Starting phenix.real_space_refine on Fri May 30 10:35:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ope_17050/05_2025/8ope_17050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ope_17050/05_2025/8ope_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_17050/05_2025/8ope_17050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ope_17050/05_2025/8ope_17050.map" model { file = "/net/cci-nas-00/data/ceres_data/8ope_17050/05_2025/8ope_17050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ope_17050/05_2025/8ope_17050.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33411 Number of models: 1 Model: "" Number of chains: 2 Chain: "Bd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Be" 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} Restraints were copied for chains: Bg, Ba, Bc, Bm, Bo, Bi, Bk, Aa, Ac, Ae, Ag, Ai, Ak, Am, Ao, Aq, As, Au, Aw, Ay, Bf, Bb, Bl, Bn, Bh, Bj, Bp, Ab, Ad, Af, Ah, Aj, Al, An, Ap, Ar, At, Av, Ax, Az Time building chain proxies: 7.94, per 1000 atoms: 0.24 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: 8.16 Conformation dependent library (CDL) restraints added in 3.8 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: 10.54 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: 9.98 Time building geometry restraints manager: 9.47 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: 45656 1.93 - 3.86: 1027 3.86 - 5.79: 126 5.79 - 7.72: 21 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 - 34.16: 20177 34.16 - 68.32: 1075 68.32 - 102.47: 21 102.47 - 136.63: 0 136.63 - 170.79: 21 Dihedral angle restraints: 21294 sinusoidal: 9744 harmonic: 11550 Sorted by residual: dihedral pdb=" O4' UAl 4 " pdb=" C1' UAl 4 " pdb=" N1 UAl 4 " pdb=" C2 UAl 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.79 -170.79 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' UBh 4 " pdb=" C1' UBh 4 " pdb=" N1 UBh 4 " pdb=" C2 UBh 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.78 -170.78 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' UAz 4 " pdb=" C1' UAz 4 " pdb=" N1 UAz 4 " pdb=" C2 UAz 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.77 -170.77 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 21291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2933 0.026 - 0.052: 1567 0.052 - 0.078: 335 0.078 - 0.103: 257 0.103 - 0.129: 179 Chirality restraints: 5271 Sorted by residual: chirality pdb=" CA ILEBo 50 " pdb=" N ILEBo 50 " pdb=" C ILEBo 50 " pdb=" CB ILEBo 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" C1' UAz 2 " pdb=" O4' UAz 2 " pdb=" C2' UAz 2 " pdb=" N1 UAz 2 " both_signs ideal model delta sigma weight residual False 2.47 2.34 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILEBi 50 " pdb=" N ILEBi 50 " pdb=" C ILEBi 50 " pdb=" CB ILEBi 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (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: 0.28 Found NCS groups: ncs_group { reference = chain 'Be' selection = chain 'Bg' selection = chain 'Ba' selection = chain 'Bc' selection = chain 'Bm' selection = chain 'Bo' selection = chain 'Bi' selection = chain 'Bk' selection = chain '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' } ncs_group { reference = chain 'Bd' selection = chain 'Bf' selection = chain 'Bb' selection = chain 'Bl' selection = chain 'Bn' selection = chain 'Bh' selection = chain 'Bj' selection = chain 'Bp' selection = chain 'Ab' selection = chain 'Ad' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Aj' selection = chain 'Al' selection = chain 'An' selection = chain 'Ap' selection = chain 'Ar' selection = chain 'At' selection = chain 'Av' selection = chain 'Ax' selection = chain 'Az' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.240 Set scattering table: 0.270 Process input model: 62.620 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.695 9.646 46851 Z= 0.456 Chirality : 0.040 0.129 5271 Planarity : 0.007 0.076 5712 Dihedral : 18.434 170.791 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 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 TRP 0.009 0.001 TRPAo 132 HIS 0.004 0.001 HISAu 217 PHE 0.011 0.002 PHEAe 163 TYR 0.018 0.002 TYRAi 143 ARG 0.005 0.001 ARGAg 212 Details of bonding type rmsd hydrogen bonds : bond 0.14025 ( 1449) hydrogen bonds : angle 5.35304 ( 4095) covalent geometry : bond 0.00523 (34293) covalent geometry : angle 0.69453 (46851) *********************** 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 : 3.668 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: 0.8258 (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: 0.7502 (mtp-110) outliers start: 8 outliers final: 2 residues processed: 1068 average time/residue: 0.4899 time to fit residues: 807.4356 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 : 3.292 ------------------------------------------------------------------------------- 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 319 optimal weight: 0.7980 chunk 286 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 220 optimal weight: 0.4980 chunk 343 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 66 ASN Ae 151 ASN Ag 151 ASN Ak 66 ASN Ao 87 GLN Aq 66 ASN Aq 151 ASN Au 129 ASN Au 151 ASN Ay 151 ASN Bc 66 ASN Be 66 ASN Be 98 GLN Bk 98 GLN Bm 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.113628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.094919 restraints weight = 39030.115| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.86 r_work: 0.2674 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34293 Z= 0.121 Angle : 0.506 6.094 46851 Z= 0.263 Chirality : 0.038 0.131 5271 Planarity : 0.005 0.046 5712 Dihedral : 15.305 176.368 5951 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.60 % Allowed : 19.52 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 3864 helix: 1.61 (0.12), residues: 1890 sheet: 0.88 (0.30), residues: 210 loop : -0.97 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAg 93 HIS 0.004 0.001 HISAy 217 PHE 0.015 0.002 PHEAc 200 TYR 0.009 0.001 TYRBg 94 ARG 0.007 0.001 ARGAc 174 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1449) hydrogen bonds : angle 4.04421 ( 4095) covalent geometry : bond 0.00274 (34293) covalent geometry : angle 0.50604 (46851) *********************** 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 1089 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1001 time to evaluate : 3.489 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7841 (mt-10) REVERT: Aa 108 MET cc_start: 0.9232 (tpt) cc_final: 0.9007 (tpt) REVERT: Ac 95 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8103 (mt-10) REVERT: Ae 134 MET cc_start: 0.7979 (ttt) cc_final: 0.7662 (ttt) REVERT: Ae 146 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7997 (ttmm) REVERT: Ag 113 ASN cc_start: 0.9007 (m-40) cc_final: 0.8739 (m-40) REVERT: Ag 116 MET cc_start: 0.9183 (ttp) cc_final: 0.8978 (ttp) REVERT: Ag 134 MET cc_start: 0.7669 (ttt) cc_final: 0.7464 (ttt) REVERT: Ai 158 GLN cc_start: 0.9249 (mt0) cc_final: 0.8940 (mt0) REVERT: Ai 181 MET cc_start: 0.8006 (tpt) cc_final: 0.7696 (tpt) REVERT: Ai 208 ARG cc_start: 0.8562 (ptm160) cc_final: 0.8231 (mtp85) REVERT: Ak 71 LEU cc_start: 0.8716 (mm) cc_final: 0.8502 (mm) REVERT: Ak 204 GLU cc_start: 0.8654 (tt0) cc_final: 0.8453 (pt0) REVERT: Ak 208 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8467 (ptp-110) REVERT: Ao 180 TYR cc_start: 0.9141 (t80) cc_final: 0.8730 (t80) REVERT: Aq 95 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8006 (mt-10) REVERT: Aq 134 MET cc_start: 0.8595 (ttt) cc_final: 0.8051 (ttt) REVERT: Aq 191 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7704 (mtp-110) REVERT: Aq 212 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7818 (ttp-170) REVERT: As 46 ARG cc_start: 0.9210 (mpt180) cc_final: 0.8996 (mpt180) REVERT: As 55 ARG cc_start: 0.8342 (tpt-90) cc_final: 0.8026 (tpt-90) REVERT: As 134 MET cc_start: 0.8464 (ttt) cc_final: 0.8099 (ttt) REVERT: As 151 ASN cc_start: 0.8652 (m-40) cc_final: 0.8019 (m110) REVERT: As 191 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7165 (mtp-110) REVERT: As 212 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7810 (ttp-170) REVERT: Au 134 MET cc_start: 0.8143 (ttt) cc_final: 0.7905 (mtp) REVERT: Au 204 GLU cc_start: 0.8986 (tt0) cc_final: 0.8726 (tt0) REVERT: Aw 134 MET cc_start: 0.7981 (ttt) cc_final: 0.7597 (ttt) REVERT: Aw 204 GLU cc_start: 0.8735 (tt0) cc_final: 0.8334 (pt0) REVERT: Ay 108 MET cc_start: 0.8282 (tpt) cc_final: 0.7615 (tpt) REVERT: Bc 50 ILE cc_start: 0.8089 (mt) cc_final: 0.7840 (mt) REVERT: Bc 55 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7936 (mmm-85) REVERT: Bc 95 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7243 (mt-10) REVERT: Bc 121 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8459 (mm-30) REVERT: Be 95 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7556 (mt-10) REVERT: Be 177 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7856 (ttmm) REVERT: Bg 160 MET cc_start: 0.9474 (mmp) cc_final: 0.9251 (mmt) REVERT: Bg 204 GLU cc_start: 0.8768 (tt0) cc_final: 0.7922 (pt0) REVERT: Bi 79 ASP cc_start: 0.8577 (m-30) cc_final: 0.8304 (m-30) REVERT: Bi 121 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8392 (mm-30) REVERT: Bi 125 SER cc_start: 0.8749 (p) cc_final: 0.8402 (t) REVERT: Bi 135 MET cc_start: 0.8143 (mmm) cc_final: 0.7841 (mmm) REVERT: Bi 136 ASP cc_start: 0.8308 (t0) cc_final: 0.8068 (t0) REVERT: Bi 168 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8419 (mt-10) REVERT: Bi 208 ARG cc_start: 0.8774 (ptm160) cc_final: 0.8509 (ptp-110) REVERT: Bk 121 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8457 (mm-30) REVERT: Bk 135 MET cc_start: 0.8609 (mmm) cc_final: 0.8319 (tpp) REVERT: Bm 55 ARG cc_start: 0.8504 (tpt-90) cc_final: 0.8010 (tpt-90) REVERT: Bm 71 LEU cc_start: 0.8866 (mm) cc_final: 0.8664 (mm) REVERT: Bm 95 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7550 (mt-10) REVERT: Bo 95 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7526 (mt-10) REVERT: Bo 141 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8915 (t) outliers start: 88 outliers final: 39 residues processed: 1028 average time/residue: 0.4822 time to fit residues: 782.1375 Evaluate side-chains 1006 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 965 time to evaluate : 3.286 ------------------------------------------------------------------------------- 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 Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 159 ILE Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 122 ASN Chi-restraints excluded: chain Ak residue 208 ARG Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 194 SER 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 141 VAL Chi-restraints excluded: chain As residue 50 ILE Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 107 GLU Chi-restraints excluded: chain Aw residue 107 GLU 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 Be residue 67 LEU Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 194 SER Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bk residue 50 ILE Chi-restraints excluded: chain Bm residue 68 GLU Chi-restraints excluded: chain Bo residue 67 LEU Chi-restraints excluded: chain Bo residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 23 optimal weight: 8.9990 chunk 312 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 151 ASN Ae 151 ASN Ag 151 ASN Am 151 ASN Ao 87 GLN Ao 151 ASN Ao 158 GLN Au 129 ASN Au 151 ASN Ay 151 ASN Ba 77 GLN Ba 151 ASN Bc 87 GLN ** Bc 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 129 ASN Be 87 GLN Bk 98 GLN ** Bk 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.101293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.082236 restraints weight = 40312.874| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.89 r_work: 0.2474 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 34293 Z= 0.288 Angle : 0.602 6.745 46851 Z= 0.315 Chirality : 0.045 0.177 5271 Planarity : 0.005 0.046 5712 Dihedral : 15.342 171.668 5945 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.40 % Allowed : 18.93 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 3864 helix: 1.16 (0.12), residues: 1890 sheet: 0.66 (0.28), residues: 252 loop : -1.05 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPBe 132 HIS 0.005 0.001 HISBc 217 PHE 0.020 0.003 PHEBa 200 TYR 0.014 0.002 TYRAg 143 ARG 0.008 0.001 ARGBi 191 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 1449) hydrogen bonds : angle 4.12420 ( 4095) covalent geometry : bond 0.00684 (34293) covalent geometry : angle 0.60180 (46851) *********************** 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 1382 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1267 time to evaluate : 3.353 Fit side-chains REVERT: Aa 55 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8341 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8500 (mt-10) REVERT: Aa 206 THR cc_start: 0.9492 (p) cc_final: 0.9279 (t) REVERT: Aa 212 ARG cc_start: 0.8814 (ttp-110) cc_final: 0.8399 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8693 (mmm160) cc_final: 0.7799 (tpt170) REVERT: Ac 91 ASP cc_start: 0.8981 (m-30) cc_final: 0.8672 (m-30) REVERT: Ac 95 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8559 (mt-10) REVERT: Ac 153 LYS cc_start: 0.9184 (mptt) cc_final: 0.8920 (mmtm) REVERT: Ae 191 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7576 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8284 (ttp-170) REVERT: Ag 67 LEU cc_start: 0.8884 (mt) cc_final: 0.8657 (mp) REVERT: Ag 84 ARG cc_start: 0.9084 (ttm170) cc_final: 0.8654 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8329 (mt-10) REVERT: Ag 151 ASN cc_start: 0.9230 (m-40) cc_final: 0.8991 (m110) REVERT: Ag 191 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7428 (mtp-110) REVERT: Ag 204 GLU cc_start: 0.9232 (tt0) cc_final: 0.8786 (tt0) REVERT: Ai 46 ARG cc_start: 0.9097 (mpt180) cc_final: 0.8858 (mpt180) REVERT: Ai 79 ASP cc_start: 0.9195 (m-30) cc_final: 0.8966 (m-30) REVERT: Ai 95 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8194 (mt-10) REVERT: Ai 172 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7829 (mt-10) REVERT: Ai 204 GLU cc_start: 0.9184 (tt0) cc_final: 0.8922 (tt0) REVERT: Ai 212 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8054 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7822 (mt-10) REVERT: Ak 71 LEU cc_start: 0.8988 (mm) cc_final: 0.8564 (mm) REVERT: Ak 190 LEU cc_start: 0.8955 (tp) cc_final: 0.8717 (tp) REVERT: Ak 206 THR cc_start: 0.9520 (p) cc_final: 0.9316 (t) REVERT: Ak 208 ARG cc_start: 0.9150 (ptp-170) cc_final: 0.8871 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8308 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7892 (mt-10) REVERT: Am 67 LEU cc_start: 0.8593 (mt) cc_final: 0.8357 (mm) REVERT: Am 71 LEU cc_start: 0.9231 (mm) cc_final: 0.9027 (mm) REVERT: Am 110 THR cc_start: 0.9281 (m) cc_final: 0.9072 (m) REVERT: Am 136 ASP cc_start: 0.8976 (t0) cc_final: 0.8568 (t0) REVERT: Am 191 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7719 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8134 (ttp80) REVERT: Ao 110 THR cc_start: 0.9153 (m) cc_final: 0.8892 (m) REVERT: Ao 134 MET cc_start: 0.9133 (ttt) cc_final: 0.8651 (ttt) REVERT: Ao 135 MET cc_start: 0.9162 (mmm) cc_final: 0.8810 (mmt) REVERT: Ao 175 ASN cc_start: 0.9009 (m-40) cc_final: 0.8611 (m110) REVERT: Ao 180 TYR cc_start: 0.9368 (t80) cc_final: 0.8930 (t80) REVERT: Ao 184 TYR cc_start: 0.9495 (t80) cc_final: 0.9252 (t80) REVERT: Ao 204 GLU cc_start: 0.9110 (tt0) cc_final: 0.8469 (tt0) REVERT: Ao 212 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8243 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8586 (tpt-90) cc_final: 0.8253 (tpt-90) REVERT: Aq 88 SER cc_start: 0.9223 (p) cc_final: 0.9002 (p) REVERT: Aq 95 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8298 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8129 (ttp-170) REVERT: As 95 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8277 (mt-10) REVERT: As 116 MET cc_start: 0.9519 (ttp) cc_final: 0.9097 (ttp) REVERT: As 160 MET cc_start: 0.9542 (mmm) cc_final: 0.9239 (mmt) REVERT: As 198 TYR cc_start: 0.9407 (m-80) cc_final: 0.9055 (m-80) REVERT: As 212 ARG cc_start: 0.8729 (ttp-110) cc_final: 0.8105 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9094 (m-30) cc_final: 0.8758 (m-30) REVERT: Au 95 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8151 (mt-10) REVERT: Au 153 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8944 (mptt) REVERT: Au 175 ASN cc_start: 0.9084 (m-40) cc_final: 0.8768 (m-40) REVERT: Au 177 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8712 (ttmm) REVERT: Au 180 TYR cc_start: 0.9275 (t80) cc_final: 0.8972 (t80) REVERT: Au 204 GLU cc_start: 0.9206 (tt0) cc_final: 0.8997 (tt0) REVERT: Au 208 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8037 (ptm160) REVERT: Au 212 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8362 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8695 (mt) cc_final: 0.8194 (mm) REVERT: Aw 71 LEU cc_start: 0.8916 (mm) cc_final: 0.8703 (mm) REVERT: Aw 112 MET cc_start: 0.9516 (mmm) cc_final: 0.9141 (mmp) REVERT: Aw 134 MET cc_start: 0.9102 (ttt) cc_final: 0.8562 (ttt) REVERT: Aw 212 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8236 (ttp-170) REVERT: Ay 95 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8326 (mt-10) REVERT: Ba 157 ARG cc_start: 0.9318 (ttm110) cc_final: 0.9097 (ttm110) REVERT: Ba 212 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8150 (ttp-170) REVERT: Ba 220 MET cc_start: 0.9049 (mtm) cc_final: 0.8778 (mtm) REVERT: Bc 55 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8361 (tpt-90) REVERT: Bc 95 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8245 (mt-10) REVERT: Bc 153 LYS cc_start: 0.9185 (mptt) cc_final: 0.8957 (mptt) REVERT: Bc 212 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8178 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7782 (mt-10) REVERT: Be 79 ASP cc_start: 0.9220 (m-30) cc_final: 0.8968 (m-30) REVERT: Be 95 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8234 (mt-10) REVERT: Be 112 MET cc_start: 0.9505 (mmp) cc_final: 0.9173 (mmp) REVERT: Be 151 ASN cc_start: 0.9405 (m-40) cc_final: 0.9128 (m-40) REVERT: Be 177 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8535 (ttmm) REVERT: Be 191 ARG cc_start: 0.8211 (mtp-110) cc_final: 0.8006 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8367 (ttp-170) REVERT: Bg 46 ARG cc_start: 0.9121 (mpt180) cc_final: 0.8783 (mpt180) REVERT: Bg 99 LEU cc_start: 0.8750 (tp) cc_final: 0.8516 (tp) REVERT: Bg 108 MET cc_start: 0.9286 (tpt) cc_final: 0.9057 (tpt) REVERT: Bg 135 MET cc_start: 0.9062 (mmm) cc_final: 0.8380 (mmt) REVERT: Bg 204 GLU cc_start: 0.9048 (tt0) cc_final: 0.8756 (tt0) REVERT: Bg 212 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8174 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9097 (mpt180) cc_final: 0.8777 (mpt180) REVERT: Bi 148 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8413 (mt) REVERT: Bi 177 LYS cc_start: 0.8781 (mttt) cc_final: 0.8334 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7541 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9299 (tt0) cc_final: 0.9044 (tt0) REVERT: Bi 208 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.7901 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8143 (ttp-170) REVERT: Bi 215 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7864 (mt-10) REVERT: Bk 67 LEU cc_start: 0.8669 (mt) cc_final: 0.8373 (mm) REVERT: Bk 110 THR cc_start: 0.9156 (m) cc_final: 0.8797 (m) REVERT: Bk 134 MET cc_start: 0.9031 (ttt) cc_final: 0.8595 (ttt) REVERT: Bk 191 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7765 (mtp-110) REVERT: Bk 212 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8280 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.8477 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8271 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8566 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8256 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8161 (mt-10) REVERT: Bo 155 THR cc_start: 0.9377 (m) cc_final: 0.9153 (m) REVERT: Bo 157 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8899 (ttm170) REVERT: Bo 212 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8381 (ttp-170) outliers start: 115 outliers final: 64 residues processed: 1328 average time/residue: 0.4739 time to fit residues: 978.6072 Evaluate side-chains 1250 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 1183 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 178 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 Ai residue 124 THR Chi-restraints excluded: chain Ak residue 51 THR Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 122 ASN 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 65 LEU 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 Aq residue 208 ARG Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 103 ILE 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 Ba residue 51 THR 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 Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU 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 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 148 ILE Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 208 ARG 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 49 optimal weight: 5.9990 chunk 208 optimal weight: 0.3980 chunk 368 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 66 ASN Ac 151 ASN Ac 158 GLN Ae 151 ASN Ae 158 GLN Ag 66 ASN Ai 66 ASN Ak 77 GLN Aq 151 ASN Aw 66 ASN Ay 158 GLN Bc 151 ASN Bi 151 ASN Bk 66 ASN Bm 69 HIS Bm 151 ASN Bo 113 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.106199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.087386 restraints weight = 39831.635| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.88 r_work: 0.2566 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34293 Z= 0.126 Angle : 0.489 6.121 46851 Z= 0.252 Chirality : 0.039 0.138 5271 Planarity : 0.005 0.056 5712 Dihedral : 15.186 177.087 5943 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.02 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 3864 helix: 1.49 (0.12), residues: 1890 sheet: 0.98 (0.27), residues: 210 loop : -1.02 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAw 132 HIS 0.003 0.001 HISAu 217 PHE 0.016 0.002 PHEAo 200 TYR 0.012 0.001 TYRBo 198 ARG 0.012 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1449) hydrogen bonds : angle 3.90326 ( 4095) covalent geometry : bond 0.00301 (34293) covalent geometry : angle 0.48856 (46851) *********************** 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 1367 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1265 time to evaluate : 4.164 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8372 (mt-10) REVERT: Aa 212 ARG cc_start: 0.8744 (ttp-110) cc_final: 0.8349 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8598 (mmm160) cc_final: 0.7814 (tpt-90) REVERT: Ae 50 ILE cc_start: 0.8213 (mt) cc_final: 0.7985 (tt) REVERT: Ae 191 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7456 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8235 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8352 (mt-10) REVERT: Ag 108 MET cc_start: 0.9183 (tpt) cc_final: 0.8929 (tpt) REVERT: Ag 177 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8553 (ttmm) REVERT: Ai 95 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9071 (m-40) cc_final: 0.8710 (m-40) REVERT: Ai 172 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7840 (mt-10) REVERT: Ai 206 THR cc_start: 0.9588 (p) cc_final: 0.9354 (t) REVERT: Ai 212 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8063 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Ai 220 MET cc_start: 0.9051 (mtm) cc_final: 0.8766 (mtm) REVERT: Ak 55 ARG cc_start: 0.8504 (tpt-90) cc_final: 0.8169 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8885 (mm) cc_final: 0.8490 (mm) REVERT: Ak 142 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: Ak 191 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7355 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9529 (p) cc_final: 0.9291 (t) REVERT: Ak 208 ARG cc_start: 0.9029 (ptp-170) cc_final: 0.8815 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8270 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7835 (mt-10) REVERT: Am 67 LEU cc_start: 0.8526 (mt) cc_final: 0.8301 (mm) REVERT: Am 71 LEU cc_start: 0.9138 (mm) cc_final: 0.8919 (mm) REVERT: Am 107 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8272 (mp0) REVERT: Am 110 THR cc_start: 0.9233 (m) cc_final: 0.8956 (m) REVERT: Am 191 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7562 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8023 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9130 (m) cc_final: 0.8730 (m) REVERT: Ao 129 ASN cc_start: 0.9219 (p0) cc_final: 0.8997 (p0) REVERT: Ao 134 MET cc_start: 0.8990 (ttt) cc_final: 0.8392 (ttt) REVERT: Ao 175 ASN cc_start: 0.8971 (m-40) cc_final: 0.8757 (m-40) REVERT: Ao 204 GLU cc_start: 0.9073 (tt0) cc_final: 0.8429 (tt0) REVERT: Ao 212 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8132 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8585 (tpt-90) cc_final: 0.8235 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8289 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.7898 (ttp-170) REVERT: As 95 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8230 (mt-10) REVERT: As 107 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8528 (pt0) REVERT: As 212 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8081 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9043 (m-30) cc_final: 0.8731 (m-30) REVERT: Au 95 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8120 (mt-10) REVERT: Au 151 ASN cc_start: 0.9074 (m-40) cc_final: 0.8847 (m110) REVERT: Au 175 ASN cc_start: 0.9056 (m-40) cc_final: 0.8766 (m-40) REVERT: Au 177 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8565 (ttmm) REVERT: Au 180 TYR cc_start: 0.9273 (t80) cc_final: 0.9067 (t80) REVERT: Au 212 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8240 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8709 (mt) cc_final: 0.8243 (mm) REVERT: Aw 71 LEU cc_start: 0.8779 (mm) cc_final: 0.8556 (mm) REVERT: Aw 110 THR cc_start: 0.9277 (m) cc_final: 0.8962 (m) REVERT: Aw 134 MET cc_start: 0.9014 (ttt) cc_final: 0.8476 (ttt) REVERT: Aw 172 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8052 (mt-10) REVERT: Aw 190 LEU cc_start: 0.8825 (tp) cc_final: 0.8468 (mp) REVERT: Aw 191 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7340 (mtp-110) REVERT: Aw 208 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7662 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8227 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8820 (mtt) cc_final: 0.8436 (mtt) REVERT: Ay 77 GLN cc_start: 0.8623 (mt0) cc_final: 0.8392 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8330 (mt-10) REVERT: Ay 151 ASN cc_start: 0.9165 (m-40) cc_final: 0.8952 (m110) REVERT: Ay 208 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8679 (ptm160) REVERT: Ba 212 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8102 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8295 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.7902 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7794 (mt-10) REVERT: Be 79 ASP cc_start: 0.9157 (m-30) cc_final: 0.8928 (m-30) REVERT: Be 95 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8206 (mt-10) REVERT: Be 151 ASN cc_start: 0.9361 (m-40) cc_final: 0.9072 (m-40) REVERT: Be 177 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8490 (ttmm) REVERT: Be 181 MET cc_start: 0.9073 (tpp) cc_final: 0.8859 (tpt) REVERT: Be 191 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7736 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8094 (ttp-170) REVERT: Bg 54 MET cc_start: 0.8636 (ptp) cc_final: 0.8434 (ptm) REVERT: Bg 153 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8741 (mptt) REVERT: Bg 212 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8021 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9215 (mpt180) cc_final: 0.8948 (mpt180) REVERT: Bi 99 LEU cc_start: 0.8770 (tp) cc_final: 0.8518 (tp) REVERT: Bi 134 MET cc_start: 0.9030 (ttt) cc_final: 0.8584 (ttt) REVERT: Bi 151 ASN cc_start: 0.9131 (m-40) cc_final: 0.8824 (m110) REVERT: Bi 157 ARG cc_start: 0.9149 (ttm170) cc_final: 0.8852 (ttm170) REVERT: Bi 177 LYS cc_start: 0.8773 (mttt) cc_final: 0.8339 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9128 (tt0) cc_final: 0.8925 (tt0) REVERT: Bi 206 THR cc_start: 0.9523 (p) cc_final: 0.9322 (t) REVERT: Bi 212 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8058 (ttp-170) REVERT: Bk 134 MET cc_start: 0.8933 (ttt) cc_final: 0.8454 (ttt) REVERT: Bk 191 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7662 (mtp-110) REVERT: Bk 212 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8078 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8611 (tpt-90) cc_final: 0.8103 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8298 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8500 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8167 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8054 (mt-10) REVERT: Bo 190 LEU cc_start: 0.9036 (tp) cc_final: 0.8737 (mp) REVERT: Bo 212 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8235 (ttp-170) outliers start: 102 outliers final: 64 residues processed: 1313 average time/residue: 0.4671 time to fit residues: 962.8300 Evaluate side-chains 1271 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1203 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 142 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 Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 54 MET 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 51 THR 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 51 THR Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 159 ILE Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 54 MET 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 Ay residue 208 ARG Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU Chi-restraints excluded: chain Be residue 64 VAL 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 64 VAL Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU 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 51 THR Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 306 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 343 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 334 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ac 158 GLN Ae 151 ASN Ag 151 ASN Am 151 ASN Ao 151 ASN Au 113 ASN Aw 151 ASN Ay 158 GLN Bc 151 ASN Bi 66 ASN Bm 151 ASN Bo 69 HIS Bo 158 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.101473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.082344 restraints weight = 40123.261| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.90 r_work: 0.2474 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 34293 Z= 0.249 Angle : 0.561 6.711 46851 Z= 0.291 Chirality : 0.043 0.162 5271 Planarity : 0.005 0.058 5712 Dihedral : 15.326 173.455 5943 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.61 % Allowed : 20.23 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 3864 helix: 1.30 (0.12), residues: 1890 sheet: 0.92 (0.26), residues: 210 loop : -0.99 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPBe 132 HIS 0.005 0.001 HISAa 217 PHE 0.016 0.002 PHEBa 200 TYR 0.018 0.002 TYRBo 198 ARG 0.011 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1449) hydrogen bonds : angle 3.97308 ( 4095) covalent geometry : bond 0.00597 (34293) covalent geometry : angle 0.56104 (46851) *********************** 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 1301 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1179 time to evaluate : 3.309 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8417 (mt-10) REVERT: Aa 121 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8712 (mm-30) REVERT: Aa 206 THR cc_start: 0.9519 (p) cc_final: 0.9300 (t) REVERT: Aa 212 ARG cc_start: 0.8749 (ttp-110) cc_final: 0.8273 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8623 (mmm160) cc_final: 0.7816 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8989 (m-30) cc_final: 0.8699 (m-30) REVERT: Ae 50 ILE cc_start: 0.8325 (mt) cc_final: 0.8069 (tt) REVERT: Ae 212 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8333 (ttp-170) REVERT: Ag 84 ARG cc_start: 0.9109 (ttm170) cc_final: 0.8709 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8401 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8513 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8230 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8213 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9200 (m-40) cc_final: 0.8833 (m-40) REVERT: Ai 175 ASN cc_start: 0.8918 (m-40) cc_final: 0.8506 (m110) REVERT: Ai 206 THR cc_start: 0.9563 (p) cc_final: 0.9348 (t) REVERT: Ai 208 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8094 (ptm160) REVERT: Ai 215 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7753 (mt-10) REVERT: Ai 220 MET cc_start: 0.9052 (mtm) cc_final: 0.8807 (mtm) REVERT: Ak 71 LEU cc_start: 0.8994 (mm) cc_final: 0.8582 (mm) REVERT: Ak 191 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7759 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9565 (p) cc_final: 0.9322 (t) REVERT: Ak 212 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8377 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7905 (mt-10) REVERT: Am 107 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8308 (mp0) REVERT: Am 191 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7559 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8200 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8253 (mt-10) REVERT: Ao 110 THR cc_start: 0.9113 (m) cc_final: 0.8810 (m) REVERT: Ao 129 ASN cc_start: 0.9229 (p0) cc_final: 0.8994 (p0) REVERT: Ao 134 MET cc_start: 0.9130 (ttt) cc_final: 0.8633 (ttt) REVERT: Ao 175 ASN cc_start: 0.9001 (m-40) cc_final: 0.8726 (m-40) REVERT: Ao 204 GLU cc_start: 0.9101 (tt0) cc_final: 0.8354 (tt0) REVERT: Ao 212 ARG cc_start: 0.8753 (ttp-110) cc_final: 0.8287 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8586 (tpt-90) cc_final: 0.8299 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8213 (mt-10) REVERT: Aq 208 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (ptm160) REVERT: Aq 212 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.7995 (ttp-170) REVERT: As 95 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8234 (mt-10) REVERT: As 116 MET cc_start: 0.9522 (ttp) cc_final: 0.9155 (ttp) REVERT: As 160 MET cc_start: 0.9508 (mmm) cc_final: 0.9209 (mmt) REVERT: As 172 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: As 212 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8022 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9056 (m-30) cc_final: 0.8750 (m-30) REVERT: Au 95 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8131 (mt-10) REVERT: Au 175 ASN cc_start: 0.9092 (m-40) cc_final: 0.8869 (m-40) REVERT: Au 177 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8582 (ttmm) REVERT: Au 208 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8002 (ptm160) REVERT: Au 212 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8225 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8786 (mt) cc_final: 0.8319 (mm) REVERT: Aw 71 LEU cc_start: 0.8925 (mm) cc_final: 0.8691 (mm) REVERT: Aw 134 MET cc_start: 0.9115 (ttt) cc_final: 0.8656 (ttt) REVERT: Aw 172 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8078 (mt-10) REVERT: Aw 190 LEU cc_start: 0.8873 (tp) cc_final: 0.8439 (mp) REVERT: Aw 208 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7772 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8270 (ttp-170) REVERT: Ay 56 MET cc_start: 0.9074 (mtt) cc_final: 0.8642 (mtt) REVERT: Ay 95 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8364 (mt-10) REVERT: Ba 191 ARG cc_start: 0.7878 (mtp-110) cc_final: 0.7484 (mtp-110) REVERT: Ba 212 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8282 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8347 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8183 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8705 (mmm-85) cc_final: 0.8418 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9147 (m-30) cc_final: 0.8925 (m-30) REVERT: Be 95 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8254 (mt-10) REVERT: Be 113 ASN cc_start: 0.9376 (m-40) cc_final: 0.9169 (m-40) REVERT: Be 151 ASN cc_start: 0.9415 (m-40) cc_final: 0.9121 (m-40) REVERT: Be 177 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8581 (ttmm) REVERT: Be 191 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7789 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8300 (ttp-170) REVERT: Bg 212 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8206 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9202 (mpt180) cc_final: 0.8889 (mpt180) REVERT: Bi 55 ARG cc_start: 0.8526 (tpt-90) cc_final: 0.8256 (tpt-90) REVERT: Bi 99 LEU cc_start: 0.8856 (tp) cc_final: 0.8608 (tp) REVERT: Bi 134 MET cc_start: 0.9066 (ttt) cc_final: 0.8645 (ttt) REVERT: Bi 151 ASN cc_start: 0.9172 (m-40) cc_final: 0.8829 (m110) REVERT: Bi 177 LYS cc_start: 0.8734 (mttt) cc_final: 0.8339 (ttmm) REVERT: Bi 191 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7628 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9159 (tt0) cc_final: 0.8943 (tt0) REVERT: Bi 208 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7953 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8701 (ttp-110) cc_final: 0.8227 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9046 (mtm) cc_final: 0.8800 (mtp) REVERT: Bk 121 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8549 (mm-30) REVERT: Bk 134 MET cc_start: 0.9029 (ttt) cc_final: 0.8631 (ttt) REVERT: Bk 212 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8160 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8318 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8521 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8118 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8084 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8165 (ttp-170) outliers start: 122 outliers final: 91 residues processed: 1242 average time/residue: 0.4714 time to fit residues: 916.7260 Evaluate side-chains 1249 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1152 time to evaluate : 3.642 ------------------------------------------------------------------------------- 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 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 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 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 173 MET Chi-restraints excluded: chain Ai residue 208 ARG Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 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 122 ASN Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 150 GLU 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 Ao residue 209 THR 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 Aq residue 208 ARG Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 142 GLU 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 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 54 MET 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 51 THR Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 54 MET 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 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 173 MET Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 50 ILE 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 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 172 GLU 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 Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 234 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 332 optimal weight: 0.0370 chunk 107 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 289 optimal weight: 0.0980 chunk 277 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 113 ASN Ae 151 ASN Ao 151 ASN As 66 ASN Ay 66 ASN Ay 158 GLN Bc 151 ASN Bm 151 ASN Bo 66 ASN Bo 158 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.105666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.086762 restraints weight = 39909.214| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.90 r_work: 0.2545 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34293 Z= 0.125 Angle : 0.488 6.612 46851 Z= 0.251 Chirality : 0.039 0.142 5271 Planarity : 0.005 0.054 5712 Dihedral : 15.180 176.658 5943 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.11 % Allowed : 20.62 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 3864 helix: 1.49 (0.12), residues: 1890 sheet: 0.78 (0.25), residues: 210 loop : -0.87 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBo 132 HIS 0.003 0.001 HISBo 217 PHE 0.014 0.002 PHEAc 200 TYR 0.016 0.001 TYRBo 198 ARG 0.014 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1449) hydrogen bonds : angle 3.87420 ( 4095) covalent geometry : bond 0.00302 (34293) covalent geometry : angle 0.48820 (46851) *********************** 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: 105 poor density : 1219 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8377 (mt-10) REVERT: Aa 212 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8228 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8595 (mmm160) cc_final: 0.7972 (tpt170) REVERT: Ac 190 LEU cc_start: 0.9005 (tp) cc_final: 0.8784 (mp) REVERT: Ae 190 LEU cc_start: 0.8985 (tp) cc_final: 0.8758 (mp) REVERT: Ag 84 ARG cc_start: 0.9069 (ttm170) cc_final: 0.8603 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8329 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8548 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8232 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8206 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9146 (m-40) cc_final: 0.8829 (m-40) REVERT: Ai 175 ASN cc_start: 0.8842 (m-40) cc_final: 0.8434 (m110) REVERT: Ai 206 THR cc_start: 0.9588 (p) cc_final: 0.9261 (t) REVERT: Ai 208 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8151 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8157 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7747 (mt-10) REVERT: Ai 220 MET cc_start: 0.8992 (mtm) cc_final: 0.8719 (mtm) REVERT: Ak 55 ARG cc_start: 0.8557 (tpt-90) cc_final: 0.8267 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8855 (mm) cc_final: 0.8403 (mm) REVERT: Ak 177 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8449 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8890 (tp) cc_final: 0.8387 (mp) REVERT: Ak 191 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7601 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9563 (p) cc_final: 0.9240 (t) REVERT: Ak 212 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8320 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7917 (mt-10) REVERT: Am 107 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8292 (mp0) REVERT: Am 191 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7603 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8163 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8258 (mt-10) REVERT: Ao 175 ASN cc_start: 0.8952 (m-40) cc_final: 0.8725 (m-40) REVERT: Ao 204 GLU cc_start: 0.9065 (tt0) cc_final: 0.8353 (tt0) REVERT: Ao 212 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8234 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8244 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8002 (ttp-170) REVERT: As 95 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8192 (mt-10) REVERT: As 136 ASP cc_start: 0.8828 (t0) cc_final: 0.8611 (t0) REVERT: As 172 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: As 212 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8059 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9056 (m-30) cc_final: 0.8767 (m-30) REVERT: Au 95 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8085 (mt-10) REVERT: Au 151 ASN cc_start: 0.9145 (m-40) cc_final: 0.8879 (m110) REVERT: Au 175 ASN cc_start: 0.9046 (m-40) cc_final: 0.8783 (m-40) REVERT: Au 177 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8523 (ttmm) REVERT: Au 208 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7968 (ptm160) REVERT: Au 212 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8146 (ttp-170) REVERT: Aw 50 ILE cc_start: 0.8315 (mt) cc_final: 0.7941 (tt) REVERT: Aw 55 ARG cc_start: 0.8612 (tpt-90) cc_final: 0.8285 (tpt-90) REVERT: Aw 134 MET cc_start: 0.9065 (ttt) cc_final: 0.8608 (ttt) REVERT: Aw 172 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7947 (mt-10) REVERT: Aw 190 LEU cc_start: 0.8810 (tp) cc_final: 0.8469 (mp) REVERT: Aw 208 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7719 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8169 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8872 (mtt) cc_final: 0.8500 (mtt) REVERT: Ay 77 GLN cc_start: 0.8691 (mt0) cc_final: 0.8478 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8379 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8113 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8313 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8095 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8317 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9081 (m-30) cc_final: 0.8834 (m-30) REVERT: Be 95 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8245 (mt-10) REVERT: Be 151 ASN cc_start: 0.9348 (m-40) cc_final: 0.9033 (m-40) REVERT: Be 177 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8509 (ttmm) REVERT: Be 191 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8240 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8738 (mptt) REVERT: Bg 212 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.8134 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9235 (mpt180) cc_final: 0.8984 (mpt180) REVERT: Bi 99 LEU cc_start: 0.8729 (tp) cc_final: 0.8501 (tp) REVERT: Bi 134 MET cc_start: 0.9059 (ttt) cc_final: 0.8601 (ttt) REVERT: Bi 151 ASN cc_start: 0.9155 (m-40) cc_final: 0.8884 (m110) REVERT: Bi 157 ARG cc_start: 0.9135 (ttm170) cc_final: 0.8896 (ttm170) REVERT: Bi 177 LYS cc_start: 0.8623 (mttt) cc_final: 0.8230 (ttmm) REVERT: Bi 178 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: Bi 204 GLU cc_start: 0.9109 (tt0) cc_final: 0.8885 (tt0) REVERT: Bi 208 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7934 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.8221 (ttp-170) REVERT: Bk 54 MET cc_start: 0.8660 (ptp) cc_final: 0.8382 (ptp) REVERT: Bk 110 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8928 (m) REVERT: Bk 134 MET cc_start: 0.8994 (ttt) cc_final: 0.8754 (ttt) REVERT: Bk 212 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8242 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8594 (tpt-90) cc_final: 0.8255 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8352 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8532 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.8107 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8289 (tpt-90) REVERT: Bo 56 MET cc_start: 0.9082 (mmt) cc_final: 0.8780 (mmt) REVERT: Bo 95 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8070 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8941 (tp) cc_final: 0.8666 (mp) REVERT: Bo 212 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8213 (ttp-170) outliers start: 105 outliers final: 83 residues processed: 1271 average time/residue: 0.4591 time to fit residues: 923.7522 Evaluate side-chains 1275 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1184 time to evaluate : 3.499 ------------------------------------------------------------------------------- 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 107 GLU Chi-restraints excluded: chain Aa residue 172 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 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 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 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 208 ARG Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 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 Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 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 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 54 MET 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 51 THR 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 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU Chi-restraints excluded: chain Bc residue 107 GLU 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 141 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 67 LEU 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 Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 68 GLU Chi-restraints excluded: chain Bi residue 107 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 51 THR 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 172 GLU 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 Bm residue 133 VAL Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 99 LEU 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 9 optimal weight: 0.0270 chunk 116 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Ac 151 ASN Ac 158 GLN Ae 151 ASN Ag 151 ASN Ak 77 GLN Am 151 ASN Ao 151 ASN Aq 113 ASN Aq 151 ASN Aw 151 ASN Ay 158 GLN Ba 158 GLN ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 189 ASN 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 = 0.2908 r_free = 0.2908 target = 0.100509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.081368 restraints weight = 40433.615| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 1.91 r_work: 0.2459 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2297 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 34293 Z= 0.287 Angle : 0.589 7.542 46851 Z= 0.304 Chirality : 0.044 0.190 5271 Planarity : 0.005 0.062 5712 Dihedral : 15.336 173.004 5943 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.85 % Allowed : 20.79 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 3864 helix: 1.31 (0.13), residues: 1764 sheet: 0.90 (0.25), residues: 210 loop : -0.84 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPBe 132 HIS 0.005 0.001 HISAa 217 PHE 0.016 0.002 PHEBa 200 TYR 0.022 0.002 TYRBo 198 ARG 0.015 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 1449) hydrogen bonds : angle 4.00795 ( 4095) covalent geometry : bond 0.00686 (34293) covalent geometry : angle 0.58852 (46851) *********************** 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 1291 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1161 time to evaluate : 3.816 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8393 (mt-10) REVERT: Aa 108 MET cc_start: 0.9424 (tpt) cc_final: 0.8934 (tpt) REVERT: Aa 206 THR cc_start: 0.9544 (p) cc_final: 0.9293 (t) REVERT: Aa 212 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8250 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8633 (mmm160) cc_final: 0.7806 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8975 (m-30) cc_final: 0.8684 (m-30) REVERT: Ae 56 MET cc_start: 0.9157 (mtt) cc_final: 0.8907 (mtt) REVERT: Ae 212 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8334 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8395 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8531 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8211 (ttp-170) REVERT: Ag 220 MET cc_start: 0.9001 (mtm) cc_final: 0.8785 (mtm) REVERT: Ai 95 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8186 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9282 (m-40) cc_final: 0.8883 (m-40) REVERT: Ai 208 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8059 (ptm160) REVERT: Ai 215 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7733 (mt-10) REVERT: Ai 220 MET cc_start: 0.9014 (mtm) cc_final: 0.8773 (mtm) REVERT: Ak 55 ARG cc_start: 0.8716 (tpt-90) cc_final: 0.8505 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.9057 (mm) cc_final: 0.8615 (mm) REVERT: Ak 177 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8476 (ttmm) REVERT: Ak 191 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9581 (p) cc_final: 0.9249 (t) REVERT: Ak 212 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8410 (ttp-170) REVERT: Am 54 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (ptp) REVERT: Am 107 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8321 (mp0) REVERT: Am 139 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: Am 212 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8240 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8255 (mt-10) REVERT: Ao 134 MET cc_start: 0.9149 (ttt) cc_final: 0.8660 (ttt) REVERT: Ao 175 ASN cc_start: 0.8996 (m-40) cc_final: 0.8701 (m-40) REVERT: Ao 204 GLU cc_start: 0.9100 (tt0) cc_final: 0.8345 (tt0) REVERT: Ao 212 ARG cc_start: 0.8791 (ttp-110) cc_final: 0.8322 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8538 (tpt-90) cc_final: 0.8334 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8174 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8020 (ttp-170) REVERT: As 160 MET cc_start: 0.9518 (mmm) cc_final: 0.9211 (mmt) REVERT: As 172 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: As 212 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8092 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9064 (m-30) cc_final: 0.8755 (m-30) REVERT: Au 95 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8152 (mt-10) REVERT: Au 175 ASN cc_start: 0.9098 (m-40) cc_final: 0.8855 (m-40) REVERT: Au 177 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8634 (ttmm) REVERT: Au 208 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8054 (ptm160) REVERT: Au 212 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8250 (ttp-170) REVERT: Aw 55 ARG cc_start: 0.8668 (tpt-90) cc_final: 0.8304 (tpt-90) REVERT: Aw 67 LEU cc_start: 0.8786 (mm) cc_final: 0.8439 (mm) REVERT: Aw 71 LEU cc_start: 0.9055 (mm) cc_final: 0.8797 (mm) REVERT: Aw 95 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8179 (mt-10) REVERT: Aw 134 MET cc_start: 0.9119 (ttt) cc_final: 0.8657 (ttt) REVERT: Aw 190 LEU cc_start: 0.8849 (tp) cc_final: 0.8445 (mp) REVERT: Aw 191 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7610 (mtp-110) REVERT: Aw 208 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7876 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8275 (ttp-170) REVERT: Ay 56 MET cc_start: 0.9140 (mtt) cc_final: 0.8678 (mtt) REVERT: Ay 95 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8368 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8308 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8379 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8204 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8416 (tpt90) REVERT: Be 68 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: Be 79 ASP cc_start: 0.9092 (m-30) cc_final: 0.8839 (m-30) REVERT: Be 95 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8265 (mt-10) REVERT: Be 151 ASN cc_start: 0.9402 (m-40) cc_final: 0.9115 (m-40) REVERT: Be 177 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8565 (ttmm) REVERT: Be 191 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7791 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8275 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8722 (mptt) REVERT: Bg 212 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8213 (ttp-170) REVERT: Bi 99 LEU cc_start: 0.8846 (tp) cc_final: 0.8585 (tp) REVERT: Bi 134 MET cc_start: 0.9065 (ttt) cc_final: 0.8641 (ttt) REVERT: Bi 151 ASN cc_start: 0.9211 (m-40) cc_final: 0.8840 (m110) REVERT: Bi 177 LYS cc_start: 0.8740 (mttt) cc_final: 0.8321 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9175 (tt0) cc_final: 0.8953 (tt0) REVERT: Bi 208 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7930 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8261 (ttp-170) REVERT: Bk 54 MET cc_start: 0.8726 (ptp) cc_final: 0.8328 (ptp) REVERT: Bk 79 ASP cc_start: 0.9096 (m-30) cc_final: 0.8848 (m-30) REVERT: Bk 134 MET cc_start: 0.9038 (ttt) cc_final: 0.8644 (ttt) REVERT: Bk 212 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8243 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8574 (tpt-90) cc_final: 0.8041 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8365 (mt-10) REVERT: Bm 142 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8515 (ttmt) REVERT: Bm 197 ARG cc_start: 0.9025 (ptm160) cc_final: 0.8756 (ptm160) REVERT: Bm 212 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8229 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8387 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8088 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8154 (ttp-170) outliers start: 130 outliers final: 103 residues processed: 1225 average time/residue: 0.4753 time to fit residues: 913.9536 Evaluate side-chains 1238 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1125 time to evaluate : 3.559 ------------------------------------------------------------------------------- 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 107 GLU 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 65 LEU 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 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 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 122 ASN Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 208 ARG 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 51 THR Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 150 GLU 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 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 67 LEU 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 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 51 THR Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 197 ARG Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 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 51 THR Chi-restraints excluded: chain Ba residue 67 LEU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 54 MET 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 67 LEU Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 107 GLU 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 51 THR Chi-restraints excluded: chain Bg residue 67 LEU 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 Bg residue 172 GLU Chi-restraints excluded: chain Bg residue 197 ARG 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 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR 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 54 MET 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 Bm residue 142 GLU Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU 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 166 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ac 158 GLN Ae 151 ASN Ag 151 ASN Am 66 ASN Ao 66 ASN Ao 151 ASN Aq 151 ASN Ay 158 GLN Ba 158 GLN ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 66 ASN Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.106010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.087047 restraints weight = 39918.083| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.90 r_work: 0.2551 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34293 Z= 0.116 Angle : 0.503 7.630 46851 Z= 0.257 Chirality : 0.039 0.151 5271 Planarity : 0.005 0.050 5712 Dihedral : 15.201 176.540 5943 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.16 % Allowed : 21.74 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 3864 helix: 1.51 (0.13), residues: 1764 sheet: 0.78 (0.25), residues: 210 loop : -0.71 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBo 132 HIS 0.003 0.001 HISAm 217 PHE 0.016 0.002 PHEAe 200 TYR 0.016 0.001 TYRBo 198 ARG 0.012 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1449) hydrogen bonds : angle 3.93438 ( 4095) covalent geometry : bond 0.00278 (34293) covalent geometry : angle 0.50271 (46851) *********************** 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 1291 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1184 time to evaluate : 3.521 Fit side-chains revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8728 (tpt-90) cc_final: 0.8506 (tpt-90) REVERT: Aa 79 ASP cc_start: 0.9022 (m-30) cc_final: 0.8773 (m-30) REVERT: Aa 95 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8345 (mt-10) REVERT: Aa 108 MET cc_start: 0.9338 (tpt) cc_final: 0.9057 (tpt) REVERT: Aa 135 MET cc_start: 0.9035 (mmm) cc_final: 0.8781 (mmm) REVERT: Aa 172 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: Aa 212 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8186 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8547 (mmm160) cc_final: 0.7796 (tpt-90) REVERT: Ac 190 LEU cc_start: 0.9004 (tp) cc_final: 0.8774 (mp) REVERT: Ag 95 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8352 (mt-10) REVERT: Ag 134 MET cc_start: 0.8725 (ttt) cc_final: 0.8255 (ttt) REVERT: Ag 177 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8546 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8221 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8194 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9149 (m-40) cc_final: 0.8814 (m-40) REVERT: Ai 208 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8110 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7734 (mt-10) REVERT: Ak 55 ARG cc_start: 0.8590 (tpt-90) cc_final: 0.8331 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8972 (mm) cc_final: 0.8499 (mm) REVERT: Ak 177 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8400 (ttmm) REVERT: Ak 191 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7615 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9587 (p) cc_final: 0.9229 (t) REVERT: Ak 212 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8401 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7855 (mt-10) REVERT: Am 54 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8255 (ptp) REVERT: Am 56 MET cc_start: 0.9031 (mmt) cc_final: 0.8821 (mmm) REVERT: Am 107 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8240 (mp0) REVERT: Am 116 MET cc_start: 0.9533 (ttp) cc_final: 0.9287 (ttp) REVERT: Am 139 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: Am 212 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8176 (ttp-170) REVERT: Ao 134 MET cc_start: 0.9011 (ttt) cc_final: 0.8482 (ttt) REVERT: Ao 175 ASN cc_start: 0.8957 (m-40) cc_final: 0.8733 (m-40) REVERT: Ao 204 GLU cc_start: 0.9060 (tt0) cc_final: 0.8399 (tt0) REVERT: Ao 212 ARG cc_start: 0.8725 (ttp-110) cc_final: 0.8255 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8161 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.7945 (ttp-170) REVERT: As 172 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: As 212 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8026 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9069 (m-30) cc_final: 0.8779 (m-30) REVERT: Au 95 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8103 (mt-10) REVERT: Au 175 ASN cc_start: 0.9012 (m-40) cc_final: 0.8719 (m-40) REVERT: Au 177 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8618 (ttmm) REVERT: Au 212 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8205 (ttp-170) REVERT: Aw 50 ILE cc_start: 0.8321 (mt) cc_final: 0.8027 (tt) REVERT: Aw 55 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8296 (tpt-90) REVERT: Aw 71 LEU cc_start: 0.8978 (mm) cc_final: 0.8680 (mm) REVERT: Aw 86 THR cc_start: 0.9418 (p) cc_final: 0.9060 (m) REVERT: Aw 134 MET cc_start: 0.9068 (ttt) cc_final: 0.8601 (ttt) REVERT: Aw 190 LEU cc_start: 0.8776 (tp) cc_final: 0.8449 (mp) REVERT: Aw 208 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7749 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8144 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8903 (mtt) cc_final: 0.8497 (mtt) REVERT: Ay 95 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8372 (mt-10) REVERT: Ay 158 GLN cc_start: 0.9388 (mt0) cc_final: 0.9179 (mt0) REVERT: Ba 212 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8277 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8282 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.8112 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9067 (m-30) cc_final: 0.8788 (m-30) REVERT: Be 95 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8259 (mt-10) REVERT: Be 151 ASN cc_start: 0.9336 (m-40) cc_final: 0.9019 (m-40) REVERT: Be 177 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8482 (ttmm) REVERT: Be 191 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7740 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8274 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8764 (mptt) REVERT: Bg 212 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8162 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9235 (mpt180) cc_final: 0.8979 (mpt180) REVERT: Bi 99 LEU cc_start: 0.8728 (tp) cc_final: 0.8496 (tp) REVERT: Bi 134 MET cc_start: 0.9047 (ttt) cc_final: 0.8577 (ttt) REVERT: Bi 151 ASN cc_start: 0.9147 (m-40) cc_final: 0.8859 (m110) REVERT: Bi 177 LYS cc_start: 0.8595 (mttt) cc_final: 0.8199 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9100 (tt0) cc_final: 0.8860 (tt0) REVERT: Bi 208 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7909 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8245 (ttp-170) REVERT: Bi 219 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7931 (tm-30) REVERT: Bk 54 MET cc_start: 0.8731 (ptp) cc_final: 0.8474 (ptp) REVERT: Bk 110 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8859 (m) REVERT: Bk 134 MET cc_start: 0.8984 (ttt) cc_final: 0.8581 (ttt) REVERT: Bk 212 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8035 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8340 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8529 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8156 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8085 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8939 (tp) cc_final: 0.8738 (mp) REVERT: Bo 212 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8170 (ttp-170) outliers start: 107 outliers final: 83 residues processed: 1235 average time/residue: 0.4599 time to fit residues: 901.2679 Evaluate side-chains 1242 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1150 time to evaluate : 3.856 ------------------------------------------------------------------------------- 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 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 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 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 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 208 ARG 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 54 MET Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 186 LEU 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 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 67 LEU 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 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 51 THR Chi-restraints excluded: chain Aw residue 64 VAL 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 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 51 THR Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 67 LEU Chi-restraints excluded: chain Bc residue 107 GLU 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 141 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR 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 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 72 GLU Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR 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 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 99 LEU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 57 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 356 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 266 optimal weight: 0.0030 chunk 122 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ac 158 GLN Ae 113 ASN Ae 151 ASN Ag 151 ASN Ak 77 GLN Ao 151 ASN Aq 113 ASN Aq 151 ASN Ba 158 GLN ** Bc 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.103553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.084435 restraints weight = 40109.643| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.91 r_work: 0.2512 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34293 Z= 0.181 Angle : 0.541 8.375 46851 Z= 0.277 Chirality : 0.041 0.171 5271 Planarity : 0.005 0.051 5712 Dihedral : 15.277 175.496 5943 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.28 % Allowed : 22.09 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 3864 helix: 1.44 (0.13), residues: 1764 sheet: 0.76 (0.25), residues: 210 loop : -0.71 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAk 132 HIS 0.004 0.001 HISBm 217 PHE 0.014 0.002 PHEBa 200 TYR 0.022 0.001 TYRAw 198 ARG 0.011 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1449) hydrogen bonds : angle 3.95377 ( 4095) covalent geometry : bond 0.00437 (34293) covalent geometry : angle 0.54102 (46851) *********************** 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 1278 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1167 time to evaluate : 3.329 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8363 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: Aa 206 THR cc_start: 0.9545 (p) cc_final: 0.9335 (t) REVERT: Aa 212 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8222 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8566 (mmm160) cc_final: 0.7829 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8933 (m-30) cc_final: 0.8656 (m-30) REVERT: Ac 190 LEU cc_start: 0.9041 (tp) cc_final: 0.8770 (mp) REVERT: Ag 84 ARG cc_start: 0.9133 (ttm170) cc_final: 0.8712 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8364 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8541 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8228 (ttp-170) REVERT: Ag 220 MET cc_start: 0.8991 (mtm) cc_final: 0.8789 (mtm) REVERT: Ai 95 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8174 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9227 (m-40) cc_final: 0.8869 (m-40) REVERT: Ai 208 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8202 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7734 (mt-10) REVERT: Ak 55 ARG cc_start: 0.8657 (tpt-90) cc_final: 0.8385 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.9010 (mm) cc_final: 0.8527 (mm) REVERT: Ak 177 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8421 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8918 (tp) cc_final: 0.8462 (mp) REVERT: Ak 191 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7594 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9619 (p) cc_final: 0.9269 (t) REVERT: Ak 212 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8443 (ttp-170) REVERT: Am 54 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8329 (ptp) REVERT: Am 107 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8263 (mp0) REVERT: Am 139 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: Am 212 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8213 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8297 (mt-10) REVERT: Ao 134 MET cc_start: 0.9096 (ttt) cc_final: 0.8584 (ttt) REVERT: Ao 175 ASN cc_start: 0.8962 (m-40) cc_final: 0.8719 (m-40) REVERT: Ao 204 GLU cc_start: 0.9086 (tt0) cc_final: 0.8332 (tt0) REVERT: Ao 212 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8295 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8245 (mt-10) REVERT: Aq 208 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8465 (ptm160) REVERT: Aq 212 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8000 (ttp-170) REVERT: As 172 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: As 198 TYR cc_start: 0.9356 (m-80) cc_final: 0.9000 (m-80) REVERT: As 212 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8032 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9068 (m-30) cc_final: 0.8750 (m-30) REVERT: Au 95 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8130 (mt-10) REVERT: Au 175 ASN cc_start: 0.9054 (m-40) cc_final: 0.8764 (m-40) REVERT: Au 177 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8620 (ttmm) REVERT: Au 212 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8282 (ttp-170) REVERT: Aw 50 ILE cc_start: 0.8376 (mt) cc_final: 0.8175 (tt) REVERT: Aw 55 ARG cc_start: 0.8547 (tpt-90) cc_final: 0.8326 (tpt-90) REVERT: Aw 67 LEU cc_start: 0.8539 (mm) cc_final: 0.8080 (mm) REVERT: Aw 71 LEU cc_start: 0.9011 (mm) cc_final: 0.8712 (mm) REVERT: Aw 95 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8208 (mt-10) REVERT: Aw 134 MET cc_start: 0.9099 (ttt) cc_final: 0.8621 (ttt) REVERT: Aw 190 LEU cc_start: 0.8838 (tp) cc_final: 0.8477 (mp) REVERT: Aw 208 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7827 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8198 (ttp-170) REVERT: Ay 56 MET cc_start: 0.9016 (mtt) cc_final: 0.8616 (mtt) REVERT: Ay 95 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8359 (mt-10) REVERT: Ba 180 TYR cc_start: 0.9265 (t80) cc_final: 0.9029 (t80) REVERT: Ba 212 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8316 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8310 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8186 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9103 (m-30) cc_final: 0.8846 (m-30) REVERT: Be 95 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8265 (mt-10) REVERT: Be 151 ASN cc_start: 0.9392 (m-40) cc_final: 0.9085 (m-40) REVERT: Be 177 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8508 (ttmm) REVERT: Be 212 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8328 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8814 (mptt) REVERT: Bg 212 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8224 (ttp-170) REVERT: Bi 55 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8064 (tpt-90) REVERT: Bi 99 LEU cc_start: 0.8799 (tp) cc_final: 0.8555 (tp) REVERT: Bi 134 MET cc_start: 0.9065 (ttt) cc_final: 0.8581 (ttt) REVERT: Bi 151 ASN cc_start: 0.9192 (m-40) cc_final: 0.8887 (m110) REVERT: Bi 177 LYS cc_start: 0.8619 (mttt) cc_final: 0.8236 (ttmm) REVERT: Bi 178 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: Bi 204 GLU cc_start: 0.9135 (tt0) cc_final: 0.8891 (tt0) REVERT: Bi 208 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7924 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8736 (ttp-110) cc_final: 0.8281 (ttp-170) REVERT: Bi 219 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7960 (tm-30) REVERT: Bk 54 MET cc_start: 0.8706 (ptp) cc_final: 0.8499 (ptp) REVERT: Bk 110 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8892 (m) REVERT: Bk 134 MET cc_start: 0.9008 (ttt) cc_final: 0.8594 (ttt) REVERT: Bk 212 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8227 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8349 (mt-10) REVERT: Bm 172 GLU cc_start: 0.8346 (tt0) cc_final: 0.7998 (tt0) REVERT: Bm 177 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8547 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8115 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8202 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8084 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8951 (tp) cc_final: 0.8647 (mp) REVERT: Bo 212 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8085 (ttp-170) outliers start: 111 outliers final: 88 residues processed: 1225 average time/residue: 0.4537 time to fit residues: 878.2460 Evaluate side-chains 1240 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1141 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 208 ARG 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 54 MET Chi-restraints excluded: chain Am residue 139 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 151 ASN Chi-restraints excluded: chain Ao residue 177 LYS 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 151 ASN Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 208 ARG 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 67 LEU 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 122 ASN Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 51 THR Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 51 THR 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 51 THR Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 178 GLU Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 67 LEU Chi-restraints excluded: chain Bc residue 107 GLU 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 141 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 67 LEU 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 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 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 51 THR 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 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 99 LEU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 91 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 377 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 350 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ac 158 GLN Ae 151 ASN Ag 151 ASN Ao 151 ASN Ay 158 GLN Ba 113 ASN Ba 158 GLN ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.103421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.084351 restraints weight = 40081.965| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 1.91 r_work: 0.2508 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34293 Z= 0.192 Angle : 0.550 9.478 46851 Z= 0.281 Chirality : 0.041 0.173 5271 Planarity : 0.005 0.051 5712 Dihedral : 15.295 175.624 5943 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.28 % Allowed : 22.42 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 3864 helix: 1.39 (0.13), residues: 1764 sheet: 0.79 (0.25), residues: 210 loop : -0.71 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAk 132 HIS 0.004 0.001 HISBm 217 PHE 0.014 0.002 PHEBa 200 TYR 0.031 0.001 TYRAw 198 ARG 0.011 0.001 ARGBe 174 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 1449) hydrogen bonds : angle 3.98744 ( 4095) covalent geometry : bond 0.00465 (34293) covalent geometry : angle 0.55002 (46851) ********************** 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 1254 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1143 time to evaluate : 3.374 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8383 (mt-10) REVERT: Aa 108 MET cc_start: 0.9387 (tpt) cc_final: 0.8953 (tpt) REVERT: Aa 172 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: Aa 206 THR cc_start: 0.9552 (p) cc_final: 0.9323 (t) REVERT: Aa 212 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8222 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8568 (mmm160) cc_final: 0.7819 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8934 (m-30) cc_final: 0.8663 (m-30) REVERT: Ac 190 LEU cc_start: 0.9015 (tp) cc_final: 0.8740 (mp) REVERT: Ag 84 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8713 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8372 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8514 (ttmm) REVERT: Ag 212 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8242 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8173 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9249 (m-40) cc_final: 0.8896 (m-40) REVERT: Ai 208 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8205 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7733 (mt-10) REVERT: Ak 55 ARG cc_start: 0.8655 (tpt-90) cc_final: 0.8397 (tpt-90) REVERT: Ak 177 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8427 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8934 (tp) cc_final: 0.8476 (mp) REVERT: Ak 191 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7555 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9633 (p) cc_final: 0.9277 (t) REVERT: Ak 212 ARG cc_start: 0.8753 (ttp-110) cc_final: 0.8454 (ttp-170) REVERT: Am 54 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (ptp) REVERT: Am 107 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8286 (mp0) REVERT: Am 139 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: Am 212 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8177 (ttp-170) REVERT: Ao 134 MET cc_start: 0.9085 (ttt) cc_final: 0.8570 (ttt) REVERT: Ao 175 ASN cc_start: 0.8954 (m-40) cc_final: 0.8708 (m-40) REVERT: Ao 204 GLU cc_start: 0.9085 (tt0) cc_final: 0.8415 (tt0) REVERT: Ao 212 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8292 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8253 (mt-10) REVERT: Aq 208 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8507 (ptm160) REVERT: Aq 212 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8002 (ttp-170) REVERT: As 116 MET cc_start: 0.9514 (ttp) cc_final: 0.9100 (ttp) REVERT: As 197 ARG cc_start: 0.9078 (ptm160) cc_final: 0.8854 (ptm160) REVERT: As 212 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8034 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9060 (m-30) cc_final: 0.8742 (m-30) REVERT: Au 95 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8120 (mt-10) REVERT: Au 175 ASN cc_start: 0.9053 (m-40) cc_final: 0.8762 (m-40) REVERT: Au 177 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8611 (ttmm) REVERT: Au 212 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.8246 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8546 (mm) cc_final: 0.8081 (mm) REVERT: Aw 71 LEU cc_start: 0.9023 (mm) cc_final: 0.8713 (mm) REVERT: Aw 95 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8178 (mt-10) REVERT: Aw 134 MET cc_start: 0.9103 (ttt) cc_final: 0.8632 (ttt) REVERT: Aw 190 LEU cc_start: 0.8841 (tp) cc_final: 0.8491 (mp) REVERT: Aw 208 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7823 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8235 (ttp-170) REVERT: Ay 56 MET cc_start: 0.9034 (mtt) cc_final: 0.8605 (mtt) REVERT: Ay 95 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8391 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8308 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8313 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8208 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9104 (m-30) cc_final: 0.8873 (m-30) REVERT: Be 95 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8259 (mt-10) REVERT: Be 151 ASN cc_start: 0.9394 (m-40) cc_final: 0.9083 (m-40) REVERT: Be 177 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8525 (ttmm) REVERT: Be 212 ARG cc_start: 0.8687 (ttp-110) cc_final: 0.8306 (ttp-170) REVERT: Bg 153 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8819 (mptt) REVERT: Bg 172 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8037 (mm-30) REVERT: Bg 212 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8230 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9218 (mpt180) cc_final: 0.8963 (mpt180) REVERT: Bi 71 LEU cc_start: 0.8955 (mm) cc_final: 0.8676 (mm) REVERT: Bi 99 LEU cc_start: 0.8808 (tp) cc_final: 0.8561 (tp) REVERT: Bi 134 MET cc_start: 0.9084 (ttt) cc_final: 0.8603 (ttt) REVERT: Bi 151 ASN cc_start: 0.9192 (m-40) cc_final: 0.8884 (m110) REVERT: Bi 177 LYS cc_start: 0.8632 (mttt) cc_final: 0.8248 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9136 (tt0) cc_final: 0.8912 (tt0) REVERT: Bi 208 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7922 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8282 (ttp-170) REVERT: Bi 219 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7972 (tm-30) REVERT: Bi 225 LEU cc_start: 0.8692 (mt) cc_final: 0.8441 (mt) REVERT: Bk 54 MET cc_start: 0.8711 (ptp) cc_final: 0.8511 (ptp) REVERT: Bk 79 ASP cc_start: 0.9075 (m-30) cc_final: 0.8836 (m-30) REVERT: Bk 110 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8880 (m) REVERT: Bk 134 MET cc_start: 0.9018 (ttt) cc_final: 0.8610 (ttt) REVERT: Bk 212 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8245 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8337 (mt-10) REVERT: Bm 172 GLU cc_start: 0.8354 (tt0) cc_final: 0.8009 (tt0) REVERT: Bm 177 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8555 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8541 (ttp-110) cc_final: 0.8127 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8093 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8957 (tp) cc_final: 0.8646 (mp) REVERT: Bo 212 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8093 (ttp-170) outliers start: 111 outliers final: 91 residues processed: 1204 average time/residue: 0.4690 time to fit residues: 897.7079 Evaluate side-chains 1235 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1135 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU 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 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 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 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 122 ASN Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Ai residue 208 ARG 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 54 MET Chi-restraints excluded: chain Am residue 139 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 186 LEU 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 121 GLU Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 208 ARG 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 67 LEU 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 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Aw residue 51 THR Chi-restraints excluded: chain Aw residue 64 VAL 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 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 51 THR Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 178 GLU 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 141 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 67 LEU 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 107 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR 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 172 GLU Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 50 ILE Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 99 LEU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 277 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 372 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ac 158 GLN Ae 113 ASN Ae 151 ASN Ag 151 ASN Am 151 ASN Ao 151 ASN Aq 151 ASN Ay 158 GLN Ba 158 GLN ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.101671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.082499 restraints weight = 40242.749| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 1.91 r_work: 0.2480 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 34293 Z= 0.240 Angle : 0.584 9.529 46851 Z= 0.299 Chirality : 0.043 0.202 5271 Planarity : 0.005 0.062 5712 Dihedral : 15.330 173.575 5943 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.28 % Allowed : 22.60 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 3864 helix: 1.29 (0.13), residues: 1764 sheet: 0.84 (0.26), residues: 210 loop : -0.73 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPBm 132 HIS 0.004 0.001 HISAa 217 PHE 0.015 0.002 PHEBa 200 TYR 0.034 0.002 TYRAw 198 ARG 0.010 0.001 ARGAa 191 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1449) hydrogen bonds : angle 4.04054 ( 4095) covalent geometry : bond 0.00577 (34293) covalent geometry : angle 0.58372 (46851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20842.27 seconds wall clock time: 359 minutes 42.44 seconds (21582.44 seconds total)