Starting phenix.real_space_refine on Sat Jun 28 19:34:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ope_17050/06_2025/8ope_17050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ope_17050/06_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_17050/06_2025/8ope_17050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ope_17050/06_2025/8ope_17050.map" model { file = "/net/cci-nas-00/data/ceres_data/8ope_17050/06_2025/8ope_17050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ope_17050/06_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-5710/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: 7.60, per 1000 atoms: 0.23 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: 7.35 Conformation dependent library (CDL) restraints added in 3.6 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: 9.59 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: 9.94 Time building geometry restraints manager: 8.77 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: 0.30 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 60.910 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.080 ------------------------------------------------------------------------------- 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 : 3.194 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: 0.5028 time to fit residues: 828.2330 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 : 3.600 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.114076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.095394 restraints weight = 38986.582| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.85 r_work: 0.2677 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 3.213 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7849 (mt-10) REVERT: Aa 108 MET cc_start: 0.9231 (tpt) cc_final: 0.9010 (tpt) REVERT: Ac 95 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8104 (mt-10) REVERT: Ae 134 MET cc_start: 0.7975 (ttt) cc_final: 0.7657 (ttt) REVERT: Ae 146 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8006 (ttmm) REVERT: Ag 113 ASN cc_start: 0.9010 (m-40) cc_final: 0.8744 (m-40) REVERT: Ag 116 MET cc_start: 0.9181 (ttp) cc_final: 0.8978 (ttp) REVERT: Ag 134 MET cc_start: 0.7668 (ttt) cc_final: 0.7463 (ttt) REVERT: Ai 158 GLN cc_start: 0.9249 (mt0) cc_final: 0.8938 (mt0) REVERT: Ai 181 MET cc_start: 0.8002 (tpt) cc_final: 0.7693 (tpt) REVERT: Ai 208 ARG cc_start: 0.8567 (ptm160) cc_final: 0.8236 (mtp85) REVERT: Ak 71 LEU cc_start: 0.8719 (mm) cc_final: 0.8505 (mm) REVERT: Ak 208 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8474 (ptp-110) REVERT: Ao 180 TYR cc_start: 0.9134 (t80) cc_final: 0.8727 (t80) REVERT: Aq 95 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8009 (mt-10) REVERT: Aq 134 MET cc_start: 0.8585 (ttt) cc_final: 0.8045 (ttt) REVERT: Aq 191 ARG cc_start: 0.7917 (mtp-110) cc_final: 0.7706 (mtp-110) REVERT: Aq 212 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7825 (ttp-170) REVERT: As 46 ARG cc_start: 0.9212 (mpt180) cc_final: 0.9000 (mpt180) REVERT: As 55 ARG cc_start: 0.8350 (tpt-90) cc_final: 0.8036 (tpt-90) REVERT: As 134 MET cc_start: 0.8461 (ttt) cc_final: 0.8099 (ttt) REVERT: As 151 ASN cc_start: 0.8651 (m-40) cc_final: 0.8020 (m110) REVERT: As 191 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7168 (mtp-110) REVERT: As 212 ARG cc_start: 0.8412 (ttp-110) cc_final: 0.7820 (ttp-170) REVERT: Au 134 MET cc_start: 0.8140 (ttt) cc_final: 0.7903 (mtp) REVERT: Au 204 GLU cc_start: 0.8987 (tt0) cc_final: 0.8725 (tt0) REVERT: Aw 134 MET cc_start: 0.7976 (ttt) cc_final: 0.7594 (ttt) REVERT: Aw 204 GLU cc_start: 0.8733 (tt0) cc_final: 0.8336 (pt0) REVERT: Ay 108 MET cc_start: 0.8278 (tpt) cc_final: 0.7613 (tpt) REVERT: Bc 50 ILE cc_start: 0.8100 (mt) cc_final: 0.7856 (mt) REVERT: Bc 55 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7936 (mmm-85) REVERT: Bc 95 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7247 (mt-10) REVERT: Bc 121 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8459 (mm-30) REVERT: Be 95 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7560 (mt-10) REVERT: Be 177 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7865 (ttmm) REVERT: Bg 160 MET cc_start: 0.9475 (mmp) cc_final: 0.9251 (mmt) REVERT: Bg 204 GLU cc_start: 0.8770 (tt0) cc_final: 0.7927 (pt0) REVERT: Bi 79 ASP cc_start: 0.8577 (m-30) cc_final: 0.8310 (m-30) REVERT: Bi 121 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8388 (mm-30) REVERT: Bi 125 SER cc_start: 0.8752 (p) cc_final: 0.8405 (t) REVERT: Bi 135 MET cc_start: 0.8144 (mmm) cc_final: 0.7845 (mmm) REVERT: Bi 136 ASP cc_start: 0.8312 (t0) cc_final: 0.8072 (t0) REVERT: Bi 168 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8415 (mt-10) REVERT: Bi 208 ARG cc_start: 0.8781 (ptm160) cc_final: 0.8519 (ptp-110) REVERT: Bk 121 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8448 (mm-30) REVERT: Bk 135 MET cc_start: 0.8601 (mmm) cc_final: 0.8315 (tpp) REVERT: Bm 55 ARG cc_start: 0.8506 (tpt-90) cc_final: 0.8016 (tpt-90) REVERT: Bm 71 LEU cc_start: 0.8873 (mm) cc_final: 0.8670 (mm) REVERT: Bm 95 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7557 (mt-10) REVERT: Bo 95 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7530 (mt-10) REVERT: Bo 141 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (t) outliers start: 88 outliers final: 39 residues processed: 1028 average time/residue: 0.4801 time to fit residues: 781.5114 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 : 3.236 ------------------------------------------------------------------------------- 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: 7.9990 chunk 309 optimal weight: 6.9990 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.101286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.082217 restraints weight = 40337.907| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.89 r_work: 0.2473 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5309 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= 0.298 Angle : 0.603 6.843 46851 Z= 0.317 Chirality : 0.045 0.176 5271 Planarity : 0.005 0.047 5712 Dihedral : 15.344 171.665 5945 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.43 % Allowed : 19.08 % Favored : 77.49 % 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: 0.26 (0.13), residues: 3864 helix: 1.18 (0.12), residues: 1890 sheet: 0.67 (0.28), residues: 252 loop : -1.05 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPBe 132 HIS 0.005 0.001 HISBa 217 PHE 0.021 0.003 PHEBa 200 TYR 0.013 0.002 TYRAg 143 ARG 0.008 0.001 ARGBi 191 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 1449) hydrogen bonds : angle 4.12105 ( 4095) covalent geometry : bond 0.00699 (34293) covalent geometry : angle 0.60341 (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 1380 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1264 time to evaluate : 3.382 Fit side-chains REVERT: Aa 55 ARG cc_start: 0.8715 (tpt-90) cc_final: 0.8341 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8500 (mt-10) REVERT: Aa 212 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.8406 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8641 (mmm160) cc_final: 0.7699 (tpt170) REVERT: Ac 91 ASP cc_start: 0.8987 (m-30) cc_final: 0.8646 (m-30) REVERT: Ae 191 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7576 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8294 (ttp-170) REVERT: Ag 67 LEU cc_start: 0.8876 (mt) cc_final: 0.8646 (mp) REVERT: Ag 84 ARG cc_start: 0.9110 (ttm170) cc_final: 0.8663 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8338 (mt-10) REVERT: Ag 191 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7439 (mtp-110) REVERT: Ag 204 GLU cc_start: 0.9236 (tt0) cc_final: 0.8791 (tt0) REVERT: Ai 46 ARG cc_start: 0.9087 (mpt180) cc_final: 0.8835 (mpt180) REVERT: Ai 79 ASP cc_start: 0.9194 (m-30) cc_final: 0.8973 (m-30) REVERT: Ai 95 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8193 (mt-10) REVERT: Ai 172 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7838 (mt-10) REVERT: Ai 204 GLU cc_start: 0.9169 (tt0) cc_final: 0.8898 (tt0) REVERT: Ai 212 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8054 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7818 (mt-10) REVERT: Ak 71 LEU cc_start: 0.8986 (mm) cc_final: 0.8557 (mm) REVERT: Ak 168 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8605 (mt-10) REVERT: Ak 175 ASN cc_start: 0.8928 (m-40) cc_final: 0.8691 (m-40) REVERT: Ak 190 LEU cc_start: 0.8959 (tp) cc_final: 0.8715 (tp) REVERT: Ak 206 THR cc_start: 0.9553 (p) cc_final: 0.9319 (t) REVERT: Ak 208 ARG cc_start: 0.9147 (ptp-170) cc_final: 0.8900 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8297 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7884 (mt-10) REVERT: Am 67 LEU cc_start: 0.8585 (mt) cc_final: 0.8365 (mm) REVERT: Am 110 THR cc_start: 0.9273 (m) cc_final: 0.9066 (m) REVERT: Am 136 ASP cc_start: 0.9015 (t0) cc_final: 0.8618 (t0) REVERT: Am 191 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7718 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8166 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9155 (m) cc_final: 0.8894 (m) REVERT: Ao 134 MET cc_start: 0.9127 (ttt) cc_final: 0.8640 (ttt) REVERT: Ao 135 MET cc_start: 0.9159 (mmm) cc_final: 0.8828 (mmt) REVERT: Ao 175 ASN cc_start: 0.9010 (m-40) cc_final: 0.8599 (m110) REVERT: Ao 180 TYR cc_start: 0.9374 (t80) cc_final: 0.8932 (t80) REVERT: Ao 184 TYR cc_start: 0.9487 (t80) cc_final: 0.9275 (t80) REVERT: Ao 204 GLU cc_start: 0.9107 (tt0) cc_final: 0.8468 (tt0) REVERT: Ao 212 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.8249 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8568 (tpt-90) cc_final: 0.8220 (tpt-90) REVERT: Aq 88 SER cc_start: 0.9227 (p) cc_final: 0.9010 (p) REVERT: Aq 95 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8297 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8131 (ttp-170) REVERT: As 95 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8269 (mt-10) REVERT: As 160 MET cc_start: 0.9541 (mmm) cc_final: 0.9230 (mmt) REVERT: As 212 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8111 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9098 (m-30) cc_final: 0.8750 (m-30) REVERT: Au 95 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8149 (mt-10) REVERT: Au 175 ASN cc_start: 0.9083 (m-40) cc_final: 0.8770 (m-40) REVERT: Au 177 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8722 (ttmm) REVERT: Au 180 TYR cc_start: 0.9278 (t80) cc_final: 0.8975 (t80) REVERT: Au 204 GLU cc_start: 0.9207 (tt0) cc_final: 0.9001 (tt0) REVERT: Au 208 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7982 (ptm160) REVERT: Au 212 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8346 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8689 (mt) cc_final: 0.8189 (mm) REVERT: Aw 71 LEU cc_start: 0.8909 (mm) cc_final: 0.8695 (mm) REVERT: Aw 112 MET cc_start: 0.9520 (mmm) cc_final: 0.9140 (mmp) REVERT: Aw 134 MET cc_start: 0.9103 (ttt) cc_final: 0.8557 (ttt) REVERT: Aw 212 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8233 (ttp-170) REVERT: Ay 95 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8328 (mt-10) REVERT: Ba 157 ARG cc_start: 0.9318 (ttm110) cc_final: 0.8828 (ttm110) REVERT: Ba 212 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8144 (ttp-170) REVERT: Ba 220 MET cc_start: 0.9053 (mtm) cc_final: 0.8781 (mtm) REVERT: Bc 55 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8378 (tpt-90) REVERT: Bc 95 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Bc 153 LYS cc_start: 0.9186 (mptt) cc_final: 0.8961 (mptt) REVERT: Bc 206 THR cc_start: 0.9507 (p) cc_final: 0.9306 (t) REVERT: Bc 212 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8020 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7773 (mt-10) REVERT: Be 79 ASP cc_start: 0.9220 (m-30) cc_final: 0.8967 (m-30) REVERT: Be 95 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8246 (mt-10) REVERT: Be 112 MET cc_start: 0.9507 (mmp) cc_final: 0.9178 (mmp) REVERT: Be 151 ASN cc_start: 0.9412 (m-40) cc_final: 0.9135 (m-40) REVERT: Be 177 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8528 (ttmm) REVERT: Be 191 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.8004 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8367 (ttp-170) REVERT: Bg 99 LEU cc_start: 0.8747 (tp) cc_final: 0.8517 (tp) REVERT: Bg 108 MET cc_start: 0.9289 (tpt) cc_final: 0.9057 (tpt) REVERT: Bg 135 MET cc_start: 0.9053 (mmm) cc_final: 0.8369 (mmt) REVERT: Bg 204 GLU cc_start: 0.9053 (tt0) cc_final: 0.8806 (tt0) REVERT: Bg 212 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8161 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9077 (mpt180) cc_final: 0.8774 (mpt180) REVERT: Bi 148 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8422 (mt) REVERT: Bi 177 LYS cc_start: 0.8787 (mttt) cc_final: 0.8343 (ttmm) REVERT: Bi 191 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7568 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9295 (tt0) cc_final: 0.9051 (tt0) REVERT: Bi 208 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7869 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8136 (ttp-170) REVERT: Bi 215 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7858 (mt-10) REVERT: Bk 67 LEU cc_start: 0.8671 (mt) cc_final: 0.8385 (mm) REVERT: Bk 110 THR cc_start: 0.9152 (m) cc_final: 0.8800 (m) REVERT: Bk 134 MET cc_start: 0.9004 (ttt) cc_final: 0.8588 (ttt) REVERT: Bk 191 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7773 (mtp-110) REVERT: Bk 206 THR cc_start: 0.9558 (p) cc_final: 0.9352 (t) REVERT: Bk 212 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8263 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8691 (tpt-90) cc_final: 0.8481 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8270 (mt-10) REVERT: Bm 116 MET cc_start: 0.9575 (ttp) cc_final: 0.9336 (ttp) REVERT: Bm 177 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8574 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8176 (ttp-170) REVERT: Bo 56 MET cc_start: 0.9232 (mmt) cc_final: 0.8944 (mmt) REVERT: Bo 95 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8167 (mt-10) REVERT: Bo 155 THR cc_start: 0.9376 (m) cc_final: 0.9153 (m) REVERT: Bo 212 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8383 (ttp-170) outliers start: 116 outliers final: 63 residues processed: 1324 average time/residue: 0.4895 time to fit residues: 1014.2033 Evaluate side-chains 1246 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1180 time to evaluate : 3.546 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 368 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.103672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.084769 restraints weight = 39989.913| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.88 r_work: 0.2523 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5488 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= 0.169 Angle : 0.514 5.897 46851 Z= 0.266 Chirality : 0.040 0.145 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.239 175.120 5943 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.25 % Allowed : 19.61 % Favored : 77.14 % 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: 0.40 (0.13), residues: 3864 helix: 1.37 (0.12), residues: 1890 sheet: 1.04 (0.27), residues: 210 loop : -1.08 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAw 132 HIS 0.004 0.001 HISAa 217 PHE 0.016 0.002 PHEAo 200 TYR 0.014 0.001 TYRBo 198 ARG 0.005 0.001 ARGAs 191 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 1449) hydrogen bonds : angle 3.94620 ( 4095) covalent geometry : bond 0.00407 (34293) covalent geometry : angle 0.51411 (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 1364 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1254 time to evaluate : 3.363 Fit side-chains REVERT: Aa 95 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8390 (mt-10) REVERT: Aa 206 THR cc_start: 0.9551 (p) cc_final: 0.9323 (t) REVERT: Aa 212 ARG cc_start: 0.8763 (ttp-110) cc_final: 0.8339 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8619 (mmm160) cc_final: 0.7838 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.9002 (m-30) cc_final: 0.8661 (m-30) REVERT: Ae 50 ILE cc_start: 0.8263 (mt) cc_final: 0.7987 (tt) REVERT: Ae 129 ASN cc_start: 0.9297 (p0) cc_final: 0.9091 (p0) REVERT: Ae 191 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7511 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8281 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8311 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8617 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9211 (tt0) cc_final: 0.9005 (tt0) REVERT: Ai 95 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8232 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9098 (m-40) cc_final: 0.8715 (m-40) REVERT: Ai 175 ASN cc_start: 0.8872 (m-40) cc_final: 0.8467 (m110) REVERT: Ai 204 GLU cc_start: 0.9112 (tt0) cc_final: 0.8883 (tt0) REVERT: Ai 206 THR cc_start: 0.9584 (p) cc_final: 0.9352 (t) REVERT: Ai 208 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8121 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8063 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Ai 220 MET cc_start: 0.9045 (mtm) cc_final: 0.8775 (mtm) REVERT: Ak 55 ARG cc_start: 0.8553 (tpt-90) cc_final: 0.8258 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8940 (mm) cc_final: 0.8541 (mm) REVERT: Ak 142 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: Ak 175 ASN cc_start: 0.8977 (m-40) cc_final: 0.8761 (m-40) REVERT: Ak 191 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7514 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9560 (p) cc_final: 0.9312 (t) REVERT: Ak 208 ARG cc_start: 0.9040 (ptp-170) cc_final: 0.8817 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8293 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7864 (mt-10) REVERT: Am 107 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8323 (mp0) REVERT: Am 110 THR cc_start: 0.9261 (m) cc_final: 0.9032 (m) REVERT: Am 191 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7619 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.8027 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9079 (m) cc_final: 0.8729 (m) REVERT: Ao 129 ASN cc_start: 0.9235 (p0) cc_final: 0.9007 (p0) REVERT: Ao 134 MET cc_start: 0.9061 (ttt) cc_final: 0.8511 (ttt) REVERT: Ao 175 ASN cc_start: 0.8970 (m-40) cc_final: 0.8708 (m-40) REVERT: Ao 204 GLU cc_start: 0.9097 (tt0) cc_final: 0.8450 (tt0) REVERT: Ao 212 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8210 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8580 (tpt-90) cc_final: 0.8226 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8265 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.7883 (ttp-170) REVERT: As 79 ASP cc_start: 0.9033 (m-30) cc_final: 0.8833 (m-30) REVERT: As 95 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8245 (mt-10) REVERT: As 107 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8514 (pt0) REVERT: As 160 MET cc_start: 0.9514 (mmm) cc_final: 0.9173 (mmt) REVERT: As 212 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8072 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9071 (m-30) cc_final: 0.8764 (m-30) REVERT: Au 95 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8030 (mt-10) REVERT: Au 110 THR cc_start: 0.9286 (m) cc_final: 0.9079 (m) REVERT: Au 151 ASN cc_start: 0.9168 (m-40) cc_final: 0.8923 (m110) REVERT: Au 175 ASN cc_start: 0.9077 (m-40) cc_final: 0.8813 (m-40) REVERT: Au 177 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8558 (ttmm) REVERT: Au 212 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8254 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8726 (mt) cc_final: 0.8329 (mm) REVERT: Aw 71 LEU cc_start: 0.8850 (mm) cc_final: 0.8628 (mm) REVERT: Aw 110 THR cc_start: 0.9302 (m) cc_final: 0.8888 (m) REVERT: Aw 134 MET cc_start: 0.9059 (ttt) cc_final: 0.8512 (ttt) REVERT: Aw 190 LEU cc_start: 0.8850 (tp) cc_final: 0.8486 (mp) REVERT: Aw 208 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7748 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8244 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8913 (mtt) cc_final: 0.8525 (mtt) REVERT: Ay 77 GLN cc_start: 0.8709 (mt0) cc_final: 0.8427 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8319 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8149 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8300 (mt-10) REVERT: Bc 97 VAL cc_start: 0.9341 (t) cc_final: 0.9066 (t) REVERT: Bc 153 LYS cc_start: 0.9138 (mptt) cc_final: 0.8913 (mptt) REVERT: Bc 206 THR cc_start: 0.9579 (p) cc_final: 0.9339 (t) REVERT: Bc 212 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8130 (ttp-170) REVERT: Be 95 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8186 (mt-10) REVERT: Be 151 ASN cc_start: 0.9370 (m-40) cc_final: 0.9074 (m-40) REVERT: Be 177 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8516 (ttmm) REVERT: Be 191 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7837 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8154 (ttp-170) REVERT: Bg 99 LEU cc_start: 0.8793 (tp) cc_final: 0.8587 (tp) REVERT: Bg 153 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8762 (mptt) REVERT: Bg 204 GLU cc_start: 0.9051 (tt0) cc_final: 0.8832 (tt0) REVERT: Bg 212 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8180 (ttp-170) REVERT: Bi 99 LEU cc_start: 0.8797 (tp) cc_final: 0.8544 (tp) REVERT: Bi 134 MET cc_start: 0.9044 (ttt) cc_final: 0.8611 (ttt) REVERT: Bi 151 ASN cc_start: 0.9122 (m-40) cc_final: 0.8734 (m110) REVERT: Bi 177 LYS cc_start: 0.8782 (mttt) cc_final: 0.8359 (ttmm) REVERT: Bi 191 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7660 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9172 (tt0) cc_final: 0.8949 (tt0) REVERT: Bi 206 THR cc_start: 0.9521 (p) cc_final: 0.9316 (t) REVERT: Bi 208 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7968 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8121 (ttp-170) REVERT: Bk 55 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8259 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9161 (m) cc_final: 0.8911 (m) REVERT: Bk 134 MET cc_start: 0.8986 (ttt) cc_final: 0.8546 (ttt) REVERT: Bk 191 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7656 (mtp-110) REVERT: Bk 206 THR cc_start: 0.9566 (p) cc_final: 0.9363 (t) REVERT: Bk 212 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8105 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8620 (tpt-90) cc_final: 0.8088 (tpt-90) REVERT: Bm 89 GLN cc_start: 0.9415 (mt0) cc_final: 0.8943 (mt0) REVERT: Bm 95 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8319 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8512 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8089 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8075 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8281 (ttp-170) outliers start: 110 outliers final: 69 residues processed: 1306 average time/residue: 0.4894 time to fit residues: 1015.2758 Evaluate side-chains 1296 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1222 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 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 208 ARG Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 142 GLU Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU 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 Ao residue 177 LYS Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 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 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 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Bg residue 51 THR 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 153 LYS Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL 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: 9.9990 chunk 154 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 151 ASN Ag 151 ASN Ao 151 ASN As 66 ASN Ay 158 GLN Bc 151 ASN Bg 66 ASN Bi 158 GLN Bm 151 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 = 0.2934 r_free = 0.2934 target = 0.102321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.083312 restraints weight = 40090.766| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 1.89 r_work: 0.2494 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2332 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34293 Z= 0.205 Angle : 0.532 6.254 46851 Z= 0.276 Chirality : 0.041 0.153 5271 Planarity : 0.005 0.050 5712 Dihedral : 15.291 174.254 5943 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.67 % Allowed : 19.70 % Favored : 76.63 % 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: 0.40 (0.13), residues: 3864 helix: 1.33 (0.12), residues: 1890 sheet: 0.93 (0.26), residues: 210 loop : -1.02 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPBe 132 HIS 0.004 0.001 HISAa 217 PHE 0.016 0.002 PHEBa 200 TYR 0.017 0.001 TYRBo 198 ARG 0.007 0.001 ARGBk 174 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1449) hydrogen bonds : angle 3.93880 ( 4095) covalent geometry : bond 0.00493 (34293) covalent geometry : angle 0.53188 (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 1331 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1207 time to evaluate : 3.460 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8408 (mt-10) REVERT: Aa 206 THR cc_start: 0.9540 (p) cc_final: 0.9308 (t) REVERT: Aa 212 ARG cc_start: 0.8734 (ttp-110) cc_final: 0.8277 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8606 (mmm160) cc_final: 0.7824 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8957 (m-30) cc_final: 0.8655 (m-30) REVERT: Ae 50 ILE cc_start: 0.8250 (mt) cc_final: 0.8020 (tt) REVERT: Ae 129 ASN cc_start: 0.9324 (p0) cc_final: 0.9102 (p0) REVERT: Ae 191 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7571 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8289 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8382 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8590 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9241 (tt0) cc_final: 0.8992 (tt0) REVERT: Ag 212 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8198 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8196 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9191 (m-40) cc_final: 0.8833 (m-40) REVERT: Ai 175 ASN cc_start: 0.8857 (m-40) cc_final: 0.8402 (m110) REVERT: Ai 204 GLU cc_start: 0.9161 (tt0) cc_final: 0.8935 (tt0) REVERT: Ai 206 THR cc_start: 0.9584 (p) cc_final: 0.9341 (t) REVERT: Ai 208 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8144 (ptm160) REVERT: Ai 212 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8160 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7743 (mt-10) REVERT: Ai 220 MET cc_start: 0.9047 (mtm) cc_final: 0.8794 (mtm) REVERT: Ak 71 LEU cc_start: 0.8960 (mm) cc_final: 0.8538 (mm) REVERT: Ak 175 ASN cc_start: 0.8981 (m-40) cc_final: 0.8763 (m-40) REVERT: Ak 206 THR cc_start: 0.9595 (p) cc_final: 0.9305 (t) REVERT: Ak 208 ARG cc_start: 0.9031 (ptp-170) cc_final: 0.8808 (ptp-110) REVERT: Ak 211 VAL cc_start: 0.9333 (t) cc_final: 0.9126 (t) REVERT: Ak 212 ARG cc_start: 0.8683 (ttp-110) cc_final: 0.8343 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7913 (mt-10) REVERT: Am 107 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8290 (mp0) REVERT: Am 191 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7747 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8151 (ttp80) REVERT: Ao 95 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8236 (mt-10) REVERT: Ao 110 THR cc_start: 0.9079 (m) cc_final: 0.8762 (m) REVERT: Ao 129 ASN cc_start: 0.9237 (p0) cc_final: 0.9006 (p0) REVERT: Ao 134 MET cc_start: 0.9118 (ttt) cc_final: 0.8601 (ttt) REVERT: Ao 175 ASN cc_start: 0.8971 (m-40) cc_final: 0.8646 (m-40) REVERT: Ao 184 TYR cc_start: 0.9469 (t80) cc_final: 0.9261 (t80) REVERT: Ao 204 GLU cc_start: 0.9101 (tt0) cc_final: 0.8378 (tt0) REVERT: Ao 212 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8259 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8478 (tpt-90) cc_final: 0.8253 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8188 (mt-10) REVERT: Aq 208 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8678 (ptm160) REVERT: Aq 212 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.7991 (ttp-170) REVERT: As 95 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8214 (mt-10) REVERT: As 107 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8537 (pt0) REVERT: As 160 MET cc_start: 0.9513 (mmm) cc_final: 0.9178 (mmt) REVERT: As 172 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: As 212 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8127 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9047 (m-30) cc_final: 0.8739 (m-30) REVERT: Au 95 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8097 (mt-10) REVERT: Au 175 ASN cc_start: 0.9071 (m-40) cc_final: 0.8798 (m-40) REVERT: Au 177 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8547 (ttmm) REVERT: Au 208 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8019 (ptm160) REVERT: Au 212 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8230 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8769 (mt) cc_final: 0.8291 (mm) REVERT: Aw 71 LEU cc_start: 0.8893 (mm) cc_final: 0.8655 (mm) REVERT: Aw 134 MET cc_start: 0.9103 (ttt) cc_final: 0.8638 (ttt) REVERT: Aw 190 LEU cc_start: 0.8877 (tp) cc_final: 0.8501 (mp) REVERT: Aw 208 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7797 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8223 (ttp-170) REVERT: Ay 56 MET cc_start: 0.9004 (mtt) cc_final: 0.8592 (mtt) REVERT: Ay 77 GLN cc_start: 0.8745 (mt0) cc_final: 0.8505 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Ba 157 ARG cc_start: 0.9255 (ttm170) cc_final: 0.8673 (ttm170) REVERT: Ba 191 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7461 (mtp-110) REVERT: Ba 212 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8259 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8300 (mt-10) REVERT: Bc 153 LYS cc_start: 0.9147 (mptt) cc_final: 0.8930 (mptt) REVERT: Bc 206 THR cc_start: 0.9562 (p) cc_final: 0.9343 (t) REVERT: Bc 212 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8137 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8414 (tpt-90) REVERT: Be 95 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Be 151 ASN cc_start: 0.9398 (m-40) cc_final: 0.9092 (m-40) REVERT: Be 177 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8556 (ttmm) REVERT: Be 191 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7757 (mtp-110) REVERT: Be 212 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8259 (ttp-170) REVERT: Bg 99 LEU cc_start: 0.8795 (tp) cc_final: 0.8574 (tp) REVERT: Bg 212 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8236 (ttp-170) REVERT: Bi 99 LEU cc_start: 0.8789 (tp) cc_final: 0.8542 (tp) REVERT: Bi 134 MET cc_start: 0.9063 (ttt) cc_final: 0.8625 (ttt) REVERT: Bi 151 ASN cc_start: 0.9184 (m-40) cc_final: 0.8879 (m110) REVERT: Bi 177 LYS cc_start: 0.8754 (mttt) cc_final: 0.8341 (ttmm) REVERT: Bi 191 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9181 (tt0) cc_final: 0.8974 (tt0) REVERT: Bi 208 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7944 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8200 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9062 (mtm) cc_final: 0.8773 (mtp) REVERT: Bk 55 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8327 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9173 (m) cc_final: 0.8763 (m) REVERT: Bk 134 MET cc_start: 0.9029 (ttt) cc_final: 0.8631 (ttt) REVERT: Bk 206 THR cc_start: 0.9565 (p) cc_final: 0.9357 (t) REVERT: Bk 212 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8043 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8350 (tpt-90) REVERT: Bm 89 GLN cc_start: 0.9409 (mt0) cc_final: 0.8938 (mt0) REVERT: Bm 95 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8318 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8514 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8273 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8191 (tpt-90) REVERT: Bo 56 MET cc_start: 0.9296 (mmt) cc_final: 0.8984 (mmt) REVERT: Bo 95 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8065 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8151 (ttp-170) outliers start: 124 outliers final: 94 residues processed: 1268 average time/residue: 0.4837 time to fit residues: 973.5243 Evaluate side-chains 1275 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1175 time to evaluate : 3.572 ------------------------------------------------------------------------------- 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 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 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 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 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 208 ARG 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 Aq residue 208 ARG 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 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 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 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 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 51 THR 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 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 54 MET 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 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 133 VAL Chi-restraints excluded: chain Bm residue 195 LEU Chi-restraints excluded: chain Bo residue 99 LEU Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 234 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 151 ASN Ae 158 GLN Ag 151 ASN Ao 151 ASN ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 158 GLN Bc 151 ASN ** Be 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 66 ASN Bi 158 GLN Bm 151 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 = 0.2934 r_free = 0.2934 target = 0.102272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.083263 restraints weight = 40110.725| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 1.90 r_work: 0.2488 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34293 Z= 0.205 Angle : 0.534 6.586 46851 Z= 0.276 Chirality : 0.041 0.159 5271 Planarity : 0.005 0.055 5712 Dihedral : 15.285 174.089 5943 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.55 % Allowed : 20.35 % Favored : 76.10 % 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: 0.41 (0.13), residues: 3864 helix: 1.32 (0.12), residues: 1890 sheet: 0.89 (0.25), residues: 210 loop : -0.96 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAk 132 HIS 0.004 0.001 HISAa 217 PHE 0.016 0.002 PHEBa 200 TYR 0.018 0.001 TYRBo 198 ARG 0.014 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 1449) hydrogen bonds : angle 3.93459 ( 4095) covalent geometry : bond 0.00493 (34293) covalent geometry : angle 0.53421 (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: 120 poor density : 1204 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8392 (mt-10) REVERT: Aa 206 THR cc_start: 0.9541 (p) cc_final: 0.9290 (t) REVERT: Aa 212 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8275 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8614 (mmm160) cc_final: 0.7831 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8967 (m-30) cc_final: 0.8651 (m-30) REVERT: Ac 190 LEU cc_start: 0.9049 (tp) cc_final: 0.8754 (mp) REVERT: Ae 191 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7585 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8314 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8366 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8624 (ttmm) REVERT: Ag 204 GLU cc_start: 0.9223 (tt0) cc_final: 0.8985 (tt0) REVERT: Ag 212 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8263 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8180 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9213 (m-40) cc_final: 0.8834 (m-40) REVERT: Ai 175 ASN cc_start: 0.8879 (m-40) cc_final: 0.8424 (m110) REVERT: Ai 204 GLU cc_start: 0.9135 (tt0) cc_final: 0.8921 (tt0) REVERT: Ai 206 THR cc_start: 0.9585 (p) cc_final: 0.9337 (t) REVERT: Ai 208 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8124 (ptm160) REVERT: Ai 215 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7730 (mt-10) REVERT: Ai 220 MET cc_start: 0.9032 (mtm) cc_final: 0.8779 (mtm) REVERT: Ak 55 ARG cc_start: 0.8665 (tpt-90) cc_final: 0.8430 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8950 (mm) cc_final: 0.8497 (mm) REVERT: Ak 175 ASN cc_start: 0.9014 (m-40) cc_final: 0.8803 (m-40) REVERT: Ak 177 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8443 (ttmm) REVERT: Ak 206 THR cc_start: 0.9612 (p) cc_final: 0.9297 (t) REVERT: Ak 208 ARG cc_start: 0.9037 (ptp-170) cc_final: 0.8818 (ptp-110) REVERT: Ak 211 VAL cc_start: 0.9345 (t) cc_final: 0.9134 (t) REVERT: Ak 212 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8357 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7945 (mt-10) REVERT: Ak 220 MET cc_start: 0.9038 (mtm) cc_final: 0.8730 (mtp) REVERT: Am 107 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8263 (mp0) REVERT: Am 191 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7667 (mtp-110) REVERT: Am 203 TYR cc_start: 0.9427 (t80) cc_final: 0.9100 (t80) REVERT: Am 212 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8231 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8273 (mt-10) REVERT: Ao 110 THR cc_start: 0.9087 (m) cc_final: 0.8766 (m) REVERT: Ao 129 ASN cc_start: 0.9236 (p0) cc_final: 0.9005 (p0) REVERT: Ao 134 MET cc_start: 0.9097 (ttt) cc_final: 0.8572 (ttt) REVERT: Ao 175 ASN cc_start: 0.8945 (m-40) cc_final: 0.8619 (m-40) REVERT: Ao 184 TYR cc_start: 0.9471 (t80) cc_final: 0.9264 (t80) REVERT: Ao 204 GLU cc_start: 0.9096 (tt0) cc_final: 0.8363 (tt0) REVERT: Ao 212 ARG cc_start: 0.8749 (ttp-110) cc_final: 0.8270 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8587 (tpt-90) cc_final: 0.8379 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8252 (mt-10) REVERT: Aq 208 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8657 (ptm160) REVERT: Aq 212 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.7987 (ttp-170) REVERT: As 95 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8216 (mt-10) REVERT: As 136 ASP cc_start: 0.8779 (t0) cc_final: 0.8566 (t0) REVERT: As 160 MET cc_start: 0.9517 (mmm) cc_final: 0.9186 (mmt) REVERT: As 172 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: As 212 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8003 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9050 (m-30) cc_final: 0.8732 (m-30) REVERT: Au 95 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8101 (mt-10) REVERT: Au 175 ASN cc_start: 0.9075 (m-40) cc_final: 0.8811 (m-40) REVERT: Au 177 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8631 (ttmm) REVERT: Au 208 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8034 (ptm160) REVERT: Au 212 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8248 (ttp-170) REVERT: Aw 67 LEU cc_start: 0.8778 (mt) cc_final: 0.8315 (mm) REVERT: Aw 71 LEU cc_start: 0.8921 (mm) cc_final: 0.8678 (mm) REVERT: Aw 95 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8205 (mt-10) REVERT: Aw 134 MET cc_start: 0.9109 (ttt) cc_final: 0.8649 (ttt) REVERT: Aw 172 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: Aw 190 LEU cc_start: 0.8873 (tp) cc_final: 0.8414 (mp) REVERT: Aw 208 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7822 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8227 (ttp-170) REVERT: Aw 220 MET cc_start: 0.9069 (mtm) cc_final: 0.8666 (mtp) REVERT: Ay 56 MET cc_start: 0.9048 (mtt) cc_final: 0.8628 (mtt) REVERT: Ay 77 GLN cc_start: 0.8771 (mt0) cc_final: 0.8480 (mm-40) REVERT: Ay 95 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8373 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8308 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8355 (mt-10) REVERT: Bc 153 LYS cc_start: 0.9142 (mptt) cc_final: 0.8928 (mptt) REVERT: Bc 206 THR cc_start: 0.9573 (p) cc_final: 0.9337 (t) REVERT: Bc 212 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8164 (ttp-170) REVERT: Be 55 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8393 (tpt90) REVERT: Be 95 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8275 (mt-10) REVERT: Be 151 ASN cc_start: 0.9398 (m-40) cc_final: 0.9087 (m-40) REVERT: Be 177 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8540 (ttmm) REVERT: Be 212 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8295 (ttp-170) REVERT: Bg 99 LEU cc_start: 0.8817 (tp) cc_final: 0.8579 (tp) REVERT: Bg 153 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8738 (mptt) REVERT: Bg 212 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8303 (ttp-170) REVERT: Bi 99 LEU cc_start: 0.8748 (tp) cc_final: 0.8492 (tp) REVERT: Bi 134 MET cc_start: 0.9068 (ttt) cc_final: 0.8627 (ttt) REVERT: Bi 151 ASN cc_start: 0.9189 (m-40) cc_final: 0.8863 (m110) REVERT: Bi 177 LYS cc_start: 0.8751 (mttt) cc_final: 0.8354 (ttmm) REVERT: Bi 191 ARG cc_start: 0.8002 (mtp-110) cc_final: 0.7578 (mtp-110) REVERT: Bi 204 GLU cc_start: 0.9153 (tt0) cc_final: 0.8944 (tt0) REVERT: Bi 208 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7913 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8260 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9101 (mtm) cc_final: 0.8760 (mtp) REVERT: Bk 54 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8383 (ptp) REVERT: Bk 55 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8339 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8872 (m) REVERT: Bk 134 MET cc_start: 0.9035 (ttt) cc_final: 0.8628 (ttt) REVERT: Bk 191 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7690 (mtp-110) REVERT: Bk 206 THR cc_start: 0.9566 (p) cc_final: 0.9352 (t) REVERT: Bk 212 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8226 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8612 (tpt-90) cc_final: 0.8258 (tpt-90) REVERT: Bm 71 LEU cc_start: 0.9125 (mm) cc_final: 0.8909 (mm) REVERT: Bm 89 GLN cc_start: 0.9402 (mt0) cc_final: 0.8926 (mt0) REVERT: Bm 95 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8343 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8495 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8138 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8406 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8080 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8138 (ttp-170) outliers start: 120 outliers final: 92 residues processed: 1263 average time/residue: 0.4804 time to fit residues: 960.8564 Evaluate side-chains 1283 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1181 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 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 64 VAL Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ai residue 172 GLU 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 Ak residue 178 GLU 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 54 MET 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 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 51 THR Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 172 GLU 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 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 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 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 178 GLU 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 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 54 MET 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 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 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 9 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 335 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 Ae 113 ASN Ae 151 ASN Ag 151 ASN Am 66 ASN Am 113 ASN Ao 66 ASN Ao 151 ASN Ay 66 ASN Ay 158 GLN ** Bc 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 151 ASN Bm 151 ASN Bo 66 ASN Bo 158 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.106995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.088141 restraints weight = 40071.392| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.89 r_work: 0.2560 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5898 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= 0.118 Angle : 0.489 6.838 46851 Z= 0.250 Chirality : 0.038 0.154 5271 Planarity : 0.005 0.055 5712 Dihedral : 15.188 176.841 5943 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.90 % Allowed : 21.38 % Favored : 75.72 % 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: 0.63 (0.13), residues: 3864 helix: 1.51 (0.12), residues: 1890 sheet: 0.79 (0.25), residues: 210 loop : -0.83 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAk 132 HIS 0.004 0.001 HISAm 217 PHE 0.015 0.002 PHEAg 200 TYR 0.016 0.001 TYRBo 198 ARG 0.015 0.001 ARGBc 191 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1449) hydrogen bonds : angle 3.87095 ( 4095) covalent geometry : bond 0.00285 (34293) covalent geometry : angle 0.48867 (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 1339 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1241 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8610 (tpt-90) cc_final: 0.8325 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8375 (mt-10) REVERT: Aa 107 GLU cc_start: 0.8728 (pt0) cc_final: 0.8299 (pt0) REVERT: Aa 108 MET cc_start: 0.9374 (tpt) cc_final: 0.9033 (tpt) REVERT: Aa 206 THR cc_start: 0.9530 (p) cc_final: 0.9321 (t) REVERT: Aa 212 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8202 (ttp-170) REVERT: Ac 55 ARG cc_start: 0.8557 (mmm160) cc_final: 0.7806 (tpt-90) REVERT: Ac 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8770 (mp) REVERT: Ae 108 MET cc_start: 0.9264 (tpt) cc_final: 0.8718 (tpt) REVERT: Ae 191 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7666 (mtp-110) REVERT: Ae 212 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8280 (ttp-170) REVERT: Ag 65 LEU cc_start: 0.9433 (mt) cc_final: 0.9119 (mp) REVERT: Ag 95 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8283 (mt-10) REVERT: Ag 172 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: Ag 212 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8237 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8231 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9145 (m-40) cc_final: 0.8786 (m-40) REVERT: Ai 206 THR cc_start: 0.9595 (p) cc_final: 0.9259 (t) REVERT: Ai 212 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8201 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7737 (mt-10) REVERT: Ai 220 MET cc_start: 0.8997 (mtm) cc_final: 0.8732 (mtm) REVERT: Ak 55 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8288 (tpt-90) REVERT: Ak 175 ASN cc_start: 0.9001 (m-40) cc_final: 0.8801 (m-40) REVERT: Ak 177 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8390 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8868 (tp) cc_final: 0.8618 (mp) REVERT: Ak 206 THR cc_start: 0.9575 (p) cc_final: 0.9228 (t) REVERT: Ak 212 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8354 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7959 (mt-10) REVERT: Ak 220 MET cc_start: 0.8970 (mtm) cc_final: 0.8687 (mtp) REVERT: Am 107 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8209 (mp0) REVERT: Am 139 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: Am 191 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7617 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8187 (ttp-170) REVERT: Ao 95 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8274 (mt-10) REVERT: Ao 175 ASN cc_start: 0.8940 (m-40) cc_final: 0.8697 (m-40) REVERT: Ao 204 GLU cc_start: 0.9081 (tt0) cc_final: 0.8342 (tt0) REVERT: Ao 212 ARG cc_start: 0.8714 (ttp-110) cc_final: 0.8247 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8595 (tpt-90) cc_final: 0.8320 (tpt-90) REVERT: Aq 56 MET cc_start: 0.9381 (mmt) cc_final: 0.9133 (mmt) REVERT: Aq 95 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8198 (mt-10) REVERT: Aq 180 TYR cc_start: 0.9277 (t80) cc_final: 0.8891 (t80) REVERT: Aq 212 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.7990 (ttp-170) REVERT: As 95 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8196 (mt-10) REVERT: As 116 MET cc_start: 0.9509 (ttp) cc_final: 0.9126 (ttp) REVERT: As 136 ASP cc_start: 0.8844 (t0) cc_final: 0.8639 (t0) REVERT: As 172 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: As 212 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8025 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9042 (m-30) cc_final: 0.8756 (m-30) REVERT: Au 95 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8175 (mt-10) REVERT: Au 175 ASN cc_start: 0.9048 (m-40) cc_final: 0.8758 (m-40) REVERT: Au 212 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8158 (ttp-170) REVERT: Aw 50 ILE cc_start: 0.8290 (mt) cc_final: 0.7991 (tt) REVERT: Aw 86 THR cc_start: 0.9423 (p) cc_final: 0.9075 (m) REVERT: Aw 95 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8167 (mt-10) REVERT: Aw 134 MET cc_start: 0.9069 (ttt) cc_final: 0.8629 (ttt) REVERT: Aw 172 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: Aw 177 LYS cc_start: 0.8867 (mttt) cc_final: 0.8528 (ttmm) REVERT: Aw 190 LEU cc_start: 0.8799 (tp) cc_final: 0.8424 (mp) REVERT: Aw 208 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7815 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8199 (ttp-170) REVERT: Aw 220 MET cc_start: 0.9032 (mtm) cc_final: 0.8618 (mtp) REVERT: Ay 56 MET cc_start: 0.8901 (mtt) cc_final: 0.8497 (mtt) REVERT: Ay 95 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8375 (mt-10) REVERT: Ay 151 ASN cc_start: 0.9171 (m-40) cc_final: 0.8931 (m110) REVERT: Ay 158 GLN cc_start: 0.9429 (mt0) cc_final: 0.9223 (mt0) REVERT: Ay 180 TYR cc_start: 0.9105 (t80) cc_final: 0.8876 (t80) REVERT: Ba 157 ARG cc_start: 0.9211 (ttm170) cc_final: 0.8632 (ttm170) REVERT: Ba 212 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8133 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8270 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.8096 (ttp-170) REVERT: Be 95 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8266 (mt-10) REVERT: Be 151 ASN cc_start: 0.9334 (m-40) cc_final: 0.9009 (m-40) REVERT: Be 177 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8483 (ttmm) REVERT: Be 212 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8264 (ttp-170) REVERT: Bg 99 LEU cc_start: 0.8816 (tp) cc_final: 0.8588 (tp) REVERT: Bg 153 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8706 (mptt) REVERT: Bg 212 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8279 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9201 (mpt180) cc_final: 0.8930 (mpt180) REVERT: Bi 71 LEU cc_start: 0.8958 (mm) cc_final: 0.8694 (mm) REVERT: Bi 134 MET cc_start: 0.9042 (ttt) cc_final: 0.8577 (ttt) REVERT: Bi 151 ASN cc_start: 0.9148 (m-40) cc_final: 0.8854 (m110) REVERT: Bi 177 LYS cc_start: 0.8653 (mttt) cc_final: 0.8275 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9109 (tt0) cc_final: 0.8853 (tt0) REVERT: Bi 212 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8218 (ttp-170) REVERT: Bi 220 MET cc_start: 0.9130 (mtm) cc_final: 0.8784 (mtp) REVERT: Bk 55 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8279 (tpt-90) REVERT: Bk 110 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8939 (m) REVERT: Bk 134 MET cc_start: 0.8972 (ttt) cc_final: 0.8725 (ttt) REVERT: Bk 191 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7609 (mtp-110) REVERT: Bk 206 THR cc_start: 0.9569 (p) cc_final: 0.9363 (t) REVERT: Bk 212 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8150 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8347 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8451 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8272 (ttp-170) REVERT: Bo 95 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8066 (mt-10) REVERT: Bo 212 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8170 (ttp-170) outliers start: 98 outliers final: 74 residues processed: 1287 average time/residue: 0.4721 time to fit residues: 973.7309 Evaluate side-chains 1271 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1190 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 172 GLU 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 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 54 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 151 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 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 172 GLU Chi-restraints excluded: chain Aw residue 208 ARG 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 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 107 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 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 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain 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 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 166 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 328 optimal weight: 0.0670 chunk 114 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 151 ASN Ag 151 ASN Am 151 ASN Ao 151 ASN Ao 158 GLN Ba 158 GLN Bi 158 GLN Bm 76 GLN Bo 69 HIS Bo 158 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.108462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.089603 restraints weight = 39865.119| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.89 r_work: 0.2591 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34293 Z= 0.098 Angle : 0.485 7.097 46851 Z= 0.246 Chirality : 0.038 0.144 5271 Planarity : 0.005 0.051 5712 Dihedral : 15.162 177.211 5943 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.48 % Allowed : 22.74 % Favored : 74.77 % 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: 0.78 (0.13), residues: 3864 helix: 1.59 (0.12), residues: 1890 sheet: 0.67 (0.24), residues: 210 loop : -0.68 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAo 132 HIS 0.003 0.001 HISAm 217 PHE 0.015 0.002 PHEAg 200 TYR 0.015 0.001 TYRBo 198 ARG 0.013 0.001 ARGAa 191 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 1449) hydrogen bonds : angle 3.86177 ( 4095) covalent geometry : bond 0.00234 (34293) covalent geometry : angle 0.48517 (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 1324 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1240 time to evaluate : 4.341 Fit side-chains REVERT: Aa 55 ARG cc_start: 0.8645 (tpt-90) cc_final: 0.8315 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8329 (mt-10) REVERT: Aa 107 GLU cc_start: 0.8683 (pt0) cc_final: 0.8298 (pt0) REVERT: Aa 108 MET cc_start: 0.9336 (tpt) cc_final: 0.8950 (tpt) REVERT: Aa 172 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: Aa 206 THR cc_start: 0.9537 (p) cc_final: 0.9321 (t) REVERT: Aa 212 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8194 (ttp-170) REVERT: Ae 212 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8283 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8291 (mt-10) REVERT: Ag 172 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: Ag 197 ARG cc_start: 0.9038 (ptm160) cc_final: 0.8687 (ptm160) REVERT: Ag 212 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.7999 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8182 (mt-10) REVERT: Ai 136 ASP cc_start: 0.8932 (t0) cc_final: 0.8583 (t0) REVERT: Ai 151 ASN cc_start: 0.9140 (m-40) cc_final: 0.8800 (m-40) REVERT: Ai 175 ASN cc_start: 0.8882 (m-40) cc_final: 0.8480 (m110) REVERT: Ai 212 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.7780 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7756 (mt-10) REVERT: Ak 55 ARG cc_start: 0.8483 (tpt-90) cc_final: 0.8195 (tpt-90) REVERT: Ak 71 LEU cc_start: 0.8927 (mm) cc_final: 0.8568 (mm) REVERT: Ak 177 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8311 (ttmm) REVERT: Ak 190 LEU cc_start: 0.8898 (tp) cc_final: 0.8692 (mp) REVERT: Ak 206 THR cc_start: 0.9527 (p) cc_final: 0.9187 (t) REVERT: Ak 212 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8281 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7928 (mt-10) REVERT: Ak 220 MET cc_start: 0.8920 (mtm) cc_final: 0.8644 (mtp) REVERT: Am 107 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8179 (mp0) REVERT: Am 191 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7533 (mtp-110) REVERT: Am 195 LEU cc_start: 0.9073 (mt) cc_final: 0.8870 (mp) REVERT: Am 212 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8075 (ttp-170) REVERT: Ao 212 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8240 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8322 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8212 (mt-10) REVERT: As 95 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8173 (mt-10) REVERT: As 172 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: As 212 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8125 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9058 (m-30) cc_final: 0.8765 (m-30) REVERT: Au 95 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8045 (mt-10) REVERT: Au 151 ASN cc_start: 0.9123 (m-40) cc_final: 0.8876 (m-40) REVERT: Au 175 ASN cc_start: 0.9073 (m-40) cc_final: 0.8788 (m-40) REVERT: Au 212 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8180 (ttp-170) REVERT: Aw 86 THR cc_start: 0.9412 (p) cc_final: 0.9075 (m) REVERT: Aw 95 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8149 (mt-10) REVERT: Aw 134 MET cc_start: 0.9019 (ttt) cc_final: 0.8564 (ttt) REVERT: Aw 172 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: Aw 177 LYS cc_start: 0.8837 (mttt) cc_final: 0.8494 (ttmm) REVERT: Aw 190 LEU cc_start: 0.8745 (tp) cc_final: 0.8499 (mp) REVERT: Aw 208 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: Aw 212 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8094 (ttp-170) REVERT: Ay 56 MET cc_start: 0.8830 (mtt) cc_final: 0.8427 (mtt) REVERT: Ay 95 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8370 (mt-10) REVERT: Ay 151 ASN cc_start: 0.9041 (m-40) cc_final: 0.8833 (m110) REVERT: Ay 177 LYS cc_start: 0.8828 (mttt) cc_final: 0.8517 (mtpt) REVERT: Ay 180 TYR cc_start: 0.9128 (t80) cc_final: 0.8887 (t80) REVERT: Ba 212 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8114 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8269 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8188 (ttp-170) REVERT: Be 95 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8265 (mt-10) REVERT: Be 136 ASP cc_start: 0.8727 (t0) cc_final: 0.8498 (t0) REVERT: Be 151 ASN cc_start: 0.9349 (m-40) cc_final: 0.9024 (m-40) REVERT: Be 177 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8466 (ttmm) REVERT: Bg 212 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8279 (ttp-170) REVERT: Bi 46 ARG cc_start: 0.9223 (mpt180) cc_final: 0.8935 (mpt180) REVERT: Bi 71 LEU cc_start: 0.8890 (mm) cc_final: 0.8585 (mm) REVERT: Bi 134 MET cc_start: 0.9000 (ttt) cc_final: 0.8527 (ttt) REVERT: Bi 151 ASN cc_start: 0.9102 (m-40) cc_final: 0.8790 (m110) REVERT: Bi 177 LYS cc_start: 0.8622 (mttt) cc_final: 0.8277 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9103 (tt0) cc_final: 0.8887 (tt0) REVERT: Bi 208 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: Bi 212 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8192 (ttp-170) REVERT: Bk 46 ARG cc_start: 0.9195 (mpt180) cc_final: 0.8889 (mpt180) REVERT: Bk 55 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8205 (tpt-90) REVERT: Bk 84 ARG cc_start: 0.9056 (ttt180) cc_final: 0.8817 (ttt-90) REVERT: Bk 110 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8941 (m) REVERT: Bk 134 MET cc_start: 0.8918 (ttt) cc_final: 0.8640 (ttt) REVERT: Bk 206 THR cc_start: 0.9544 (p) cc_final: 0.9288 (t) REVERT: Bm 95 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8302 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8482 (ttmt) REVERT: Bm 212 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8128 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8611 (tpt-90) cc_final: 0.8317 (tpt-90) REVERT: Bo 95 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8050 (mt-10) outliers start: 84 outliers final: 63 residues processed: 1282 average time/residue: 0.5367 time to fit residues: 1105.6578 Evaluate side-chains 1263 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1193 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 172 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 172 GLU Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 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 As residue 51 THR Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 107 GLU 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 172 GLU Chi-restraints excluded: chain Aw residue 208 ARG 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 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 Bg residue 51 THR Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bi residue 208 ARG Chi-restraints excluded: chain Bk residue 51 THR 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 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9358 > 50: distance: 78 - 85: 9.861 distance: 85 - 86: 10.525 distance: 86 - 87: 8.236 distance: 86 - 89: 7.571 distance: 87 - 88: 8.568 distance: 87 - 93: 9.119 distance: 89 - 90: 9.679 distance: 90 - 91: 12.972 distance: 91 - 92: 16.119 distance: 93 - 94: 13.413 distance: 93 - 99: 13.961 distance: 94 - 95: 15.143 distance: 94 - 97: 17.509 distance: 95 - 96: 19.351 distance: 95 - 100: 13.471 distance: 96 - 127: 28.607 distance: 97 - 98: 21.147 distance: 98 - 99: 14.226 distance: 100 - 101: 10.957 distance: 101 - 102: 8.198 distance: 102 - 103: 15.065 distance: 102 - 111: 7.845 distance: 103 - 135: 13.616 distance: 104 - 105: 6.176 distance: 108 - 109: 3.864 distance: 111 - 112: 5.602 distance: 112 - 113: 7.089 distance: 112 - 115: 6.012 distance: 113 - 114: 15.000 distance: 113 - 123: 35.031 distance: 114 - 142: 24.344 distance: 116 - 117: 3.929 distance: 116 - 118: 6.321 distance: 117 - 119: 3.362 distance: 118 - 120: 6.983 distance: 119 - 121: 7.933 distance: 120 - 121: 6.638 distance: 121 - 122: 8.118 distance: 123 - 124: 10.640 distance: 124 - 125: 37.991 distance: 125 - 126: 12.237 distance: 125 - 127: 34.687 distance: 127 - 128: 26.301 distance: 128 - 129: 27.242 distance: 128 - 131: 23.735 distance: 129 - 130: 16.464 distance: 129 - 135: 19.476 distance: 131 - 132: 10.109 distance: 132 - 133: 15.172 distance: 132 - 134: 17.286 distance: 135 - 136: 14.583 distance: 136 - 137: 15.991 distance: 136 - 139: 6.629 distance: 137 - 138: 26.643 distance: 137 - 142: 22.701 distance: 139 - 141: 20.409 distance: 142 - 143: 10.762 distance: 143 - 144: 19.507 distance: 143 - 146: 9.093 distance: 144 - 145: 9.275 distance: 144 - 153: 22.077 distance: 146 - 147: 12.647 distance: 147 - 148: 8.639 distance: 148 - 149: 8.108 distance: 149 - 150: 4.346 distance: 150 - 152: 4.165 distance: 153 - 154: 9.792 distance: 154 - 155: 21.057 distance: 154 - 157: 18.181 distance: 155 - 156: 21.489 distance: 155 - 161: 26.328 distance: 157 - 158: 32.155 distance: 158 - 159: 21.675 distance: 158 - 160: 5.322 distance: 161 - 162: 7.726 distance: 162 - 163: 14.292 distance: 162 - 165: 4.964 distance: 163 - 164: 5.343 distance: 163 - 169: 25.105 distance: 165 - 166: 12.381 distance: 166 - 167: 8.914 distance: 166 - 168: 13.352