191 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7707 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7717 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (mtt180) REVERT: Ak 191 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8287 (mtt-85) REVERT: Am 53 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7768 (mtmt) REVERT: Am 95 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8219 (mt-10) REVERT: Am 191 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7964 (mtt180) REVERT: Am 245 ASN cc_start: 0.9130 (t0) cc_final: 0.8870 (t0) REVERT: Ao 53 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7770 (mtmt) REVERT: Ao 112 MET cc_start: 0.9041 (mmp) cc_final: 0.8783 (mmp) REVERT: Ao 113 ASN cc_start: 0.8700 (m110) cc_final: 0.8326 (m110) REVERT: Ao 212 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7971 (ttt90) REVERT: Aq 72 GLU cc_start: 0.7896 (pt0) cc_final: 0.7246 (pp20) REVERT: Aq 91 ASP cc_start: 0.8544 (m-30) cc_final: 0.8237 (m-30) REVERT: Aq 191 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: As 53 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7939 (mttp) REVERT: As 72 GLU cc_start: 0.8062 (pt0) cc_final: 0.7192 (pp20) REVERT: As 191 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7753 (mtt180) REVERT: As 231 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8276 (mmm160) REVERT: Au 60 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8701 (mttm) REVERT: Au 98 GLN cc_start: 0.8567 (tt0) cc_final: 0.8204 (tt0) REVERT: Au 191 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8028 (mtt180) REVERT: Aw 79 ASP cc_start: 0.8896 (m-30) cc_final: 0.8651 (m-30) REVERT: Aw 113 ASN cc_start: 0.8683 (m-40) cc_final: 0.8187 (m110) REVERT: Aw 231 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7977 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8686 (m-30) cc_final: 0.8459 (m-30) REVERT: Ay 191 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7699 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8036 (mttm) REVERT: Ba 122 ASN cc_start: 0.9122 (m-40) cc_final: 0.8911 (m110) REVERT: Ba 160 MET cc_start: 0.9429 (mmm) cc_final: 0.9166 (mmm) REVERT: Bc 191 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7952 (mtt180) REVERT: Be 54 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8680 (ttp) REVERT: Be 95 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8148 (mt-10) REVERT: Bg 231 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8073 (mmt180) REVERT: Bi 212 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8105 (ttp80) REVERT: Bk 108 MET cc_start: 0.8964 (tpt) cc_final: 0.8556 (tpp) REVERT: Bm 53 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7982 (mttp) REVERT: Bm 72 GLU cc_start: 0.7983 (pt0) cc_final: 0.7258 (pp20) REVERT: Bm 153 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8294 (mptt) REVERT: Bm 191 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8192 (mtt-85) REVERT: Bm 208 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8502 (mtt90) REVERT: Bo 72 GLU cc_start: 0.8028 (pt0) cc_final: 0.7343 (pp20) REVERT: Bo 79 ASP cc_start: 0.9002 (m-30) cc_final: 0.8756 (m-30) REVERT: Bo 95 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8110 (mt-10) REVERT: Bo 122 ASN cc_start: 0.9108 (m-40) cc_final: 0.8868 (m-40) REVERT: Bo 191 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7840 (mtt180) REVERT: Bq 95 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8082 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8174 (tp30) cc_final: 0.7954 (mm-30) REVERT: Bq 153 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8446 (mptt) REVERT: Bs 72 GLU cc_start: 0.8073 (pt0) cc_final: 0.7311 (pp20) REVERT: Bs 108 MET cc_start: 0.8875 (tpt) cc_final: 0.8670 (tpt) REVERT: Bs 153 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8222 (mttt) REVERT: Bu 113 ASN cc_start: 0.8550 (m110) cc_final: 0.8085 (m110) REVERT: Bw 91 ASP cc_start: 0.8606 (m-30) cc_final: 0.8186 (m-30) REVERT: Bw 113 ASN cc_start: 0.8759 (m110) cc_final: 0.8455 (m110) REVERT: Bw 197 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7878 (ptm160) REVERT: Bw 212 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.8062 (ttt-90) REVERT: By 53 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7680 (mtmt) REVERT: By 72 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7833 (pp20) REVERT: By 95 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8306 (mt-10) REVERT: Ca 53 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7760 (mtmt) REVERT: Ca 113 ASN cc_start: 0.8315 (m110) cc_final: 0.8041 (m-40) REVERT: Ca 258 MET cc_start: 0.6352 (mtt) cc_final: 0.5827 (mmt) REVERT: Cc 95 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8180 (mt-10) REVERT: Cc 134 MET cc_start: 0.8835 (ttt) cc_final: 0.8542 (ttt) REVERT: Cc 191 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7988 (mtt-85) outliers start: 140 outliers final: 99 residues processed: 1029 average time/residue: 1.4419 time to fit residues: 1831.6247 Evaluate side-chains 1003 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 885 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 191 ARG Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 250 THR Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Bc residue 135 MET Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 54 MET Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 250 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 267 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 236 ASP Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 20 optimal weight: 30.0000 chunk 490 optimal weight: 0.8980 chunk 252 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 595 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 449 optimal weight: 0.6980 chunk 535 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN ** Ak 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** By 189 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.094915 restraints weight = 67947.588| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.02 r_work: 0.2839 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 54376 Z= 0.153 Angle : 0.501 12.155 74144 Z= 0.248 Chirality : 0.038 0.141 8372 Planarity : 0.004 0.050 9184 Dihedral : 10.398 59.385 9100 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 30.19 % Favored : 67.69 % 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: 0.31 (0.11), residues: 6272 helix: 1.49 (0.11), residues: 2492 sheet: 0.01 (0.25), residues: 392 loop : -0.75 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAw 132 HIS 0.002 0.000 HISAk 69 PHE 0.012 0.002 PHEBs 202 TYR 0.013 0.001 TYRCc 180 ARG 0.008 0.000 ARGAa 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 963 time to evaluate : 4.419 Fit side-chains REVERT: Aa 98 GLN cc_start: 0.8620 (tt0) cc_final: 0.8411 (tt0) REVERT: Aa 191 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7990 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8832 (m110) cc_final: 0.8485 (m110) REVERT: Ac 231 ARG cc_start: 0.8467 (mmt180) cc_final: 0.8167 (mmm160) REVERT: Ag 47 ILE cc_start: 0.9358 (pt) cc_final: 0.9150 (mp) REVERT: Ag 53 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7604 (mtmt) REVERT: Ag 56 MET cc_start: 0.9214 (mtp) cc_final: 0.8936 (ttm) REVERT: Ag 150 GLU cc_start: 0.8406 (pt0) cc_final: 0.8191 (pt0) REVERT: Ag 153 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: Ag 191 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7679 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7770 (mtmt) REVERT: Ak 191 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8289 (mtt-85) REVERT: Am 95 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8216 (mt-10) REVERT: Am 191 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7945 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7802 (mtmt) REVERT: Ao 113 ASN cc_start: 0.8600 (m110) cc_final: 0.8278 (m110) REVERT: Ao 212 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7914 (ttt90) REVERT: Aq 72 GLU cc_start: 0.7904 (pt0) cc_final: 0.7260 (pp20) REVERT: Aq 91 ASP cc_start: 0.8556 (m-30) cc_final: 0.8257 (m-30) REVERT: Aq 191 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7966 (mtt180) REVERT: As 53 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7819 (mttm) REVERT: As 72 GLU cc_start: 0.8048 (pt0) cc_final: 0.7237 (pp20) REVERT: As 95 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8235 (mt-10) REVERT: As 113 ASN cc_start: 0.8203 (m-40) cc_final: 0.8000 (m110) REVERT: As 191 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7716 (mtt180) REVERT: As 208 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8421 (mtt90) REVERT: As 231 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (mmm160) REVERT: Au 98 GLN cc_start: 0.8587 (tt0) cc_final: 0.8227 (tt0) REVERT: Au 191 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8102 (mtt180) REVERT: Aw 113 ASN cc_start: 0.8602 (m-40) cc_final: 0.8220 (m110) REVERT: Aw 231 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7850 (mmt180) REVERT: Ay 91 ASP cc_start: 0.8730 (m-30) cc_final: 0.8503 (m-30) REVERT: Ay 160 MET cc_start: 0.9415 (mmm) cc_final: 0.9183 (mmm) REVERT: Ay 191 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7715 (mtt180) REVERT: Ay 212 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.8170 (ttt90) REVERT: Ba 53 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8055 (mttm) REVERT: Ba 122 ASN cc_start: 0.9097 (m-40) cc_final: 0.8867 (m110) REVERT: Ba 160 MET cc_start: 0.9418 (mmm) cc_final: 0.9149 (mmm) REVERT: Bc 191 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7929 (mtt180) REVERT: Be 95 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8103 (mt-10) REVERT: Be 191 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: Bg 231 ARG cc_start: 0.8441 (mmm160) cc_final: 0.7875 (mmt180) REVERT: Bi 267 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3215 (ptm) REVERT: Bk 108 MET cc_start: 0.8948 (tpt) cc_final: 0.8515 (tpp) REVERT: Bk 191 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: Bm 53 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8016 (mttp) REVERT: Bm 72 GLU cc_start: 0.7979 (pt0) cc_final: 0.7279 (pp20) REVERT: Bm 134 MET cc_start: 0.8693 (ttt) cc_final: 0.8370 (ttt) REVERT: Bm 153 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8375 (tptt) REVERT: Bm 191 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8201 (mtt-85) REVERT: Bm 208 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8475 (mtt90) REVERT: Bo 72 GLU cc_start: 0.8034 (pt0) cc_final: 0.7385 (pp20) REVERT: Bo 79 ASP cc_start: 0.8873 (m-30) cc_final: 0.8628 (m-30) REVERT: Bo 95 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8176 (mt-10) REVERT: Bo 122 ASN cc_start: 0.9077 (m-40) cc_final: 0.8847 (m-40) REVERT: Bo 153 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8211 (mttt) REVERT: Bo 191 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7850 (mtt180) REVERT: Bq 95 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8058 (mt-10) REVERT: Bq 105 GLU cc_start: 0.8128 (tp30) cc_final: 0.7902 (mm-30) REVERT: Bq 153 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8412 (mptt) REVERT: Bs 153 LYS cc_start: 0.9022 (mmpt) cc_final: 0.8247 (mttt) REVERT: Bu 113 ASN cc_start: 0.8448 (m110) cc_final: 0.8020 (m110) REVERT: Bu 122 ASN cc_start: 0.8882 (m110) cc_final: 0.8663 (m-40) REVERT: Bw 91 ASP cc_start: 0.8613 (m-30) cc_final: 0.8209 (m-30) REVERT: Bw 113 ASN cc_start: 0.8700 (m110) cc_final: 0.8389 (m110) REVERT: Bw 197 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: Bw 212 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.8055 (ttt-90) REVERT: By 53 LYS cc_start: 0.8405 (mmtt) cc_final: 0.7663 (mtmt) REVERT: By 72 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7778 (pp20) REVERT: By 95 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8318 (mt-10) REVERT: By 113 ASN cc_start: 0.8052 (m110) cc_final: 0.7718 (m110) REVERT: Ca 53 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7813 (mtmt) REVERT: Ca 98 GLN cc_start: 0.8565 (tt0) cc_final: 0.8210 (tt0) REVERT: Ca 113 ASN cc_start: 0.8180 (m110) cc_final: 0.7937 (m110) REVERT: Ca 258 MET cc_start: 0.6371 (mtt) cc_final: 0.5841 (mmt) REVERT: Cc 53 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7673 (mtmt) REVERT: Cc 95 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8185 (mt-10) REVERT: Cc 134 MET cc_start: 0.8801 (ttt) cc_final: 0.8545 (ttt) REVERT: Cc 191 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7987 (mtt-85) outliers start: 116 outliers final: 78 residues processed: 1044 average time/residue: 1.4678 time to fit residues: 1889.4000 Evaluate side-chains 1002 residues out of total 5488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 905 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 191 ARG Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 153 LYS Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 250 THR Chi-restraints excluded: chain Ay residue 258 MET Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 191 ARG Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 250 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 267 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bw residue 54 MET Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 197 ARG Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 54 optimal weight: 0.5980 chunk 234 optimal weight: 9.9990 chunk 548 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 451 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 513 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Am 98 GLN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN Ao 98 GLN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 GLN ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 113 ASN ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 77 GLN ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** By 189 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.092116 restraints weight = 68520.148| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.03 r_work: 0.2801 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 54376 Z= 0.250 Angle : 0.544 12.640 74144 Z= 0.269 Chirality : 0.040 0.146 8372 Planarity : 0.004 0.050 9184 Dihedral : 10.670 59.735 9100 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.39 % Allowed : 30.32 % Favored : 67.29 % 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: 0.22 (0.11), residues: 6272 helix: 1.37 (0.11), residues: 2492 sheet: -0.09 (0.25), residues: 392 loop : -0.75 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAw 132 HIS 0.002 0.000 HISAm 259 PHE 0.013 0.002 PHEBm 202 TYR 0.016 0.001 TYRBi 198 ARG 0.008 0.000 ARGAa 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34699.01 seconds wall clock time: 593 minutes 9.10 seconds (35589.10 seconds total)