Starting phenix.real_space_refine on Sun Aug 9 07:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.map" model { file = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ope_17050/08_2026/8ope_17050.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 105 5.49 5 S 252 5.16 5 C 20727 2.51 5 N 5670 2.21 5 O 6657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33411 Number of models: 1 Model: "" Number of chains: 2 Chain: "Aa" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} Chain: "Ab" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNAv2': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Restraints were copied for chains: Ac, Ae, Ag, Ai, Ak, Am, Ao, Aq, As, Au, Aw, Ay, Ba, Bc, Be, Bg, Bi, Bk, Bm, Bo, Ad, Af, Ah, Aj, Al, An, Ap, Ar, At, Av, Ax, Az, Bb, Bd, Bf, Bh, Bj, Bl, Bn, Bp Time building chain proxies: 3.23, per 1000 atoms: 0.10 Number of scatterers: 33411 At special positions: 0 Unit cell: (142.442, 141.379, 155.198, 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 252 16.00 P 105 15.00 O 6657 8.00 N 5670 7.00 C 20727 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 42 sheets defined 56.5% alpha, 5.4% beta 0 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAa 72 " --> pdb=" O GLUAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAa 80 " --> pdb=" O GLNAa 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAa 81 " --> pdb=" O ILEAa 78 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 152 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 195 through 199 Processing helix chain 'Aa' and resid 210 through 226 Processing helix chain 'Ac' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAc 72 " --> pdb=" O GLUAc 68 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAc 80 " --> pdb=" O GLNAc 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAc 81 " --> pdb=" O ILEAc 78 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 152 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 195 through 199 Processing helix chain 'Ac' and resid 210 through 226 Processing helix chain 'Ae' and resid 66 through 73 removed outlier: 3.740A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAe 80 " --> pdb=" O GLNAe 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAe 81 " --> pdb=" O ILEAe 78 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 152 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 195 through 199 Processing helix chain 'Ae' and resid 210 through 226 Processing helix chain 'Ag' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAg 80 " --> pdb=" O GLNAg 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAg 81 " --> pdb=" O ILEAg 78 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.551A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 152 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 195 through 199 Processing helix chain 'Ag' and resid 210 through 226 Processing helix chain 'Ai' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAi 72 " --> pdb=" O GLUAi 68 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAi 80 " --> pdb=" O GLNAi 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAi 81 " --> pdb=" O ILEAi 78 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 152 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 195 through 199 Processing helix chain 'Ai' and resid 210 through 226 Processing helix chain 'Ak' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAk 72 " --> pdb=" O GLUAk 68 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAk 81 " --> pdb=" O ILEAk 78 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 152 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 Processing helix chain 'Ak' and resid 182 through 188 Processing helix chain 'Ak' and resid 195 through 199 Processing helix chain 'Ak' and resid 210 through 226 Processing helix chain 'Am' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAm 81 " --> pdb=" O ILEAm 78 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 152 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 Processing helix chain 'Am' and resid 182 through 188 Processing helix chain 'Am' and resid 195 through 199 Processing helix chain 'Am' and resid 210 through 226 Processing helix chain 'Ao' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAo 81 " --> pdb=" O ILEAo 78 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 152 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 Processing helix chain 'Ao' and resid 182 through 188 Processing helix chain 'Ao' and resid 195 through 199 Processing helix chain 'Ao' and resid 210 through 226 Processing helix chain 'Aq' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAq 72 " --> pdb=" O GLUAq 68 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 76 through 81 removed outlier: 3.595A pdb=" N ILEAq 80 " --> pdb=" O GLNAq 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAq 81 " --> pdb=" O ILEAq 78 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 152 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 176 Processing helix chain 'Aq' and resid 182 through 188 Processing helix chain 'Aq' and resid 195 through 199 Processing helix chain 'Aq' and resid 210 through 226 Processing helix chain 'As' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAs 72 " --> pdb=" O GLUAs 68 " (cutoff:3.500A) Processing helix chain 'As' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAs 80 " --> pdb=" O GLNAs 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAs 81 " --> pdb=" O ILEAs 78 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 152 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 176 Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 195 through 199 Processing helix chain 'As' and resid 210 through 226 Processing helix chain 'Au' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAu 72 " --> pdb=" O GLUAu 68 " (cutoff:3.500A) Processing helix chain 'Au' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAu 80 " --> pdb=" O GLNAu 77 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SERAu 81 " --> pdb=" O ILEAu 78 " (cutoff:3.500A) Processing helix chain 'Au' and resid 86 through 102 Processing helix chain 'Au' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 152 Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 176 Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 195 through 199 Processing helix chain 'Au' and resid 210 through 226 Processing helix chain 'Aw' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAw 72 " --> pdb=" O GLUAw 68 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAw 80 " --> pdb=" O GLNAw 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAw 81 " --> pdb=" O ILEAw 78 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 86 through 102 Processing helix chain 'Aw' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 152 Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 176 Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 195 through 199 Processing helix chain 'Aw' and resid 210 through 226 Processing helix chain 'Ay' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAy 72 " --> pdb=" O GLUAy 68 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAy 80 " --> pdb=" O GLNAy 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAy 81 " --> pdb=" O ILEAy 78 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 86 through 102 Processing helix chain 'Ay' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAy 111 " --> pdb=" O GLUAy 107 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 145 through 152 Processing helix chain 'Ay' and resid 155 through 161 Processing helix chain 'Ay' and resid 163 through 176 Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 195 through 199 Processing helix chain 'Ay' and resid 210 through 226 Processing helix chain 'Ba' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBa 72 " --> pdb=" O GLUBa 68 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBa 80 " --> pdb=" O GLNBa 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBa 81 " --> pdb=" O ILEBa 78 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 86 through 102 Processing helix chain 'Ba' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALBa 111 " --> pdb=" O GLUBa 107 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 145 through 152 Processing helix chain 'Ba' and resid 155 through 161 Processing helix chain 'Ba' and resid 163 through 176 Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 195 through 199 Processing helix chain 'Ba' and resid 210 through 226 Processing helix chain 'Bc' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBc 72 " --> pdb=" O GLUBc 68 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 76 through 81 removed outlier: 3.595A pdb=" N ILEBc 80 " --> pdb=" O GLNBc 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBc 81 " --> pdb=" O ILEBc 78 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 86 through 102 Processing helix chain 'Bc' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBc 111 " --> pdb=" O GLUBc 107 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 145 through 152 Processing helix chain 'Bc' and resid 155 through 161 Processing helix chain 'Bc' and resid 163 through 176 Processing helix chain 'Bc' and resid 182 through 188 Processing helix chain 'Bc' and resid 195 through 199 Processing helix chain 'Bc' and resid 210 through 226 Processing helix chain 'Be' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBe 72 " --> pdb=" O GLUBe 68 " (cutoff:3.500A) Processing helix chain 'Be' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBe 80 " --> pdb=" O GLNBe 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERBe 81 " --> pdb=" O ILEBe 78 " (cutoff:3.500A) Processing helix chain 'Be' and resid 86 through 102 Processing helix chain 'Be' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBe 111 " --> pdb=" O GLUBe 107 " (cutoff:3.500A) Processing helix chain 'Be' and resid 145 through 152 Processing helix chain 'Be' and resid 155 through 161 Processing helix chain 'Be' and resid 163 through 176 Processing helix chain 'Be' and resid 182 through 188 Processing helix chain 'Be' and resid 195 through 199 Processing helix chain 'Be' and resid 210 through 226 Processing helix chain 'Bg' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBg 72 " --> pdb=" O GLUBg 68 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBg 80 " --> pdb=" O GLNBg 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERBg 81 " --> pdb=" O ILEBg 78 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 86 through 102 Processing helix chain 'Bg' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBg 111 " --> pdb=" O GLUBg 107 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 145 through 152 Processing helix chain 'Bg' and resid 155 through 161 Processing helix chain 'Bg' and resid 163 through 176 Processing helix chain 'Bg' and resid 182 through 188 Processing helix chain 'Bg' and resid 195 through 199 Processing helix chain 'Bg' and resid 210 through 226 Processing helix chain 'Bi' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBi 72 " --> pdb=" O GLUBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBi 80 " --> pdb=" O GLNBi 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBi 81 " --> pdb=" O ILEBi 78 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 86 through 102 Processing helix chain 'Bi' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBi 111 " --> pdb=" O GLUBi 107 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 145 through 152 Processing helix chain 'Bi' and resid 155 through 161 Processing helix chain 'Bi' and resid 163 through 176 Processing helix chain 'Bi' and resid 182 through 188 Processing helix chain 'Bi' and resid 195 through 199 Processing helix chain 'Bi' and resid 210 through 226 Processing helix chain 'Bk' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBk 72 " --> pdb=" O GLUBk 68 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBk 80 " --> pdb=" O GLNBk 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBk 81 " --> pdb=" O ILEBk 78 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 86 through 102 Processing helix chain 'Bk' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBk 111 " --> pdb=" O GLUBk 107 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 152 Processing helix chain 'Bk' and resid 155 through 161 Processing helix chain 'Bk' and resid 163 through 176 Processing helix chain 'Bk' and resid 182 through 188 Processing helix chain 'Bk' and resid 195 through 199 Processing helix chain 'Bk' and resid 210 through 226 Processing helix chain 'Bm' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBm 72 " --> pdb=" O GLUBm 68 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBm 80 " --> pdb=" O GLNBm 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBm 81 " --> pdb=" O ILEBm 78 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 86 through 102 Processing helix chain 'Bm' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBm 111 " --> pdb=" O GLUBm 107 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 152 Processing helix chain 'Bm' and resid 155 through 161 Processing helix chain 'Bm' and resid 163 through 176 Processing helix chain 'Bm' and resid 182 through 188 Processing helix chain 'Bm' and resid 195 through 199 Processing helix chain 'Bm' and resid 210 through 226 Processing helix chain 'Bo' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBo 72 " --> pdb=" O GLUBo 68 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBo 80 " --> pdb=" O GLNBo 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBo 81 " --> pdb=" O ILEBo 78 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 86 through 102 Processing helix chain 'Bo' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBo 111 " --> pdb=" O GLUBo 107 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 145 through 152 Processing helix chain 'Bo' and resid 155 through 161 Processing helix chain 'Bo' and resid 163 through 176 Processing helix chain 'Bo' and resid 182 through 188 Processing helix chain 'Bo' and resid 195 through 199 Processing helix chain 'Bo' 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 1449 hydrogen bonds defined for protein. 4095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6226 1.32 - 1.45: 8662 1.45 - 1.57: 18733 1.57 - 1.69: 189 1.69 - 1.81: 483 Bond restraints: 34293 Sorted by residual: bond pdb=" C ALAAo 196 " pdb=" N ARGAo 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.22e+01 bond pdb=" C ALAAm 196 " pdb=" N ARGAm 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" C ALABc 196 " pdb=" N ARGBc 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" C ALABe 196 " pdb=" N ARGBe 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.20e+01 bond pdb=" C ALABo 196 " pdb=" N ARGBo 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.20e+01 ... (remaining 34288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 45445 1.93 - 3.86: 1175 3.86 - 5.79: 168 5.79 - 7.72: 42 7.72 - 9.65: 21 Bond angle restraints: 46851 Sorted by residual: angle pdb=" C PROAa 45 " pdb=" CA PROAa 45 " pdb=" CB PROAa 45 " ideal model delta sigma weight residual 111.40 104.95 6.45 9.10e-01 1.21e+00 5.02e+01 angle pdb=" C PROBg 45 " pdb=" CA PROBg 45 " pdb=" CB PROBg 45 " ideal model delta sigma weight residual 111.40 104.96 6.44 9.10e-01 1.21e+00 5.01e+01 angle pdb=" C PROAy 45 " pdb=" CA PROAy 45 " pdb=" CB PROAy 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 5.00e+01 angle pdb=" C PROAe 45 " pdb=" CA PROAe 45 " pdb=" CB PROAe 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 5.00e+01 angle pdb=" C PROBk 45 " pdb=" CA PROBk 45 " pdb=" CB PROBk 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 4.99e+01 ... (remaining 46846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 17634 14.88 - 29.75: 1980 29.75 - 44.63: 1155 44.63 - 59.50: 441 59.50 - 74.38: 84 Dihedral angle restraints: 21294 sinusoidal: 9744 harmonic: 11550 Sorted by residual: dihedral pdb=" C4' UAv 4 " pdb=" C3' UAv 4 " pdb=" C2' UAv 4 " pdb=" C1' UAv 4 " ideal model delta sinusoidal sigma weight residual 36.34 -38.03 74.38 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' UBb 4 " pdb=" C3' UBb 4 " pdb=" C2' UBb 4 " pdb=" C1' UBb 4 " ideal model delta sinusoidal sigma weight residual 36.34 -38.01 74.35 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' UAz 4 " pdb=" C3' UAz 4 " pdb=" C2' UAz 4 " pdb=" C1' UAz 4 " ideal model delta sinusoidal sigma weight residual 36.34 -38.01 74.35 1 3.10e+00 1.04e-01 7.30e+02 ... (remaining 21291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4421 0.056 - 0.112: 628 0.112 - 0.168: 96 0.168 - 0.224: 62 0.224 - 0.280: 64 Chirality restraints: 5271 Sorted by residual: chirality pdb=" C3' UBn 4 " pdb=" C4' UBn 4 " pdb=" O3' UBn 4 " pdb=" C2' UBn 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' UAr 4 " pdb=" C4' UAr 4 " pdb=" O3' UAr 4 " pdb=" C2' UAr 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' UAd 4 " pdb=" C4' UAd 4 " pdb=" O3' UAd 4 " pdb=" C2' UAd 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5268 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PROBm 45 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C PROBm 45 " 0.035 2.00e-02 2.50e+03 pdb=" O PROBm 45 " -0.013 2.00e-02 2.50e+03 pdb=" N ARGBm 46 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAo 45 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C PROAo 45 " 0.035 2.00e-02 2.50e+03 pdb=" O PROAo 45 " -0.013 2.00e-02 2.50e+03 pdb=" N ARGAo 46 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROBg 45 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C PROBg 45 " -0.035 2.00e-02 2.50e+03 pdb=" O PROBg 45 " 0.013 2.00e-02 2.50e+03 pdb=" N ARGBg 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 15661 2.94 - 3.43: 35800 3.43 - 3.92: 58418 3.92 - 4.41: 70627 4.41 - 4.90: 108364 Nonbonded interactions: 288870 Sorted by model distance: nonbonded pdb=" OE2 GLUBe 121 " pdb=" OH TYRBe 180 " model vdw 2.456 3.040 nonbonded pdb=" OE2 GLUBg 121 " pdb=" OH TYRBg 180 " model vdw 2.456 3.040 nonbonded pdb=" OE2 GLUBo 121 " pdb=" OH TYRBo 180 " model vdw 2.456 3.040 nonbonded pdb=" OE2 GLUAu 121 " pdb=" OH TYRAu 180 " model vdw 2.456 3.040 nonbonded pdb=" OE2 GLUAc 121 " pdb=" OH TYRAc 180 " model vdw 2.456 3.040 ... (remaining 288865 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: 0.13 Found NCS groups: ncs_group { reference = chain 'Aa' 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 'Ba' selection = chain 'Bc' selection = chain 'Be' selection = chain 'Bg' selection = chain 'Bi' selection = chain 'Bk' selection = chain 'Bm' selection = chain 'Bo' } ncs_group { reference = 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 'Bb' selection = chain 'Bd' selection = chain 'Bf' selection = chain 'Bh' selection = chain 'Bj' selection = chain 'Bl' selection = chain 'Bn' selection = chain 'Bp' } 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.047 34293 Z= 0.344 Angle : 0.743 9.646 46851 Z= 0.457 Chirality : 0.054 0.280 5271 Planarity : 0.007 0.076 5712 Dihedral : 18.118 74.376 13818 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.24 % Allowed : 19.05 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 3864 helix: 1.19 (0.12), residues: 1890 sheet: 0.57 (0.32), residues: 252 loop : -1.21 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAg 212 TYR 0.018 0.002 TYRAi 143 PHE 0.011 0.002 PHEAe 163 TRP 0.009 0.001 TRPAo 132 HIS 0.004 0.001 HISAu 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.34 (34293) covalent geometry : angle 0.74270 / 0.46 (46851) hydrogen bonds : bond 0.14025 / 9.04 ( 1449) hydrogen bonds : angle 5.35304 / 3.77 ( 4095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1064 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7117 (mt-10) REVERT: Ac 95 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7380 (mt-10) REVERT: Ae 134 MET cc_start: 0.7317 (ttt) cc_final: 0.7085 (ttt) REVERT: Ae 146 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8113 (ttmm) REVERT: Ak 60 LYS cc_start: 0.8503 (mmtp) cc_final: 0.7944 (mmtp) REVERT: Am 60 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8075 (mmtp) REVERT: Ao 112 MET cc_start: 0.8393 (mmm) cc_final: 0.8120 (mmp) REVERT: Aq 95 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7580 (mt-10) REVERT: Aq 134 MET cc_start: 0.8073 (ttt) cc_final: 0.7589 (ttt) REVERT: As 54 MET cc_start: 0.7579 (ttp) cc_final: 0.7364 (ttp) REVERT: As 134 MET cc_start: 0.7625 (ttt) cc_final: 0.7371 (ttt) REVERT: As 146 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8144 (tppt) REVERT: As 151 ASN cc_start: 0.8959 (m-40) cc_final: 0.8565 (m110) REVERT: Au 46 ARG cc_start: 0.9015 (mpt180) cc_final: 0.8798 (mpt180) REVERT: Au 173 MET cc_start: 0.7871 (ttp) cc_final: 0.7591 (tmm) REVERT: Aw 134 MET cc_start: 0.7437 (ttt) cc_final: 0.7158 (ttt) REVERT: Ay 60 LYS cc_start: 0.8464 (mmtp) cc_final: 0.8218 (mmtp) REVERT: Ay 134 MET cc_start: 0.7868 (ttt) cc_final: 0.7341 (ttt) REVERT: Ba 50 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7913 (tt) REVERT: Ba 60 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8456 (mmtm) REVERT: Ba 125 SER cc_start: 0.8812 (p) cc_final: 0.8541 (p) REVERT: Be 89 GLN cc_start: 0.8478 (mt0) cc_final: 0.8090 (mt0) REVERT: Be 95 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6680 (mt-10) REVERT: Be 191 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: Bi 50 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7800 (mt) REVERT: Bi 60 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8419 (mmtm) REVERT: Bi 121 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8218 (mm-30) REVERT: Bi 134 MET cc_start: 0.8016 (ttt) cc_final: 0.7767 (ttt) REVERT: Bi 208 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8185 (ptm160) REVERT: Bk 121 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8051 (mm-30) REVERT: Bm 55 ARG cc_start: 0.8313 (tpt-90) cc_final: 0.7951 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6723 (mt-10) REVERT: Bm 191 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.7501 (mtp-110) outliers start: 8 outliers final: 2 residues processed: 1068 average time/residue: 0.2144 time to fit residues: 359.8106 Evaluate side-chains 962 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 958 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 50 ILE Chi-restraints excluded: chain Ba residue 50 ILE Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bo residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 151 ASN Ae 151 ASN Ag 151 ASN Ao 87 GLN Aq 151 ASN Au 151 ASN Ay 151 ASN Bc 66 ASN Be 98 GLN Bk 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.113761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.094805 restraints weight = 38777.482| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.83 r_work: 0.2673 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34293 Z= 0.152 Angle : 0.710 14.771 46851 Z= 0.314 Chirality : 0.065 0.659 5271 Planarity : 0.005 0.045 5712 Dihedral : 12.854 59.954 5951 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.05 % Allowed : 18.90 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 3864 helix: 1.34 (0.12), residues: 1890 sheet: 0.87 (0.30), residues: 210 loop : -0.97 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBc 208 TYR 0.010 0.001 TYRAc 184 PHE 0.018 0.002 PHEAo 200 TRP 0.009 0.001 TRPAg 93 HIS 0.005 0.001 HISAw 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (34293) covalent geometry : angle 0.70988 / 0.31 (46851) hydrogen bonds : bond 0.03703 / 2.42 ( 1449) hydrogen bonds : angle 4.12351 / 2.93 ( 4095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1104 time to evaluate : 1.207 Fit side-chains REVERT: Aa 55 ARG cc_start: 0.8554 (mtp180) cc_final: 0.8297 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8027 (mt-10) REVERT: Ac 95 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8212 (mt-10) REVERT: Ac 181 MET cc_start: 0.9190 (tpp) cc_final: 0.8977 (tpp) REVERT: Ae 108 MET cc_start: 0.9295 (tpt) cc_final: 0.8584 (tpt) REVERT: Ae 134 MET cc_start: 0.8540 (ttt) cc_final: 0.8282 (ttt) REVERT: Ae 146 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8207 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9079 (tt0) cc_final: 0.8571 (tt0) REVERT: Ai 46 ARG cc_start: 0.8623 (mpt180) cc_final: 0.8339 (mpt180) REVERT: Ai 65 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9089 (mp) REVERT: Ai 95 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7955 (mt-10) REVERT: Ai 139 GLU cc_start: 0.7798 (tp30) cc_final: 0.7336 (tm-30) REVERT: Ai 158 GLN cc_start: 0.9414 (mt0) cc_final: 0.9117 (mt0) REVERT: Ai 173 MET cc_start: 0.8251 (ttp) cc_final: 0.8022 (ttp) REVERT: Ai 212 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7597 (ttp-170) REVERT: Ak 71 LEU cc_start: 0.8820 (mm) cc_final: 0.8577 (mm) REVERT: Ak 180 TYR cc_start: 0.9168 (t80) cc_final: 0.8959 (t80) REVERT: Ak 208 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8667 (ptp-110) REVERT: Am 71 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8836 (mm) REVERT: Am 110 THR cc_start: 0.8844 (m) cc_final: 0.8604 (m) REVERT: Am 191 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7661 (mtp-110) REVERT: Ao 180 TYR cc_start: 0.9249 (t80) cc_final: 0.8790 (t80) REVERT: Aq 55 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.8029 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8220 (mt-10) REVERT: Aq 113 ASN cc_start: 0.8951 (m-40) cc_final: 0.8417 (m-40) REVERT: Aq 134 MET cc_start: 0.8910 (ttt) cc_final: 0.8453 (ttt) REVERT: Aq 180 TYR cc_start: 0.9113 (t80) cc_final: 0.8811 (t80) REVERT: Aq 181 MET cc_start: 0.9064 (tpp) cc_final: 0.8706 (tpp) REVERT: Aq 191 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7569 (mtp-110) REVERT: Aq 212 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.7967 (ttp-170) REVERT: Aq 214 ARG cc_start: 0.8865 (ttp-170) cc_final: 0.8640 (ttp80) REVERT: Aq 220 MET cc_start: 0.8829 (mtp) cc_final: 0.8509 (mtm) REVERT: As 46 ARG cc_start: 0.9294 (mpt180) cc_final: 0.8993 (mpt180) REVERT: As 55 ARG cc_start: 0.8429 (tpt-90) cc_final: 0.8134 (tpt-90) REVERT: As 95 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8095 (mt-10) REVERT: As 148 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (mt) REVERT: As 160 MET cc_start: 0.9322 (mmm) cc_final: 0.9014 (mmt) REVERT: As 191 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7255 (mtp-110) REVERT: As 201 ASP cc_start: 0.8515 (t0) cc_final: 0.8310 (t0) REVERT: As 212 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.7966 (ttp-170) REVERT: Au 46 ARG cc_start: 0.9162 (mpt180) cc_final: 0.8654 (mpt180) REVERT: Aw 95 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8030 (mt-10) REVERT: Aw 134 MET cc_start: 0.8521 (ttt) cc_final: 0.8072 (ttt) REVERT: Ay 46 ARG cc_start: 0.8635 (mpt180) cc_final: 0.8392 (mpt180) REVERT: Ay 56 MET cc_start: 0.8154 (mtt) cc_final: 0.7722 (mtt) REVERT: Ay 108 MET cc_start: 0.8696 (tpt) cc_final: 0.8165 (tpt) REVERT: Ay 204 GLU cc_start: 0.8854 (tt0) cc_final: 0.8350 (tt0) REVERT: Ba 191 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7611 (mtp-110) REVERT: Bc 95 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7581 (mt-10) REVERT: Bc 112 MET cc_start: 0.9109 (mmp) cc_final: 0.8885 (mmm) REVERT: Bc 212 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7540 (ttp-170) REVERT: Be 89 GLN cc_start: 0.9157 (mt0) cc_final: 0.8924 (mt0) REVERT: Be 95 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7808 (mt-10) REVERT: Be 177 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8196 (ttmm) REVERT: Bg 55 ARG cc_start: 0.7859 (tpt-90) cc_final: 0.7628 (tpt-90) REVERT: Bg 212 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7683 (ttp-170) REVERT: Bi 79 ASP cc_start: 0.8831 (m-30) cc_final: 0.8508 (m-30) REVERT: Bi 95 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7826 (mt-10) REVERT: Bi 125 SER cc_start: 0.8808 (p) cc_final: 0.8532 (t) REVERT: Bi 135 MET cc_start: 0.8661 (mmm) cc_final: 0.8318 (mmm) REVERT: Bi 204 GLU cc_start: 0.8910 (tt0) cc_final: 0.8652 (tt0) REVERT: Bi 212 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7503 (ttp-170) REVERT: Bk 121 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8441 (mm-30) REVERT: Bk 212 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7612 (ptm-80) REVERT: Bm 55 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.7993 (tpt-90) REVERT: Bm 69 HIS cc_start: 0.8550 (t-90) cc_final: 0.8283 (t70) REVERT: Bm 95 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7799 (mt-10) REVERT: Bm 180 TYR cc_start: 0.8956 (t80) cc_final: 0.8726 (t80) REVERT: Bo 55 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8007 (tpt-90) REVERT: Bo 65 LEU cc_start: 0.8700 (mp) cc_final: 0.8496 (mt) REVERT: Bo 95 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Bo 204 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: Bo 215 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7767 (mt-10) outliers start: 103 outliers final: 43 residues processed: 1147 average time/residue: 0.2052 time to fit residues: 372.6951 Evaluate side-chains 1104 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1056 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 159 ILE Chi-restraints excluded: chain Ai residue 65 LEU Chi-restraints excluded: chain Ai residue 159 ILE Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 208 ARG Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 65 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 142 GLU Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 50 ILE Chi-restraints excluded: chain As residue 148 ILE Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Aw residue 159 ILE Chi-restraints excluded: chain Ay residue 107 GLU Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ba residue 50 ILE Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 122 ASN Chi-restraints excluded: chain Be residue 67 LEU Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bk residue 50 ILE Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 68 GLU Chi-restraints excluded: chain Bo residue 67 LEU Chi-restraints excluded: chain Bo residue 178 GLU Chi-restraints excluded: chain Bo residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 355 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 281 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 113 ASN Ae 151 ASN Ag 151 ASN Am 98 GLN Am 151 ASN Ao 87 GLN Ao 151 ASN Ao 158 GLN Aq 151 ASN Au 129 ASN Ay 151 ASN Ba 151 ASN Bc 151 ASN Be 98 GLN ** Bk 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.103796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.084666 restraints weight = 39570.487| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 1.88 r_work: 0.2513 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 34293 Z= 0.238 Angle : 0.688 10.095 46851 Z= 0.316 Chirality : 0.063 0.598 5271 Planarity : 0.005 0.055 5712 Dihedral : 14.759 132.252 5945 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.28 % Allowed : 19.08 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 3864 helix: 1.19 (0.12), residues: 1890 sheet: 1.12 (0.28), residues: 210 loop : -1.02 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBi 191 TYR 0.014 0.002 TYRAg 143 PHE 0.018 0.002 PHEAm 200 TRP 0.013 0.001 TRPBe 132 HIS 0.005 0.001 HISBa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (34293) covalent geometry : angle 0.68833 / 0.32 (46851) hydrogen bonds : bond 0.04422 / 2.88 ( 1449) hydrogen bonds : angle 4.06421 / 2.89 ( 4095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1265 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8538 (mtp180) cc_final: 0.8329 (tpt-90) REVERT: Aa 79 ASP cc_start: 0.9097 (m-30) cc_final: 0.8893 (m-30) REVERT: Aa 95 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8454 (mt-10) REVERT: Aa 108 MET cc_start: 0.9404 (tpt) cc_final: 0.9072 (tpt) REVERT: Aa 191 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7641 (mtp-110) REVERT: Aa 206 THR cc_start: 0.9499 (p) cc_final: 0.9268 (t) REVERT: Aa 212 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8337 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8620 (mmm160) cc_final: 0.7828 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8996 (m-30) cc_final: 0.8708 (m-30) REVERT: Ac 153 LYS cc_start: 0.9186 (mptt) cc_final: 0.8860 (mmtm) REVERT: Ac 181 MET cc_start: 0.9176 (tpp) cc_final: 0.8769 (tpp) REVERT: Ae 187 VAL cc_start: 0.9340 (t) cc_final: 0.9137 (m) REVERT: Ae 191 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7601 (mtp-110) REVERT: Ag 95 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8367 (mt-10) REVERT: Ag 112 MET cc_start: 0.9495 (mmt) cc_final: 0.9291 (mmm) REVERT: Ag 177 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8659 (mtpt) REVERT: Ag 204 GLU cc_start: 0.9218 (tt0) cc_final: 0.8984 (tt0) REVERT: Ai 95 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8211 (mt-10) REVERT: Ai 174 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8666 (mmm-85) REVERT: Ai 206 THR cc_start: 0.9520 (p) cc_final: 0.9232 (t) REVERT: Ai 212 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8075 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7791 (mt-10) REVERT: Ak 46 ARG cc_start: 0.9073 (mpt180) cc_final: 0.8738 (mpt180) REVERT: Ak 71 LEU cc_start: 0.8895 (mm) cc_final: 0.8518 (mm) REVERT: Ak 79 ASP cc_start: 0.9131 (m-30) cc_final: 0.8884 (m-30) REVERT: Ak 134 MET cc_start: 0.9087 (ttt) cc_final: 0.8769 (ttt) REVERT: Ak 142 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: Ak 190 LEU cc_start: 0.9010 (tp) cc_final: 0.8803 (tp) REVERT: Ak 191 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7569 (mtp-110) REVERT: Ak 204 GLU cc_start: 0.9209 (tt0) cc_final: 0.8988 (tt0) REVERT: Ak 212 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8337 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7875 (mt-10) REVERT: Am 67 LEU cc_start: 0.8546 (mt) cc_final: 0.8335 (mm) REVERT: Am 71 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9028 (mm) REVERT: Am 110 THR cc_start: 0.9280 (m) cc_final: 0.9077 (m) REVERT: Am 136 ASP cc_start: 0.8999 (t0) cc_final: 0.8635 (t0) REVERT: Ao 110 THR cc_start: 0.9114 (m) cc_final: 0.8825 (m) REVERT: Ao 134 MET cc_start: 0.9087 (ttt) cc_final: 0.8606 (ttt) REVERT: Ao 175 ASN cc_start: 0.8969 (m-40) cc_final: 0.8548 (m110) REVERT: Ao 180 TYR cc_start: 0.9362 (t80) cc_final: 0.8966 (t80) REVERT: Ao 212 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8226 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8223 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8270 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9275 (m-40) cc_final: 0.9059 (m110) REVERT: Aq 212 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8096 (ttp-170) REVERT: As 55 ARG cc_start: 0.8693 (tpt-90) cc_final: 0.8185 (tpt-90) REVERT: As 95 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8268 (mt-10) REVERT: As 160 MET cc_start: 0.9536 (mmm) cc_final: 0.9229 (mmt) REVERT: As 191 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7316 (mtp-110) REVERT: As 212 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8094 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9063 (m-30) cc_final: 0.8818 (m-30) REVERT: Au 95 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8075 (mt-10) REVERT: Au 177 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8595 (ttmm) REVERT: Au 180 TYR cc_start: 0.9276 (t80) cc_final: 0.8986 (t80) REVERT: Au 208 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8169 (mtt90) REVERT: Aw 67 LEU cc_start: 0.8708 (mt) cc_final: 0.8211 (mm) REVERT: Aw 71 LEU cc_start: 0.8862 (mm) cc_final: 0.8642 (mm) REVERT: Aw 134 MET cc_start: 0.9092 (ttt) cc_final: 0.8537 (ttt) REVERT: Aw 190 LEU cc_start: 0.8936 (tp) cc_final: 0.8734 (tp) REVERT: Ay 46 ARG cc_start: 0.9130 (mpt180) cc_final: 0.8863 (mpt180) REVERT: Ay 95 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8317 (mt-10) REVERT: Ay 184 TYR cc_start: 0.9316 (t80) cc_final: 0.9103 (t80) REVERT: Ay 208 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (ptm160) REVERT: Ba 180 TYR cc_start: 0.9330 (t80) cc_final: 0.9126 (t80) REVERT: Ba 212 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.8092 (ttp-170) REVERT: Bc 55 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8267 (tpt-90) REVERT: Bc 95 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8251 (mt-10) REVERT: Bc 206 THR cc_start: 0.9493 (p) cc_final: 0.9292 (t) REVERT: Bc 212 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8011 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7761 (mt-10) REVERT: Be 55 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8444 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9139 (m-30) cc_final: 0.8867 (m-30) REVERT: Be 95 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8212 (mt-10) REVERT: Be 151 ASN cc_start: 0.9411 (m-40) cc_final: 0.9168 (m-40) REVERT: Be 177 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8568 (ttmm) REVERT: Be 191 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7907 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8274 (ttp-170) REVERT: Bg 46 ARG cc_start: 0.9122 (mpt180) cc_final: 0.8721 (mpt180) REVERT: Bg 99 LEU cc_start: 0.8745 (tp) cc_final: 0.8508 (tp) REVERT: Bg 135 MET cc_start: 0.9055 (mmm) cc_final: 0.8357 (mmt) REVERT: Bg 153 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8714 (mptt) REVERT: Bg 204 GLU cc_start: 0.9024 (tt0) cc_final: 0.8791 (tt0) REVERT: Bg 212 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8114 (ttp-170) REVERT: Bi 95 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8272 (mt-10) REVERT: Bi 151 ASN cc_start: 0.9237 (m-40) cc_final: 0.8862 (m110) REVERT: Bi 177 LYS cc_start: 0.8752 (mttt) cc_final: 0.8315 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7529 (mtp-110) REVERT: Bi 208 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7716 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8033 (ttp-170) REVERT: Bk 67 LEU cc_start: 0.8654 (mt) cc_final: 0.8357 (mm) REVERT: Bk 102 ASP cc_start: 0.8421 (t70) cc_final: 0.8127 (t0) REVERT: Bk 110 THR cc_start: 0.9175 (m) cc_final: 0.8819 (m) REVERT: Bk 134 MET cc_start: 0.9035 (ttt) cc_final: 0.8422 (ttt) REVERT: Bk 174 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8694 (mtp180) REVERT: Bk 212 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8203 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8246 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8524 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8167 (ttp-170) REVERT: Bo 56 MET cc_start: 0.9222 (mmt) cc_final: 0.9002 (mmt) REVERT: Bo 95 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8065 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8212 (ttp-170) outliers start: 111 outliers final: 64 residues processed: 1324 average time/residue: 0.2208 time to fit residues: 466.2706 Evaluate side-chains 1233 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1164 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 122 ASN Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ak residue 51 THR Chi-restraints excluded: chain Ak residue 122 ASN Chi-restraints excluded: chain Ak residue 142 GLU Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 65 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Ay residue 103 ILE Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 208 ARG Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 44 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 178 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 153 LYS Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 68 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 182 optimal weight: 6.9990 chunk 348 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 151 ASN Ac 158 GLN Ae 151 ASN Ae 158 GLN Ag 151 ASN Ao 151 ASN Ay 151 ASN Ay 158 GLN Bg 158 GLN Bi 158 GLN Bk 66 ASN Bm 151 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.103677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.084615 restraints weight = 39756.312| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.88 r_work: 0.2503 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2341 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34293 Z= 0.228 Angle : 0.663 9.458 46851 Z= 0.304 Chirality : 0.063 0.588 5271 Planarity : 0.005 0.057 5712 Dihedral : 15.146 135.939 5943 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.43 % Allowed : 19.67 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 3864 helix: 1.20 (0.12), residues: 1890 sheet: 1.01 (0.27), residues: 210 loop : -1.02 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGBc 174 TYR 0.016 0.001 TYRBo 198 PHE 0.017 0.002 PHEBa 200 TRP 0.012 0.001 TRPBe 132 HIS 0.004 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (34293) covalent geometry : angle 0.66277 / 0.30 (46851) hydrogen bonds : bond 0.04106 / 2.67 ( 1449) hydrogen bonds : angle 3.96773 / 2.82 ( 4095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1205 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8415 (mt-10) REVERT: Aa 191 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7592 (mtp85) REVERT: Aa 206 THR cc_start: 0.9545 (p) cc_final: 0.9317 (t) REVERT: Aa 212 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8328 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8579 (mmm160) cc_final: 0.7883 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.9002 (m-30) cc_final: 0.8676 (m-30) REVERT: Ae 50 ILE cc_start: 0.8412 (mt) cc_final: 0.8119 (tt) REVERT: Ae 187 VAL cc_start: 0.9356 (t) cc_final: 0.9112 (m) REVERT: Ag 95 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8370 (mt-10) REVERT: Ag 112 MET cc_start: 0.9482 (mmt) cc_final: 0.9268 (mmm) REVERT: Ag 177 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8611 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9216 (tt0) cc_final: 0.8963 (tt0) REVERT: Ai 95 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8223 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9139 (m-40) cc_final: 0.8755 (m-40) REVERT: Ai 172 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8061 (mm-30) REVERT: Ai 175 ASN cc_start: 0.8916 (m-40) cc_final: 0.8077 (m110) REVERT: Ai 215 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7772 (mt-10) REVERT: Ak 71 LEU cc_start: 0.8944 (mm) cc_final: 0.8526 (mm) REVERT: Ak 79 ASP cc_start: 0.9106 (m-30) cc_final: 0.8880 (m-30) REVERT: Ak 134 MET cc_start: 0.9033 (ttt) cc_final: 0.8791 (ttt) REVERT: Ak 142 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: Ak 168 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8644 (mt-10) REVERT: Ak 191 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7603 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8345 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7941 (mt-10) REVERT: Am 110 THR cc_start: 0.9296 (m) cc_final: 0.9093 (m) REVERT: Am 139 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: Am 191 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7694 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8220 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9123 (m) cc_final: 0.8808 (m) REVERT: Ao 129 ASN cc_start: 0.9266 (p0) cc_final: 0.9010 (p0) REVERT: Ao 134 MET cc_start: 0.9058 (ttt) cc_final: 0.8541 (ttt) REVERT: Ao 175 ASN cc_start: 0.8984 (m-40) cc_final: 0.8676 (m-40) REVERT: Ao 180 TYR cc_start: 0.9363 (t80) cc_final: 0.9152 (t80) REVERT: Ao 212 ARG cc_start: 0.8744 (ttp-110) cc_final: 0.8275 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.8265 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8251 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9329 (m-40) cc_final: 0.9091 (m110) REVERT: Aq 212 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8052 (ttp-170) REVERT: As 55 ARG cc_start: 0.8698 (tpt-90) cc_final: 0.8094 (tpt-90) REVERT: As 95 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8251 (mt-10) REVERT: As 160 MET cc_start: 0.9485 (mmm) cc_final: 0.9164 (mmt) REVERT: As 212 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.7963 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9047 (m-30) cc_final: 0.8724 (m-30) REVERT: Au 95 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8038 (mt-10) REVERT: Au 177 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8598 (ttmm) REVERT: Au 208 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8112 (mtt90) REVERT: Aw 67 LEU cc_start: 0.8784 (mt) cc_final: 0.8383 (mm) REVERT: Aw 71 LEU cc_start: 0.8911 (mm) cc_final: 0.8686 (mm) REVERT: Aw 134 MET cc_start: 0.9103 (ttt) cc_final: 0.8518 (ttt) REVERT: Ay 46 ARG cc_start: 0.9179 (mpt180) cc_final: 0.8886 (mpt180) REVERT: Ay 56 MET cc_start: 0.9027 (mtt) cc_final: 0.8597 (mtt) REVERT: Ay 77 GLN cc_start: 0.8810 (mt0) cc_final: 0.8559 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8350 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8489 (ttmm) REVERT: Ba 180 TYR cc_start: 0.9364 (t80) cc_final: 0.9128 (t80) REVERT: Ba 212 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.8136 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8319 (mt-10) REVERT: Bc 97 VAL cc_start: 0.9400 (t) cc_final: 0.9149 (t) REVERT: Bc 206 THR cc_start: 0.9545 (p) cc_final: 0.9293 (t) REVERT: Bc 212 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8151 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9132 (m-30) cc_final: 0.8891 (m-30) REVERT: Be 95 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8215 (mt-10) REVERT: Be 177 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8562 (ttmm) REVERT: Be 191 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7764 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8261 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8771 (mptt) REVERT: Bg 204 GLU cc_start: 0.9125 (tt0) cc_final: 0.8887 (tt0) REVERT: Bg 212 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8194 (ttp-170) REVERT: Bg 220 MET cc_start: 0.9093 (mtm) cc_final: 0.8876 (mtp) REVERT: Bi 95 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8247 (mt-10) REVERT: Bi 151 ASN cc_start: 0.9192 (m-40) cc_final: 0.8810 (m110) REVERT: Bi 177 LYS cc_start: 0.8728 (mttt) cc_final: 0.8321 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7619 (mtp-110) REVERT: Bi 208 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8144 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9044 (mtm) cc_final: 0.8660 (mtp) REVERT: Bk 134 MET cc_start: 0.9064 (ttt) cc_final: 0.8793 (ttt) REVERT: Bk 212 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.8077 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8125 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8356 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8501 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7950 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8075 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8406 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8043 (mt-10) REVERT: Bo 157 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8853 (ttm110) REVERT: Bo 212 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8315 (ttp-170) outliers start: 116 outliers final: 80 residues processed: 1260 average time/residue: 0.2070 time to fit residues: 415.9320 Evaluate side-chains 1244 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1159 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 122 ASN Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ae residue 194 SER Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 178 GLU Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 186 LEU Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 67 LEU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 142 GLU Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Ao residue 50 ILE Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 103 ILE Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Bc residue 50 ILE Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 122 ASN Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 153 LYS Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 68 GLU Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 99 LEU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 70 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 369 optimal weight: 6.9990 chunk 278 optimal weight: 0.0870 chunk 143 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 76 GLN Ac 151 ASN Ac 158 GLN Ae 151 ASN Ae 158 GLN Ag 151 ASN Ak 66 ASN Ao 151 ASN Aq 66 ASN Au 189 ASN Aw 66 ASN Ay 151 ASN Ba 151 ASN Bc 151 ASN Be 66 ASN Be 189 ASN Bg 66 ASN Bm 151 ASN Bo 113 ASN Bo 158 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.106304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.087328 restraints weight = 39768.015| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.88 r_work: 0.2553 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34293 Z= 0.142 Angle : 0.597 7.935 46851 Z= 0.274 Chirality : 0.055 0.470 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.051 132.580 5943 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.34 % Allowed : 20.32 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.13), residues: 3864 helix: 1.50 (0.13), residues: 1764 sheet: 0.84 (0.26), residues: 210 loop : -0.80 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBk 191 TYR 0.017 0.001 TYRBo 198 PHE 0.016 0.002 PHEBa 200 TRP 0.009 0.001 TRPAa 132 HIS 0.004 0.001 HISAs 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (34293) covalent geometry : angle 0.59677 / 0.27 (46851) hydrogen bonds : bond 0.03524 / 2.30 ( 1449) hydrogen bonds : angle 3.85464 / 2.73 ( 4095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1227 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: Aa 79 ASP cc_start: 0.8962 (m-30) cc_final: 0.8751 (m-30) REVERT: Aa 95 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8394 (mt-10) REVERT: Aa 206 THR cc_start: 0.9529 (p) cc_final: 0.9263 (t) REVERT: Aa 212 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8281 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8583 (mmm160) cc_final: 0.7793 (tpt-90) REVERT: Ac 190 LEU cc_start: 0.9009 (tp) cc_final: 0.8780 (mp) REVERT: Ae 108 MET cc_start: 0.9281 (tpt) cc_final: 0.8701 (tpt) REVERT: Ae 160 MET cc_start: 0.9544 (mmm) cc_final: 0.8545 (mmt) REVERT: Ae 187 VAL cc_start: 0.9374 (t) cc_final: 0.9157 (m) REVERT: Ae 191 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7558 (mtp-110) REVERT: Ag 55 ARG cc_start: 0.8537 (tpt-90) cc_final: 0.8213 (tpt-90) REVERT: Ag 95 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8312 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8599 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9182 (tt0) cc_final: 0.8972 (tt0) REVERT: Ag 212 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8191 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8271 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9093 (m-40) cc_final: 0.8757 (m-40) REVERT: Ai 172 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: Ai 212 ARG cc_start: 0.8541 (ttp-110) cc_final: 0.8036 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7761 (mt-10) REVERT: Ak 67 LEU cc_start: 0.8835 (mt) cc_final: 0.8321 (mm) REVERT: Ak 71 LEU cc_start: 0.8850 (mm) cc_final: 0.8402 (mm) REVERT: Ak 177 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8423 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8871 (tp) cc_final: 0.8409 (mp) REVERT: Ak 191 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7619 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8315 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7873 (mt-10) REVERT: Am 50 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8115 (tt) REVERT: Am 110 THR cc_start: 0.9288 (m) cc_final: 0.9073 (m) REVERT: Am 116 MET cc_start: 0.9552 (ttp) cc_final: 0.9290 (ttp) REVERT: Am 139 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: Am 191 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7560 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8191 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9160 (m) cc_final: 0.8813 (m) REVERT: Ao 129 ASN cc_start: 0.9246 (p0) cc_final: 0.8992 (p0) REVERT: Ao 134 MET cc_start: 0.9006 (ttt) cc_final: 0.8478 (ttt) REVERT: Ao 175 ASN cc_start: 0.8930 (m-40) cc_final: 0.8670 (m-40) REVERT: Ao 212 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8221 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8650 (tpt-90) cc_final: 0.8336 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8203 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9233 (m-40) cc_final: 0.8972 (m110) REVERT: Aq 212 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.8060 (ttp-170) REVERT: As 55 ARG cc_start: 0.8633 (tpt-90) cc_final: 0.7919 (tpt-90) REVERT: As 95 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8208 (mt-10) REVERT: As 212 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8073 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9029 (m-30) cc_final: 0.8750 (m-30) REVERT: Au 95 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8145 (mt-10) REVERT: Au 208 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8130 (mtt90) REVERT: Aw 50 ILE cc_start: 0.8311 (mt) cc_final: 0.7991 (tt) REVERT: Aw 67 LEU cc_start: 0.8752 (mt) cc_final: 0.8277 (mm) REVERT: Aw 71 LEU cc_start: 0.8869 (mm) cc_final: 0.8619 (mm) REVERT: Aw 86 THR cc_start: 0.9423 (p) cc_final: 0.9070 (m) REVERT: Aw 110 THR cc_start: 0.9297 (m) cc_final: 0.8874 (m) REVERT: Aw 134 MET cc_start: 0.9082 (ttt) cc_final: 0.8538 (ttt) REVERT: Aw 190 LEU cc_start: 0.8821 (tp) cc_final: 0.8462 (mp) REVERT: Aw 208 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7742 (ptm160) REVERT: Ay 56 MET cc_start: 0.8950 (mtt) cc_final: 0.8530 (mtt) REVERT: Ay 77 GLN cc_start: 0.8728 (mt0) cc_final: 0.8518 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8352 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8546 (ttmm) REVERT: Ba 180 TYR cc_start: 0.9378 (t80) cc_final: 0.9110 (t80) REVERT: Bc 55 ARG cc_start: 0.8634 (tpt-90) cc_final: 0.8047 (tpt-90) REVERT: Bc 56 MET cc_start: 0.8898 (mmm) cc_final: 0.8660 (mmt) REVERT: Bc 95 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8276 (mt-10) REVERT: Bc 206 THR cc_start: 0.9558 (p) cc_final: 0.9269 (t) REVERT: Bc 212 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8147 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8730 (tpt-90) cc_final: 0.8269 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9117 (m-30) cc_final: 0.8719 (m-30) REVERT: Be 95 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8232 (mt-10) REVERT: Be 151 ASN cc_start: 0.9332 (m-40) cc_final: 0.9040 (m-40) REVERT: Be 177 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8532 (ttmm) REVERT: Be 191 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7940 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8244 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8760 (mptt) REVERT: Bg 204 GLU cc_start: 0.9088 (tt0) cc_final: 0.8820 (tt0) REVERT: Bg 212 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8109 (ttp-170) REVERT: Bi 95 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8207 (mt-10) REVERT: Bi 134 MET cc_start: 0.9001 (ttt) cc_final: 0.8503 (ttt) REVERT: Bi 151 ASN cc_start: 0.9145 (m-40) cc_final: 0.8771 (m110) REVERT: Bi 157 ARG cc_start: 0.9179 (ttm170) cc_final: 0.8921 (ttm170) REVERT: Bi 177 LYS cc_start: 0.8691 (mttt) cc_final: 0.8307 (ttmm) REVERT: Bi 178 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: Bi 208 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8578 (ptp-110) REVERT: Bi 212 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8122 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9034 (mtm) cc_final: 0.8642 (mtp) REVERT: Bk 55 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8320 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8970 (m) REVERT: Bk 134 MET cc_start: 0.9033 (ttt) cc_final: 0.8799 (ttt) REVERT: Bk 174 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8646 (mtp180) REVERT: Bk 212 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8028 (ttp-170) REVERT: Bk 220 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8763 (mtp) REVERT: Bm 95 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Bm 168 GLU cc_start: 0.8748 (tt0) cc_final: 0.8496 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8490 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7812 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8247 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8047 (tpt-90) REVERT: Bo 65 LEU cc_start: 0.9355 (mt) cc_final: 0.9142 (mt) REVERT: Bo 95 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8024 (mt-10) REVERT: Bo 157 ARG cc_start: 0.9117 (ttm110) cc_final: 0.8680 (ttm110) REVERT: Bo 190 LEU cc_start: 0.9030 (tp) cc_final: 0.8707 (mp) REVERT: Bo 212 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8090 (ttp-170) outliers start: 113 outliers final: 78 residues processed: 1284 average time/residue: 0.1992 time to fit residues: 411.1983 Evaluate side-chains 1270 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1182 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Ao residue 50 ILE Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 122 ASN Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 122 ASN Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 153 LYS Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 220 MET Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 165 optimal weight: 0.3980 chunk 100 optimal weight: 0.1980 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 376 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 203 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 113 ASN Ac 77 GLN Ac 158 GLN Ae 113 ASN Ae 151 ASN Ag 151 ASN Am 113 ASN Aq 89 GLN As 66 ASN Ay 151 ASN Ba 151 ASN Ba 158 GLN Bc 98 GLN Bc 151 ASN Bi 158 GLN Bm 151 ASN Bo 69 HIS Bo 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.111997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.093204 restraints weight = 39281.361| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.86 r_work: 0.2623 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 34293 Z= 0.103 Angle : 0.569 8.399 46851 Z= 0.260 Chirality : 0.051 0.396 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.036 131.450 5943 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.87 % Allowed : 21.24 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.13), residues: 3864 helix: 1.65 (0.13), residues: 1764 sheet: 0.64 (0.25), residues: 210 loop : -0.63 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGBi 191 TYR 0.013 0.001 TYRBo 198 PHE 0.015 0.002 PHEAg 200 TRP 0.008 0.001 TRPAy 132 HIS 0.003 0.001 HISAs 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (34293) covalent geometry : angle 0.56932 / 0.26 (46851) hydrogen bonds : bond 0.03060 / 2.00 ( 1449) hydrogen bonds : angle 3.81191 / 2.70 ( 4095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1227 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8306 (mt-10) REVERT: Aa 135 MET cc_start: 0.8986 (mmm) cc_final: 0.8769 (mmm) REVERT: Aa 206 THR cc_start: 0.9549 (p) cc_final: 0.9319 (t) REVERT: Aa 212 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8177 (ttp-170) REVERT: Ac 181 MET cc_start: 0.9171 (tpp) cc_final: 0.8927 (tpp) REVERT: Ac 187 VAL cc_start: 0.9450 (t) cc_final: 0.9238 (m) REVERT: Ae 108 MET cc_start: 0.9269 (tpt) cc_final: 0.8768 (tpt) REVERT: Ag 95 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8315 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9129 (tt0) cc_final: 0.8921 (tt0) REVERT: Ag 208 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8869 (ptm160) REVERT: Ag 212 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8184 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8232 (mt-10) REVERT: Ai 136 ASP cc_start: 0.8842 (t0) cc_final: 0.8546 (t0) REVERT: Ai 151 ASN cc_start: 0.9049 (m-40) cc_final: 0.8746 (m-40) REVERT: Ai 172 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7895 (mm-30) REVERT: Ai 191 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7911 (mtp-110) REVERT: Ai 212 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8008 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7745 (mt-10) REVERT: Ak 67 LEU cc_start: 0.8769 (mt) cc_final: 0.8270 (mm) REVERT: Ak 71 LEU cc_start: 0.8826 (mm) cc_final: 0.8426 (mm) REVERT: Ak 79 ASP cc_start: 0.8990 (m-30) cc_final: 0.8688 (m-30) REVERT: Ak 177 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8320 (ttmm) REVERT: Ak 212 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8312 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7828 (mt-10) REVERT: Am 110 THR cc_start: 0.9256 (m) cc_final: 0.8956 (m) REVERT: Am 191 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7498 (mtp-110) REVERT: Ao 175 ASN cc_start: 0.8914 (m-40) cc_final: 0.8685 (m-40) REVERT: Ao 212 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8174 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8660 (tpt-90) cc_final: 0.8355 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8228 (mt-10) REVERT: Aq 134 MET cc_start: 0.8884 (ttt) cc_final: 0.8471 (ttt) REVERT: Aq 151 ASN cc_start: 0.9131 (m-40) cc_final: 0.8886 (m110) REVERT: As 55 ARG cc_start: 0.8546 (tpt-90) cc_final: 0.7839 (tpt-90) REVERT: As 95 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8142 (mt-10) REVERT: As 212 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8035 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9012 (m-30) cc_final: 0.8713 (m-30) REVERT: Au 95 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8112 (mt-10) REVERT: Aw 50 ILE cc_start: 0.8145 (mt) cc_final: 0.7727 (tt) REVERT: Aw 86 THR cc_start: 0.9397 (p) cc_final: 0.9081 (m) REVERT: Aw 110 THR cc_start: 0.9290 (m) cc_final: 0.8866 (m) REVERT: Aw 134 MET cc_start: 0.9010 (ttt) cc_final: 0.8478 (ttt) REVERT: Aw 177 LYS cc_start: 0.8834 (mttt) cc_final: 0.8482 (ttmm) REVERT: Aw 190 LEU cc_start: 0.8810 (tp) cc_final: 0.8502 (mp) REVERT: Aw 195 LEU cc_start: 0.9008 (mt) cc_final: 0.8731 (mt) REVERT: Aw 208 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7725 (ptm160) REVERT: Ay 56 MET cc_start: 0.8801 (mtt) cc_final: 0.8356 (mtt) REVERT: Ay 95 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8332 (mt-10) REVERT: Ay 129 ASN cc_start: 0.9174 (p0) cc_final: 0.8961 (p0) REVERT: Ay 134 MET cc_start: 0.9031 (ttt) cc_final: 0.8734 (ttt) REVERT: Ay 150 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: Ay 177 LYS cc_start: 0.8764 (mttt) cc_final: 0.8466 (mtpt) REVERT: Ba 177 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8539 (ttmm) REVERT: Ba 180 TYR cc_start: 0.9360 (t80) cc_final: 0.9087 (t80) REVERT: Bc 95 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8244 (mt-10) REVERT: Bc 113 ASN cc_start: 0.8895 (m-40) cc_final: 0.8608 (m-40) REVERT: Bc 212 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8086 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8653 (tpt-90) cc_final: 0.8235 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9061 (m-30) cc_final: 0.8828 (m-30) REVERT: Be 95 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8213 (mt-10) REVERT: Be 151 ASN cc_start: 0.9306 (m-40) cc_final: 0.9008 (m-40) REVERT: Be 177 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8451 (ttmm) REVERT: Be 191 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7757 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8141 (ttp-170) REVERT: Bg 204 GLU cc_start: 0.9032 (tt0) cc_final: 0.8764 (tt0) REVERT: Bg 212 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8115 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9173 (mpt180) cc_final: 0.8904 (mpt180) REVERT: Bi 95 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8144 (mt-10) REVERT: Bi 129 ASN cc_start: 0.9307 (p0) cc_final: 0.9064 (p0) REVERT: Bi 151 ASN cc_start: 0.9095 (m-40) cc_final: 0.8723 (m110) REVERT: Bi 177 LYS cc_start: 0.8531 (mttt) cc_final: 0.8188 (ttmm) REVERT: Bi 208 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8518 (ptp-110) REVERT: Bi 212 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8110 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9018 (mtm) cc_final: 0.8639 (mtp) REVERT: Bk 55 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8222 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8967 (m) REVERT: Bk 115 LEU cc_start: 0.9333 (tp) cc_final: 0.9068 (tp) REVERT: Bk 212 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8174 (ttp-170) REVERT: Bk 220 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8812 (mtp) REVERT: Bm 95 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8318 (mt-10) REVERT: Bm 168 GLU cc_start: 0.8674 (tt0) cc_final: 0.8449 (tt0) REVERT: Bm 177 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8466 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7779 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8060 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8334 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7999 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8923 (tp) cc_final: 0.8690 (mp) outliers start: 97 outliers final: 71 residues processed: 1269 average time/residue: 0.1953 time to fit residues: 403.1212 Evaluate side-chains 1256 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1177 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 175 ASN Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 50 ILE Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 150 GLU Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 51 THR Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 72 GLU Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 220 MET Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 345 optimal weight: 7.9990 chunk 327 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 113 ASN Ac 76 GLN Ac 151 ASN Ac 158 GLN Ae 113 ASN Ae 151 ASN Ae 158 GLN Ag 151 ASN Ai 113 ASN Am 151 ASN Aw 113 ASN Aw 151 ASN Ay 151 ASN Ay 158 GLN Ba 151 ASN Ba 158 GLN Bg 151 ASN Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.103366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.084185 restraints weight = 40032.494| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 1.90 r_work: 0.2506 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2343 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34293 Z= 0.229 Angle : 0.665 9.366 46851 Z= 0.304 Chirality : 0.063 0.608 5271 Planarity : 0.005 0.049 5712 Dihedral : 15.184 136.841 5943 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.73 % Allowed : 21.33 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 3864 helix: 1.41 (0.13), residues: 1764 sheet: 0.78 (0.24), residues: 210 loop : -0.67 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBi 191 TYR 0.021 0.001 TYRBo 198 PHE 0.015 0.002 PHEBa 200 TRP 0.012 0.001 TRPAi 132 HIS 0.005 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (34293) covalent geometry : angle 0.66508 / 0.30 (46851) hydrogen bonds : bond 0.04047 / 2.64 ( 1449) hydrogen bonds : angle 3.92983 / 2.79 ( 4095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1148 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8386 (mt-10) REVERT: Aa 206 THR cc_start: 0.9545 (p) cc_final: 0.9309 (t) REVERT: Aa 212 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8252 (ttp-170) REVERT: Ac 91 ASP cc_start: 0.8972 (m-30) cc_final: 0.8667 (m-30) REVERT: Ag 95 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8370 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9227 (tt0) cc_final: 0.8988 (tt0) REVERT: Ag 212 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8141 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8249 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9213 (m-40) cc_final: 0.8813 (m-40) REVERT: Ai 172 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: Ai 212 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8019 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7740 (mt-10) REVERT: Ak 67 LEU cc_start: 0.8875 (mt) cc_final: 0.8375 (mm) REVERT: Ak 71 LEU cc_start: 0.8999 (mm) cc_final: 0.8651 (mm) REVERT: Ak 79 ASP cc_start: 0.9086 (m-30) cc_final: 0.8815 (m-30) REVERT: Ak 177 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8425 (ttmm) REVERT: Ak 212 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8429 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7869 (mt-10) REVERT: Am 139 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: Am 191 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7613 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8118 (ttp-170) REVERT: Ao 108 MET cc_start: 0.9142 (tpp) cc_final: 0.8811 (tpt) REVERT: Ao 134 MET cc_start: 0.9072 (ttt) cc_final: 0.8570 (ttt) REVERT: Ao 172 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7936 (mt-10) REVERT: Ao 175 ASN cc_start: 0.8960 (m-40) cc_final: 0.8670 (m-40) REVERT: Ao 212 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8278 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8411 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8279 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9297 (m-40) cc_final: 0.9050 (m110) REVERT: Aq 212 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.8047 (ttp-170) REVERT: As 55 ARG cc_start: 0.8632 (tpt-90) cc_final: 0.7942 (tpt-90) REVERT: As 95 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8189 (mt-10) REVERT: As 116 MET cc_start: 0.9553 (ttp) cc_final: 0.9069 (ttp) REVERT: As 160 MET cc_start: 0.9478 (mmm) cc_final: 0.9175 (mmt) REVERT: As 197 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8746 (ptm160) REVERT: As 212 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8006 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9042 (m-30) cc_final: 0.8743 (m-30) REVERT: Au 95 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8408 (mt-10) REVERT: Aw 67 LEU cc_start: 0.8823 (mm) cc_final: 0.8449 (mm) REVERT: Aw 71 LEU cc_start: 0.9042 (mm) cc_final: 0.8786 (mm) REVERT: Aw 134 MET cc_start: 0.9125 (ttt) cc_final: 0.8657 (ttt) REVERT: Aw 190 LEU cc_start: 0.8908 (tp) cc_final: 0.8541 (mp) REVERT: Aw 208 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7850 (ptm160) REVERT: Ay 56 MET cc_start: 0.9097 (mtt) cc_final: 0.8657 (mtt) REVERT: Ay 95 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8367 (mt-10) REVERT: Ay 158 GLN cc_start: 0.9460 (mt0) cc_final: 0.9255 (mt0) REVERT: Ba 177 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8518 (ttmm) REVERT: Bc 95 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8322 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8184 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9128 (m-30) cc_final: 0.8866 (m-30) REVERT: Be 95 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8250 (mt-10) REVERT: Be 177 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8500 (ttmm) REVERT: Be 191 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7821 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.7975 (ttp-170) REVERT: Bg 212 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8232 (ttp-170) REVERT: Bi 95 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8271 (mt-10) REVERT: Bi 151 ASN cc_start: 0.9171 (m-40) cc_final: 0.8764 (m110) REVERT: Bi 177 LYS cc_start: 0.8635 (mttt) cc_final: 0.8250 (ttmm) REVERT: Bi 208 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8157 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9065 (mtm) cc_final: 0.8649 (mtp) REVERT: Bk 55 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8406 (tpt-90) REVERT: Bk 134 MET cc_start: 0.8987 (ttt) cc_final: 0.8354 (ttt) REVERT: Bk 212 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8232 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8353 (mt-10) REVERT: Bm 168 GLU cc_start: 0.8700 (tt0) cc_final: 0.8418 (tt0) REVERT: Bm 172 GLU cc_start: 0.8357 (tt0) cc_final: 0.8032 (tt0) REVERT: Bm 177 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8484 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7767 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8203 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8297 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8046 (mt-10) outliers start: 126 outliers final: 93 residues processed: 1211 average time/residue: 0.2100 time to fit residues: 410.7709 Evaluate side-chains 1217 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1117 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 186 LEU Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 177 LYS Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 178 GLU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 103 ILE Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 50 ILE Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 67 LEU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 122 ASN Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 363 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 374 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 76 GLN Ac 129 ASN Ae 151 ASN Ag 151 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN Aq 89 GLN Ay 151 ASN Ay 189 ASN Ba 151 ASN Ba 158 GLN Bm 77 GLN Bo 158 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.108102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.089026 restraints weight = 39608.098| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.89 r_work: 0.2576 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34293 Z= 0.129 Angle : 0.601 8.067 46851 Z= 0.275 Chirality : 0.054 0.442 5271 Planarity : 0.005 0.049 5712 Dihedral : 15.050 132.237 5943 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 22.03 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 3864 helix: 1.50 (0.13), residues: 1764 sheet: 0.74 (0.25), residues: 210 loop : -0.57 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBc 191 TYR 0.018 0.001 TYRBo 198 PHE 0.014 0.002 PHEBa 200 TRP 0.009 0.001 TRPAm 132 HIS 0.003 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (34293) covalent geometry : angle 0.60113 / 0.27 (46851) hydrogen bonds : bond 0.03373 / 2.20 ( 1449) hydrogen bonds : angle 3.89072 / 2.76 ( 4095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1183 time to evaluate : 1.262 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8355 (mt-10) REVERT: Aa 108 MET cc_start: 0.9350 (tpt) cc_final: 0.8937 (tpt) REVERT: Aa 135 MET cc_start: 0.8983 (mmm) cc_final: 0.8748 (mmm) REVERT: Aa 172 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: Aa 206 THR cc_start: 0.9541 (p) cc_final: 0.9316 (t) REVERT: Aa 212 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8221 (ttp-170) REVERT: Ae 108 MET cc_start: 0.9279 (tpt) cc_final: 0.8749 (tpt) REVERT: Ae 160 MET cc_start: 0.9540 (mmm) cc_final: 0.8476 (mmt) REVERT: Ag 95 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8313 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9171 (tt0) cc_final: 0.8949 (tt0) REVERT: Ag 212 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8166 (ttp-170) REVERT: Ag 220 MET cc_start: 0.8932 (mtm) cc_final: 0.8713 (mtm) REVERT: Ai 95 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8216 (mt-10) REVERT: Ai 136 ASP cc_start: 0.8814 (t0) cc_final: 0.8474 (t0) REVERT: Ai 151 ASN cc_start: 0.9173 (m-40) cc_final: 0.8802 (m-40) REVERT: Ai 172 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: Ai 175 ASN cc_start: 0.8855 (m-40) cc_final: 0.8355 (m110) REVERT: Ai 212 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.7934 (ttp-170) REVERT: Ak 79 ASP cc_start: 0.8994 (m-30) cc_final: 0.8700 (m-30) REVERT: Ak 177 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8359 (ttmm) REVERT: Am 191 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7597 (mtp-110) REVERT: Am 203 TYR cc_start: 0.9351 (t80) cc_final: 0.9106 (t80) REVERT: Am 212 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8052 (ttp-170) REVERT: Ao 212 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8229 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9184 (m-40) cc_final: 0.8918 (m110) REVERT: Aq 212 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.8041 (ttp-170) REVERT: As 55 ARG cc_start: 0.8604 (tpt-90) cc_final: 0.7875 (tpt-90) REVERT: As 95 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8148 (mt-10) REVERT: As 197 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8582 (ptm160) REVERT: As 212 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8132 (ttp-170) REVERT: Au 46 ARG cc_start: 0.9271 (mpt180) cc_final: 0.8999 (mpt180) REVERT: Au 55 ARG cc_start: 0.8676 (tpt-90) cc_final: 0.8368 (tpt-90) REVERT: Au 79 ASP cc_start: 0.9047 (m-30) cc_final: 0.8771 (m-30) REVERT: Au 95 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8096 (mt-10) REVERT: Aw 71 LEU cc_start: 0.8976 (mm) cc_final: 0.8714 (mm) REVERT: Aw 110 THR cc_start: 0.9282 (m) cc_final: 0.8868 (m) REVERT: Aw 134 MET cc_start: 0.9043 (ttt) cc_final: 0.8553 (ttt) REVERT: Aw 177 LYS cc_start: 0.8856 (mttt) cc_final: 0.8508 (ttmm) REVERT: Aw 190 LEU cc_start: 0.8824 (tp) cc_final: 0.8505 (mp) REVERT: Aw 208 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7853 (ptm160) REVERT: Ay 56 MET cc_start: 0.8940 (mtt) cc_final: 0.8617 (mtt) REVERT: Ay 95 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8348 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8506 (ttmm) REVERT: Bc 95 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8251 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8207 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9094 (m-30) cc_final: 0.8857 (m-30) REVERT: Be 95 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8231 (mt-10) REVERT: Be 151 ASN cc_start: 0.9318 (m-40) cc_final: 0.9010 (m-40) REVERT: Be 172 GLU cc_start: 0.8331 (tt0) cc_final: 0.8008 (tt0) REVERT: Be 177 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8430 (ttmm) REVERT: Be 212 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8187 (ttp-170) REVERT: Bg 212 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8195 (ttp-170) REVERT: Bi 95 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8200 (mt-10) REVERT: Bi 151 ASN cc_start: 0.9114 (m-40) cc_final: 0.8731 (m110) REVERT: Bi 177 LYS cc_start: 0.8636 (mttt) cc_final: 0.8269 (ttmm) REVERT: Bi 208 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8530 (ptp-110) REVERT: Bi 212 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8117 (ttp-170) REVERT: Bk 115 LEU cc_start: 0.9350 (tp) cc_final: 0.9105 (tp) REVERT: Bk 134 MET cc_start: 0.8911 (ttt) cc_final: 0.8270 (ttt) REVERT: Bk 212 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8237 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8340 (mt-10) REVERT: Bm 172 GLU cc_start: 0.8288 (tt0) cc_final: 0.7938 (tt0) REVERT: Bm 177 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8495 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8044 (mtp-110) cc_final: 0.7743 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8109 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8020 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8921 (tp) cc_final: 0.8677 (mp) outliers start: 112 outliers final: 86 residues processed: 1234 average time/residue: 0.1992 time to fit residues: 399.0099 Evaluate side-chains 1250 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1158 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 186 LEU Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 178 GLU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 151 ASN Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 51 THR Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 166 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 30 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 337 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 76 GLN Ae 151 ASN Ag 76 GLN Ag 151 ASN Am 151 ASN Ao 151 ASN Ao 158 GLN Ay 151 ASN Ay 158 GLN Ba 113 ASN Ba 151 ASN Ba 158 GLN Be 140 GLN Bg 158 GLN Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.102723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.083492 restraints weight = 39973.801| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 1.91 r_work: 0.2492 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2331 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 34293 Z= 0.244 Angle : 0.690 9.571 46851 Z= 0.316 Chirality : 0.065 0.633 5271 Planarity : 0.005 0.062 5712 Dihedral : 15.203 137.064 5943 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.43 % Allowed : 22.36 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 3864 helix: 1.30 (0.13), residues: 1764 sheet: 0.85 (0.25), residues: 210 loop : -0.65 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGBc 191 TYR 0.022 0.002 TYRBo 198 PHE 0.014 0.002 PHEBa 200 TRP 0.013 0.002 TRPBm 132 HIS 0.004 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (34293) covalent geometry : angle 0.69028 / 0.32 (46851) hydrogen bonds : bond 0.04178 / 2.72 ( 1449) hydrogen bonds : angle 3.98801 / 2.84 ( 4095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1136 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8362 (mt-10) REVERT: Aa 121 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8698 (mm-30) REVERT: Aa 172 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: Aa 206 THR cc_start: 0.9543 (p) cc_final: 0.9323 (t) REVERT: Aa 212 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8252 (ttp-170) REVERT: Ac 91 ASP cc_start: 0.8953 (m-30) cc_final: 0.8697 (m-30) REVERT: Ac 181 MET cc_start: 0.9125 (tpp) cc_final: 0.8787 (tpp) REVERT: Ae 212 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8034 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8346 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9220 (tt0) cc_final: 0.8979 (tt0) REVERT: Ag 212 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8292 (ttp-170) REVERT: Ag 220 MET cc_start: 0.8950 (mtm) cc_final: 0.8727 (mtm) REVERT: Ai 95 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8190 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9281 (m-40) cc_final: 0.8880 (m-40) REVERT: Ai 172 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: Ai 212 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8054 (ttp-170) REVERT: Ak 79 ASP cc_start: 0.9090 (m-30) cc_final: 0.8831 (m-30) REVERT: Ak 177 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8431 (ttmm) REVERT: Am 139 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: Am 191 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7700 (mtp-110) REVERT: Ao 108 MET cc_start: 0.9132 (tpp) cc_final: 0.8781 (tpt) REVERT: Ao 134 MET cc_start: 0.9061 (ttt) cc_final: 0.8558 (ttt) REVERT: Ao 175 ASN cc_start: 0.8911 (m-40) cc_final: 0.8597 (m110) REVERT: Ao 212 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.8288 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8257 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9326 (m-40) cc_final: 0.9047 (m110) REVERT: Aq 212 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8053 (ttp-170) REVERT: As 55 ARG cc_start: 0.8646 (tpt-90) cc_final: 0.8239 (tpt-90) REVERT: As 160 MET cc_start: 0.9487 (mmm) cc_final: 0.9167 (mmt) REVERT: As 197 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8665 (ptm160) REVERT: As 212 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8136 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9089 (m-30) cc_final: 0.8763 (m-30) REVERT: Au 95 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8139 (mt-10) REVERT: Aw 67 LEU cc_start: 0.8692 (mm) cc_final: 0.8320 (mm) REVERT: Aw 71 LEU cc_start: 0.9050 (mm) cc_final: 0.8768 (mm) REVERT: Aw 134 MET cc_start: 0.9130 (ttt) cc_final: 0.8646 (ttt) REVERT: Aw 190 LEU cc_start: 0.8893 (tp) cc_final: 0.8546 (mp) REVERT: Aw 208 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7888 (ptm160) REVERT: Ay 95 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8440 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8511 (ttmm) REVERT: Bc 95 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8298 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8301 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8576 (tpt90) cc_final: 0.8223 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9090 (m-30) cc_final: 0.8852 (m-30) REVERT: Be 95 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8257 (mt-10) REVERT: Be 172 GLU cc_start: 0.8397 (tt0) cc_final: 0.8092 (tt0) REVERT: Be 177 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8492 (ttmm) REVERT: Be 212 ARG cc_start: 0.8711 (ttp-110) cc_final: 0.8047 (ttp-170) REVERT: Bg 50 ILE cc_start: 0.8427 (mt) cc_final: 0.7994 (tt) REVERT: Bg 212 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8247 (ttp-170) REVERT: Bi 55 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8207 (tpt90) REVERT: Bi 95 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8292 (mt-10) REVERT: Bi 151 ASN cc_start: 0.9196 (m-40) cc_final: 0.8778 (m110) REVERT: Bi 177 LYS cc_start: 0.8633 (mttt) cc_final: 0.8253 (ttmm) REVERT: Bi 208 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8176 (ttp-170) REVERT: Bk 115 LEU cc_start: 0.9373 (tp) cc_final: 0.9108 (tp) REVERT: Bk 134 MET cc_start: 0.9024 (ttt) cc_final: 0.8388 (ttt) REVERT: Bk 212 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8255 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8351 (mt-10) REVERT: Bm 116 MET cc_start: 0.9554 (ttp) cc_final: 0.9296 (ttp) REVERT: Bm 172 GLU cc_start: 0.8344 (tt0) cc_final: 0.8029 (tt0) REVERT: Bm 177 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8487 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7814 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8130 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8059 (mt-10) outliers start: 116 outliers final: 95 residues processed: 1197 average time/residue: 0.2130 time to fit residues: 411.1139 Evaluate side-chains 1220 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1118 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 186 LEU Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Ao residue 50 ILE Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 50 ILE Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 178 GLU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 151 ASN Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 50 ILE Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 51 THR Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 122 ASN Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 140 GLN Chi-restraints excluded: chain Be residue 166 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 195 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 323 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 354 optimal weight: 0.9990 chunk 377 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 66 ASN Ac 66 ASN Ac 76 GLN Ae 151 ASN Ag 151 ASN Ai 66 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 76 GLN Ao 66 ASN Ao 151 ASN Ao 158 GLN Aq 89 GLN Ay 151 ASN Ba 151 ASN Ba 158 GLN Be 140 GLN Bo 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.108483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.089281 restraints weight = 39656.393| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.90 r_work: 0.2576 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34293 Z= 0.126 Angle : 0.614 8.268 46851 Z= 0.281 Chirality : 0.054 0.448 5271 Planarity : 0.005 0.063 5712 Dihedral : 15.092 132.896 5943 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.81 % Allowed : 22.77 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.13), residues: 3864 helix: 1.43 (0.13), residues: 1764 sheet: 0.75 (0.26), residues: 210 loop : -0.56 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGBc 191 TYR 0.019 0.001 TYRAi 180 PHE 0.015 0.002 PHEAe 200 TRP 0.008 0.001 TRPAm 132 HIS 0.003 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (34293) covalent geometry : angle 0.61377 / 0.28 (46851) hydrogen bonds : bond 0.03423 / 2.23 ( 1449) hydrogen bonds : angle 3.96968 / 2.82 ( 4095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1143 time to evaluate : 1.144 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8363 (mt-10) REVERT: Aa 108 MET cc_start: 0.9340 (tpt) cc_final: 0.8923 (tpt) REVERT: Aa 135 MET cc_start: 0.8960 (mmm) cc_final: 0.8726 (mmm) REVERT: Aa 172 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: Aa 206 THR cc_start: 0.9518 (p) cc_final: 0.9295 (t) REVERT: Aa 212 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8248 (ttp-170) REVERT: Ae 108 MET cc_start: 0.9281 (tpt) cc_final: 0.8750 (tpt) REVERT: Ae 160 MET cc_start: 0.9548 (mmm) cc_final: 0.8489 (mmt) REVERT: Ag 95 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8278 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9173 (tt0) cc_final: 0.8955 (tt0) REVERT: Ag 212 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8176 (ttp-170) REVERT: Ag 220 MET cc_start: 0.8908 (mtm) cc_final: 0.8700 (mtm) REVERT: Ai 95 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8248 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9166 (m-40) cc_final: 0.8794 (m-40) REVERT: Ai 172 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: Ai 175 ASN cc_start: 0.8827 (m-40) cc_final: 0.8272 (m110) REVERT: Ai 212 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8032 (ttp-170) REVERT: Ak 79 ASP cc_start: 0.9032 (m-30) cc_final: 0.8744 (m-30) REVERT: Ak 177 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8335 (ttmm) REVERT: Am 116 MET cc_start: 0.9539 (ttp) cc_final: 0.9300 (ttp) REVERT: Am 191 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7586 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8076 (ttp-170) REVERT: Ao 212 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8238 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8279 (mt-10) REVERT: Aq 151 ASN cc_start: 0.9186 (m-40) cc_final: 0.8980 (m110) REVERT: Aq 212 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.7867 (ttp-170) REVERT: As 55 ARG cc_start: 0.8603 (tpt-90) cc_final: 0.8225 (tpt-90) REVERT: As 197 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8566 (ptm160) REVERT: As 212 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8006 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9082 (m-30) cc_final: 0.8823 (m-30) REVERT: Au 95 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8171 (mt-10) REVERT: Aw 67 LEU cc_start: 0.8550 (mm) cc_final: 0.8052 (mm) REVERT: Aw 71 LEU cc_start: 0.8986 (mm) cc_final: 0.8695 (mm) REVERT: Aw 134 MET cc_start: 0.8993 (ttt) cc_final: 0.8502 (ttt) REVERT: Aw 177 LYS cc_start: 0.8846 (mttt) cc_final: 0.8509 (ttmm) REVERT: Aw 190 LEU cc_start: 0.8862 (tp) cc_final: 0.8549 (mp) REVERT: Aw 208 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7866 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8067 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8940 (mtt) cc_final: 0.8634 (mtt) REVERT: Ay 95 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8381 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8559 (ttmm) REVERT: Bc 95 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8304 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8190 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9056 (m-30) cc_final: 0.8755 (m-30) REVERT: Be 95 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8288 (mt-10) REVERT: Be 151 ASN cc_start: 0.9326 (m-40) cc_final: 0.9013 (m-40) REVERT: Be 172 GLU cc_start: 0.8325 (tt0) cc_final: 0.8014 (tt0) REVERT: Be 177 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8377 (ttmm) REVERT: Bg 135 MET cc_start: 0.8939 (mmm) cc_final: 0.8686 (mmt) REVERT: Bg 212 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8180 (ttp-170) REVERT: Bg 220 MET cc_start: 0.9069 (mtm) cc_final: 0.8786 (mtp) REVERT: Bi 68 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8330 (mm-30) REVERT: Bi 95 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8252 (mt-10) REVERT: Bi 157 ARG cc_start: 0.9117 (ttm170) cc_final: 0.8892 (ttm170) REVERT: Bi 177 LYS cc_start: 0.8652 (mttt) cc_final: 0.8290 (ttmm) REVERT: Bi 208 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8570 (ptp-110) REVERT: Bi 212 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8136 (ttp-170) REVERT: Bk 115 LEU cc_start: 0.9351 (tp) cc_final: 0.9116 (tp) REVERT: Bk 134 MET cc_start: 0.8934 (ttt) cc_final: 0.8278 (ttt) REVERT: Bk 212 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8222 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8345 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8442 (ttmt) REVERT: Bm 191 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7700 (mtp-110) REVERT: Bm 212 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8142 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8075 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8941 (tp) cc_final: 0.8685 (mp) outliers start: 95 outliers final: 80 residues processed: 1185 average time/residue: 0.2158 time to fit residues: 415.5687 Evaluate side-chains 1228 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1141 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 186 LEU Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Aw residue 44 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 151 ASN Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 142 GLU Chi-restraints excluded: chain Ba residue 177 LYS Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 197 ARG Chi-restraints excluded: chain Be residue 51 THR Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Bg residue 71 LEU Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 68 GLU Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 367 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 350 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 113 ASN Ac 76 GLN Ac 129 ASN Ae 151 ASN Ag 76 GLN Ak 76 GLN Am 151 ASN Ao 151 ASN Ao 158 GLN Au 76 GLN Ay 151 ASN Ba 113 ASN Ba 158 GLN Bi 151 ASN Bo 113 ASN Bo 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.105696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.086482 restraints weight = 39837.651| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.90 r_work: 0.2541 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34293 Z= 0.173 Angle : 0.643 8.392 46851 Z= 0.294 Chirality : 0.058 0.523 5271 Planarity : 0.005 0.061 5712 Dihedral : 15.144 134.507 5943 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.11 % Allowed : 22.86 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 3864 helix: 1.39 (0.13), residues: 1764 sheet: 0.81 (0.26), residues: 210 loop : -0.54 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGBc 191 TYR 0.021 0.001 TYRBo 198 PHE 0.014 0.002 PHEBa 200 TRP 0.010 0.001 TRPAi 132 HIS 0.004 0.001 HISAa 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (34293) covalent geometry : angle 0.64297 / 0.29 (46851) hydrogen bonds : bond 0.03746 / 2.45 ( 1449) hydrogen bonds : angle 3.96972 / 2.82 ( 4095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9625.97 seconds wall clock time: 165 minutes 3.92 seconds (9903.92 seconds total)