Starting phenix.real_space_refine on Mon Mar 18 22:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/03_2024/8opf_17051.pdb" } resolution = 2.83 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= 0.016 sd= 0.289 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: 4 Type Number sf(0) Gaussians S 209 5.16 5 C 14193 2.51 5 N 3800 2.21 5 O 4199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Al TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Am TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "An TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ar TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "As TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22401 Number of models: 1 Model: "" Number of chains: 19 Chain: "Aa" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ab" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ac" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ad" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ae" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Af" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ag" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ah" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ai" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Aj" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ak" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Al" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Am" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "An" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ao" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ap" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Aq" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "Ar" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Chain: "As" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Time building chain proxies: 11.85, per 1000 atoms: 0.53 Number of scatterers: 22401 At special positions: 0 Unit cell: (132.05, 132.05, 158.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 209 16.00 O 4199 8.00 N 3800 7.00 C 14193 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 - 3.50 Amino acid : False - 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: 7.48 Conformation dependent library (CDL) restraints added in 3.4 seconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5320 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 38 sheets defined 44.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAa 71 " --> pdb=" O LEUAa 67 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 150 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 Processing helix chain 'Ab' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAb 71 " --> pdb=" O LEUAb 67 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 150 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 176 Processing helix chain 'Ac' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAc 71 " --> pdb=" O LEUAc 67 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 150 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 Processing helix chain 'Ad' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAd 71 " --> pdb=" O LEUAd 67 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 150 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 176 Processing helix chain 'Ae' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAe 71 " --> pdb=" O LEUAe 67 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 150 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 Processing helix chain 'Af' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAf 71 " --> pdb=" O LEUAf 67 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 150 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 176 Processing helix chain 'Ag' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAg 71 " --> pdb=" O LEUAg 67 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 150 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 Processing helix chain 'Ah' and resid 66 through 71 removed outlier: 3.743A pdb=" N LEUAh 71 " --> pdb=" O LEUAh 67 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 150 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 176 Processing helix chain 'Ai' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAi 71 " --> pdb=" O LEUAi 67 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 150 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 Processing helix chain 'Aj' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAj 71 " --> pdb=" O LEUAj 67 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 150 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 176 Processing helix chain 'Ak' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAk 71 " --> pdb=" O LEUAk 67 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 150 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 Processing helix chain 'Al' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAl 71 " --> pdb=" O LEUAl 67 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 Processing helix chain 'Al' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 150 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 176 Processing helix chain 'Am' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAm 71 " --> pdb=" O LEUAm 67 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 150 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 Processing helix chain 'An' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAn 71 " --> pdb=" O LEUAn 67 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 150 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 176 Processing helix chain 'Ao' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAo 71 " --> pdb=" O LEUAo 67 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 150 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 Processing helix chain 'Ap' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAp 71 " --> pdb=" O LEUAp 67 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 150 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 176 Processing helix chain 'Aq' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAq 71 " --> pdb=" O LEUAq 67 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 150 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 176 Processing helix chain 'Ar' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAr 71 " --> pdb=" O LEUAr 67 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 Processing helix chain 'Ar' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 150 Processing helix chain 'Ar' and resid 155 through 161 Processing helix chain 'Ar' and resid 163 through 176 Processing helix chain 'As' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAs 71 " --> pdb=" O LEUAs 67 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 150 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 176 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 'Ab' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 131 through 135 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 131 through 135 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 131 through 135 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 131 through 135 Processing sheet with id=AB2, first strand: chain 'Af' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Af' and resid 131 through 135 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 131 through 135 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 131 through 135 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 131 through 135 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 131 through 135 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 131 through 135 Processing sheet with id=AC5, first strand: chain 'Al' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Al' and resid 131 through 135 Processing sheet with id=AC7, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Am' and resid 131 through 135 Processing sheet with id=AC9, first strand: chain 'An' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'An' and resid 131 through 135 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 131 through 135 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 131 through 135 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 131 through 135 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 131 through 135 Processing sheet with id=AE1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'As' and resid 131 through 135 874 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 8.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7103 1.34 - 1.45: 2897 1.45 - 1.57: 12515 1.57 - 1.69: 0 1.69 - 1.81: 399 Bond restraints: 22914 Sorted by residual: bond pdb=" C LYSAg 48 " pdb=" N ALAAg 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.31e+00 bond pdb=" C LYSAc 48 " pdb=" N ALAAc 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.16e+00 bond pdb=" C LYSAk 48 " pdb=" N ALAAk 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.07e+00 bond pdb=" C LYSAm 48 " pdb=" N ALAAm 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.06e+00 bond pdb=" C LYSAi 48 " pdb=" N ALAAi 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.05e+00 ... (remaining 22909 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.17: 1105 107.17 - 113.89: 12812 113.89 - 120.61: 8789 120.61 - 127.33: 8077 127.33 - 134.05: 320 Bond angle restraints: 31103 Sorted by residual: angle pdb=" N ILEAq 47 " pdb=" CA ILEAq 47 " pdb=" C ILEAq 47 " ideal model delta sigma weight residual 109.21 112.46 -3.25 1.36e+00 5.41e-01 5.70e+00 angle pdb=" N ILEAe 47 " pdb=" CA ILEAe 47 " pdb=" C ILEAe 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.65e+00 angle pdb=" N ILEAi 47 " pdb=" CA ILEAi 47 " pdb=" C ILEAi 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.64e+00 angle pdb=" N ILEAc 47 " pdb=" CA ILEAc 47 " pdb=" C ILEAc 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.64e+00 angle pdb=" N ILEAa 47 " pdb=" CA ILEAa 47 " pdb=" C ILEAa 47 " ideal model delta sigma weight residual 109.21 112.43 -3.22 1.36e+00 5.41e-01 5.60e+00 ... (remaining 31098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 12350 16.61 - 33.21: 994 33.21 - 49.82: 488 49.82 - 66.43: 209 66.43 - 83.03: 38 Dihedral angle restraints: 14079 sinusoidal: 5852 harmonic: 8227 Sorted by residual: dihedral pdb=" CA ARGAn 174 " pdb=" CB ARGAn 174 " pdb=" CG ARGAn 174 " pdb=" CD ARGAn 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.25 57.25 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ARGAp 174 " pdb=" CB ARGAp 174 " pdb=" CG ARGAp 174 " pdb=" CD ARGAp 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.21 57.21 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ARGAb 174 " pdb=" CB ARGAb 174 " pdb=" CG ARGAb 174 " pdb=" CD ARGAb 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.20 57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1818 0.026 - 0.052: 1019 0.052 - 0.077: 362 0.077 - 0.103: 174 0.103 - 0.129: 47 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CG LEUAf 71 " pdb=" CB LEUAf 71 " pdb=" CD1 LEUAf 71 " pdb=" CD2 LEUAf 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CG LEUAe 71 " pdb=" CB LEUAe 71 " pdb=" CD1 LEUAe 71 " pdb=" CD2 LEUAe 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CG LEUAg 71 " pdb=" CB LEUAg 71 " pdb=" CD1 LEUAg 71 " pdb=" CD2 LEUAg 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 3417 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYSAa 48 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LYSAa 48 " 0.031 2.00e-02 2.50e+03 pdb=" O LYSAa 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAa 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAf 48 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LYSAf 48 " 0.030 2.00e-02 2.50e+03 pdb=" O LYSAf 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAf 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAm 48 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LYSAm 48 " 0.030 2.00e-02 2.50e+03 pdb=" O LYSAm 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAm 49 " -0.010 2.00e-02 2.50e+03 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 9198 2.93 - 3.43: 21177 3.43 - 3.92: 37396 3.92 - 4.41: 42820 4.41 - 4.90: 70201 Nonbonded interactions: 180792 Sorted by model distance: nonbonded pdb=" O PROAo 75 " pdb=" NH1 ARGAp 174 " model vdw 2.443 2.520 nonbonded pdb=" NH1 ARGAa 174 " pdb=" O PROAq 75 " model vdw 2.458 2.520 nonbonded pdb=" NH1 ARGAd 174 " pdb=" O PROAs 75 " model vdw 2.459 2.520 nonbonded pdb=" O PROAm 75 " pdb=" NH1 ARGAn 174 " model vdw 2.466 2.520 nonbonded pdb=" O PROAg 75 " pdb=" NH1 ARGAh 174 " model vdw 2.467 2.520 ... (remaining 180787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' } 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=0.00 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: 1.440 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: 6.890 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 55.330 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22914 Z= 0.244 Angle : 0.586 4.635 31103 Z= 0.327 Chirality : 0.039 0.129 3420 Planarity : 0.006 0.039 4009 Dihedral : 17.430 83.032 8759 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.53 % Allowed : 22.55 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 2755 helix: -0.40 (0.14), residues: 1102 sheet: 2.86 (0.35), residues: 190 loop : -1.86 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAo 132 HIS 0.002 0.001 HISAm 42 PHE 0.004 0.001 PHEAk 163 TYR 0.005 0.001 TYRAp 73 ARG 0.003 0.001 ARGAl 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 736 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 134 MET cc_start: 0.8918 (ttt) cc_final: 0.8338 (ttt) REVERT: Aa 160 MET cc_start: 0.9072 (mmp) cc_final: 0.8834 (mmt) REVERT: Aa 168 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7524 (mt-10) REVERT: Aa 173 MET cc_start: 0.7501 (ttp) cc_final: 0.6945 (ttt) REVERT: Aa 177 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7637 (mptt) REVERT: Ab 76 GLN cc_start: 0.8425 (mt0) cc_final: 0.7954 (mt0) REVERT: Ab 127 ASN cc_start: 0.8432 (t0) cc_final: 0.8198 (t0) REVERT: Ab 173 MET cc_start: 0.7560 (ttp) cc_final: 0.7206 (ttt) REVERT: Ac 71 LEU cc_start: 0.8816 (mm) cc_final: 0.8611 (mt) REVERT: Ac 157 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8236 (ttp-110) REVERT: Ac 173 MET cc_start: 0.7468 (ttp) cc_final: 0.7131 (ttt) REVERT: Ac 181 MET cc_start: 0.7066 (mmt) cc_final: 0.6844 (mtm) REVERT: Ad 56 MET cc_start: 0.8646 (mmp) cc_final: 0.8392 (mmm) REVERT: Ad 139 GLU cc_start: 0.7507 (pt0) cc_final: 0.6764 (pm20) REVERT: Ad 157 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (ttp-110) REVERT: Ad 160 MET cc_start: 0.9142 (mmp) cc_final: 0.8626 (mmp) REVERT: Ad 173 MET cc_start: 0.7446 (ttp) cc_final: 0.7086 (ttt) REVERT: Ae 56 MET cc_start: 0.8736 (mmp) cc_final: 0.8527 (mmt) REVERT: Ae 139 GLU cc_start: 0.7384 (pt0) cc_final: 0.6695 (pm20) REVERT: Af 46 ARG cc_start: 0.9147 (mpt180) cc_final: 0.8938 (mpt180) REVERT: Af 153 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8395 (mmtt) REVERT: Af 168 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7424 (mt-10) REVERT: Af 173 MET cc_start: 0.7540 (ttp) cc_final: 0.7126 (ttp) REVERT: Af 177 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7594 (mptt) REVERT: Ag 50 ILE cc_start: 0.8201 (mm) cc_final: 0.7913 (mm) REVERT: Ag 91 ASP cc_start: 0.8786 (m-30) cc_final: 0.8494 (m-30) REVERT: Ag 116 MET cc_start: 0.9048 (ttm) cc_final: 0.8482 (ttm) REVERT: Ag 139 GLU cc_start: 0.7504 (pt0) cc_final: 0.6831 (pm20) REVERT: Ag 173 MET cc_start: 0.7526 (ttp) cc_final: 0.7298 (ttp) REVERT: Ag 177 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7462 (mptt) REVERT: Ah 91 ASP cc_start: 0.8862 (m-30) cc_final: 0.8657 (m-30) REVERT: Ah 108 MET cc_start: 0.9236 (tpt) cc_final: 0.8455 (tpt) REVERT: Ah 173 MET cc_start: 0.7442 (ttp) cc_final: 0.6931 (ttt) REVERT: Ah 177 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7478 (mptt) REVERT: Ah 181 MET cc_start: 0.6969 (mmt) cc_final: 0.6679 (mtm) REVERT: Ai 56 MET cc_start: 0.8693 (mmp) cc_final: 0.8483 (mmm) REVERT: Ai 108 MET cc_start: 0.9251 (tpt) cc_final: 0.8706 (tpt) REVERT: Ai 173 MET cc_start: 0.7497 (ttp) cc_final: 0.7067 (ttt) REVERT: Ai 177 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7577 (mptt) REVERT: Aj 139 GLU cc_start: 0.7382 (pt0) cc_final: 0.6718 (pm20) REVERT: Aj 158 GLN cc_start: 0.8900 (mt0) cc_final: 0.8647 (mt0) REVERT: Aj 168 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7547 (mt-10) REVERT: Aj 173 MET cc_start: 0.7611 (ttp) cc_final: 0.7219 (ttt) REVERT: Ak 157 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8268 (ttp-110) REVERT: Ak 173 MET cc_start: 0.7541 (ttp) cc_final: 0.7029 (ttt) REVERT: Ak 177 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7522 (mptt) REVERT: Ak 181 MET cc_start: 0.6970 (mmt) cc_final: 0.6704 (mtm) REVERT: Al 153 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8463 (mmtt) REVERT: Al 177 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7512 (mptt) REVERT: Am 139 GLU cc_start: 0.7509 (pt0) cc_final: 0.7190 (pt0) REVERT: Am 173 MET cc_start: 0.7510 (ttp) cc_final: 0.7094 (ttt) REVERT: Am 177 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7535 (mptt) REVERT: An 108 MET cc_start: 0.9212 (tpt) cc_final: 0.8875 (tpt) REVERT: An 135 MET cc_start: 0.8990 (mmm) cc_final: 0.8692 (mmm) REVERT: An 173 MET cc_start: 0.7419 (ttp) cc_final: 0.6997 (ttt) REVERT: An 177 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7725 (mtmm) REVERT: Ao 56 MET cc_start: 0.8735 (mmp) cc_final: 0.8431 (mmt) REVERT: Ao 91 ASP cc_start: 0.8763 (m-30) cc_final: 0.8474 (m-30) REVERT: Ao 135 MET cc_start: 0.9062 (mmm) cc_final: 0.8770 (mmm) REVERT: Ao 173 MET cc_start: 0.7410 (ttp) cc_final: 0.6891 (ttt) REVERT: Ao 177 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7689 (mptt) REVERT: Ap 116 MET cc_start: 0.9030 (ttm) cc_final: 0.8825 (ttp) REVERT: Ap 160 MET cc_start: 0.9091 (mmp) cc_final: 0.8498 (mmp) REVERT: Ap 168 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7485 (mt-10) REVERT: Ap 173 MET cc_start: 0.7407 (ttp) cc_final: 0.7085 (ttt) REVERT: Aq 60 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8276 (mmtm) REVERT: Aq 139 GLU cc_start: 0.7514 (pt0) cc_final: 0.6813 (pm20) REVERT: Ar 91 ASP cc_start: 0.8821 (m-30) cc_final: 0.8604 (m-30) REVERT: Ar 139 GLU cc_start: 0.7507 (pt0) cc_final: 0.6738 (pm20) REVERT: Ar 173 MET cc_start: 0.7519 (ttp) cc_final: 0.7029 (ttt) REVERT: Ar 177 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7538 (mptt) REVERT: As 173 MET cc_start: 0.7460 (ttp) cc_final: 0.7096 (ttt) REVERT: As 177 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7719 (mptt) outliers start: 13 outliers final: 0 residues processed: 740 average time/residue: 1.5228 time to fit residues: 1255.4599 Evaluate side-chains 694 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 693 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 157 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 0.0020 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 208 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 overall best weight: 2.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 175 ASN Ac 113 ASN ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ad 175 ASN Ae 113 ASN Ae 158 GLN Af 113 ASN Ag 113 ASN ** Ag 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 113 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 113 ASN ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN Am 175 ASN An 175 ASN Ao 113 ASN Ap 113 ASN Ap 175 ASN Aq 113 ASN Ar 113 ASN Ar 175 ASN As 113 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22914 Z= 0.294 Angle : 0.585 6.079 31103 Z= 0.298 Chirality : 0.043 0.178 3420 Planarity : 0.005 0.035 4009 Dihedral : 4.165 21.257 3044 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.49 % Allowed : 21.21 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.47 (0.16), residues: 2755 helix: 1.19 (0.16), residues: 1007 sheet: 1.87 (0.33), residues: 228 loop : -1.82 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAh 132 HIS 0.002 0.000 HISAc 69 PHE 0.013 0.002 PHEAi 163 TYR 0.018 0.001 TYRAq 180 ARG 0.005 0.001 ARGAr 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 759 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8636 (m-30) cc_final: 0.8435 (m-30) REVERT: Aa 134 MET cc_start: 0.9074 (ttt) cc_final: 0.8572 (ttt) REVERT: Aa 160 MET cc_start: 0.9126 (mmp) cc_final: 0.8642 (mmt) REVERT: Aa 168 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7452 (mt-10) REVERT: Ab 76 GLN cc_start: 0.8457 (mt0) cc_final: 0.7974 (mt0) REVERT: Ab 99 LEU cc_start: 0.8586 (tt) cc_final: 0.8268 (tp) REVERT: Ab 121 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7316 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8435 (t0) cc_final: 0.8186 (t0) REVERT: Ab 173 MET cc_start: 0.7695 (ttp) cc_final: 0.7401 (ttp) REVERT: Ab 177 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7886 (mptt) REVERT: Ac 121 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7390 (tm-30) REVERT: Ac 173 MET cc_start: 0.7616 (ttp) cc_final: 0.7297 (ttp) REVERT: Ac 177 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7744 (mptt) REVERT: Ad 56 MET cc_start: 0.8780 (mmp) cc_final: 0.8475 (mmm) REVERT: Ad 60 LYS cc_start: 0.8529 (mptm) cc_final: 0.8289 (mmtm) REVERT: Ad 168 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7524 (mt-10) REVERT: Ad 173 MET cc_start: 0.7827 (ttp) cc_final: 0.7551 (ttp) REVERT: Ae 56 MET cc_start: 0.8754 (mmp) cc_final: 0.8528 (mmt) REVERT: Ae 173 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: Af 46 ARG cc_start: 0.9211 (mpt180) cc_final: 0.8935 (mpt180) REVERT: Af 69 HIS cc_start: 0.8167 (m-70) cc_final: 0.6846 (t-90) REVERT: Af 95 GLU cc_start: 0.8220 (mp0) cc_final: 0.7877 (mp0) REVERT: Af 153 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8519 (mmtt) REVERT: Af 168 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7472 (mt-10) REVERT: Af 177 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7829 (mptt) REVERT: Ag 50 ILE cc_start: 0.8269 (mm) cc_final: 0.7958 (mm) REVERT: Ag 116 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8857 (tmm) REVERT: Ag 139 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: Ag 177 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7663 (mptt) REVERT: Ah 71 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8532 (mt) REVERT: Ah 76 GLN cc_start: 0.8488 (mt0) cc_final: 0.8095 (mt0) REVERT: Ah 91 ASP cc_start: 0.8731 (m-30) cc_final: 0.8517 (m-30) REVERT: Ah 116 MET cc_start: 0.8989 (ttp) cc_final: 0.8734 (ttp) REVERT: Ah 173 MET cc_start: 0.7721 (ttp) cc_final: 0.7243 (ttt) REVERT: Ah 177 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7570 (mptt) REVERT: Ah 181 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6836 (mtm) REVERT: Ai 99 LEU cc_start: 0.8637 (tt) cc_final: 0.8239 (tp) REVERT: Ai 108 MET cc_start: 0.9012 (tpt) cc_final: 0.8803 (tpt) REVERT: Ai 153 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.7220 (mptp) REVERT: Ai 173 MET cc_start: 0.7804 (ttp) cc_final: 0.7454 (ttt) REVERT: Aj 67 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (mp) REVERT: Aj 139 GLU cc_start: 0.7562 (pt0) cc_final: 0.7313 (pt0) REVERT: Aj 158 GLN cc_start: 0.9033 (mt0) cc_final: 0.8833 (mt0) REVERT: Aj 168 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7551 (mt-10) REVERT: Aj 173 MET cc_start: 0.7741 (ttp) cc_final: 0.7510 (ttp) REVERT: Aj 177 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7742 (mptt) REVERT: Aj 181 MET cc_start: 0.6892 (mmt) cc_final: 0.6652 (mtm) REVERT: Ak 173 MET cc_start: 0.7637 (ttp) cc_final: 0.7187 (ttt) REVERT: Ak 177 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7670 (mptt) REVERT: Ak 181 MET cc_start: 0.7064 (mmt) cc_final: 0.6781 (mtm) REVERT: Al 168 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7486 (mt-10) REVERT: Al 177 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7834 (mtmm) REVERT: Am 99 LEU cc_start: 0.8719 (tt) cc_final: 0.8307 (tp) REVERT: Am 108 MET cc_start: 0.9076 (tpt) cc_final: 0.8827 (tpt) REVERT: Am 139 GLU cc_start: 0.7586 (pt0) cc_final: 0.7236 (pt0) REVERT: Am 168 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7579 (mt-10) REVERT: Am 173 MET cc_start: 0.7693 (ttp) cc_final: 0.7484 (ttp) REVERT: An 67 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8546 (mp) REVERT: An 99 LEU cc_start: 0.8510 (tt) cc_final: 0.8091 (tp) REVERT: An 108 MET cc_start: 0.8983 (tpt) cc_final: 0.8299 (tpt) REVERT: An 135 MET cc_start: 0.9033 (mmm) cc_final: 0.8740 (mmm) REVERT: An 173 MET cc_start: 0.7605 (ttp) cc_final: 0.7174 (ttt) REVERT: Ao 56 MET cc_start: 0.8704 (mmp) cc_final: 0.8394 (mmt) REVERT: Ao 91 ASP cc_start: 0.8677 (m-30) cc_final: 0.8381 (m-30) REVERT: Ao 135 MET cc_start: 0.9123 (mmm) cc_final: 0.8827 (mmm) REVERT: Ao 153 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7633 (mptp) REVERT: Ao 173 MET cc_start: 0.7732 (ttp) cc_final: 0.7377 (ttt) REVERT: Ap 60 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7471 (mptt) REVERT: Ap 91 ASP cc_start: 0.8692 (m-30) cc_final: 0.8491 (m-30) REVERT: Ap 116 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8852 (ttp) REVERT: Ap 168 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7373 (mt-10) REVERT: Ap 173 MET cc_start: 0.7753 (ttp) cc_final: 0.7412 (ttt) REVERT: Aq 60 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8257 (mmtm) REVERT: Aq 160 MET cc_start: 0.9253 (mmt) cc_final: 0.8857 (mmt) REVERT: Aq 181 MET cc_start: 0.7047 (mmt) cc_final: 0.6825 (mtm) REVERT: Ar 67 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8560 (mp) REVERT: Ar 91 ASP cc_start: 0.8758 (m-30) cc_final: 0.8545 (m-30) REVERT: Ar 168 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7384 (mt-10) REVERT: Ar 173 MET cc_start: 0.7759 (ttp) cc_final: 0.7351 (ttt) REVERT: Ar 175 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: As 56 MET cc_start: 0.8663 (mmt) cc_final: 0.8442 (mmt) outliers start: 111 outliers final: 21 residues processed: 780 average time/residue: 1.5589 time to fit residues: 1349.9262 Evaluate side-chains 793 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 758 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 153 LYS Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 139 GLU Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 71 LEU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 67 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 175 ASN Chi-restraints excluded: chain As residue 175 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ad 175 ASN Ae 113 ASN Af 113 ASN Ag 113 ASN Ag 175 ASN Ah 113 ASN Ah 175 ASN Ai 113 ASN Aj 113 ASN ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 113 ASN ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN Aq 113 ASN Ar 175 ASN As 113 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22914 Z= 0.366 Angle : 0.605 5.988 31103 Z= 0.306 Chirality : 0.044 0.194 3420 Planarity : 0.005 0.038 4009 Dihedral : 4.353 15.724 3040 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.94 % Allowed : 23.72 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.34 (0.16), residues: 2755 helix: 1.32 (0.15), residues: 988 sheet: 1.53 (0.34), residues: 228 loop : -1.65 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.001 HISAk 162 PHE 0.014 0.002 PHEAi 163 TYR 0.018 0.002 TYRAs 180 ARG 0.006 0.001 ARGAp 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 778 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8689 (m-30) cc_final: 0.8466 (m-30) REVERT: Aa 160 MET cc_start: 0.9111 (mmp) cc_final: 0.8766 (mmt) REVERT: Aa 177 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7726 (mptt) REVERT: Ab 76 GLN cc_start: 0.8475 (mt0) cc_final: 0.8014 (mt0) REVERT: Ab 99 LEU cc_start: 0.8627 (tt) cc_final: 0.8283 (tp) REVERT: Ab 113 ASN cc_start: 0.8966 (m110) cc_final: 0.8763 (m-40) REVERT: Ab 121 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: Ab 173 MET cc_start: 0.7663 (ttp) cc_final: 0.7338 (ttp) REVERT: Ab 177 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7872 (mptt) REVERT: Ac 88 SER cc_start: 0.8735 (p) cc_final: 0.8418 (p) REVERT: Ac 173 MET cc_start: 0.7687 (ttp) cc_final: 0.7211 (ttp) REVERT: Ac 177 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7793 (mptt) REVERT: Ad 60 LYS cc_start: 0.8519 (mptm) cc_final: 0.8079 (mmtm) REVERT: Ad 76 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8032 (mm110) REVERT: Ad 173 MET cc_start: 0.7834 (ttp) cc_final: 0.7583 (ttp) REVERT: Ae 56 MET cc_start: 0.8825 (mmp) cc_final: 0.8545 (mmt) REVERT: Ae 95 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: Ae 173 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7780 (ttp) REVERT: Af 46 ARG cc_start: 0.9237 (mpt180) cc_final: 0.9017 (mpt180) REVERT: Af 69 HIS cc_start: 0.8094 (m-70) cc_final: 0.6951 (t70) REVERT: Af 95 GLU cc_start: 0.8148 (mp0) cc_final: 0.7851 (mp0) REVERT: Af 168 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7486 (mt-10) REVERT: Af 181 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6697 (mtm) REVERT: Ag 116 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8923 (tmm) REVERT: Ag 153 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8485 (mmtm) REVERT: Ag 168 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7489 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7631 (mptt) REVERT: Ag 181 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6747 (mtm) REVERT: Ah 76 GLN cc_start: 0.8532 (mt0) cc_final: 0.8112 (mt0) REVERT: Ah 91 ASP cc_start: 0.8757 (m-30) cc_final: 0.8538 (m-30) REVERT: Ah 116 MET cc_start: 0.8993 (ttp) cc_final: 0.8773 (ttp) REVERT: Ah 173 MET cc_start: 0.7734 (ttp) cc_final: 0.7333 (ttt) REVERT: Ah 177 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7601 (mptt) REVERT: Ah 181 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6868 (mtm) REVERT: Ai 99 LEU cc_start: 0.8606 (tt) cc_final: 0.8234 (tp) REVERT: Ai 108 MET cc_start: 0.9006 (tpt) cc_final: 0.8777 (tpt) REVERT: Ai 153 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7131 (mptp) REVERT: Ai 168 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7515 (mt-10) REVERT: Ai 173 MET cc_start: 0.7837 (ttp) cc_final: 0.7472 (ttt) REVERT: Ai 177 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7771 (mptt) REVERT: Aj 177 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7770 (mptt) REVERT: Aj 181 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: Ak 173 MET cc_start: 0.7679 (ttp) cc_final: 0.7228 (ttt) REVERT: Ak 177 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7733 (mptt) REVERT: Ak 181 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6751 (mtm) REVERT: Am 168 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7578 (mt-10) REVERT: An 67 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8545 (mp) REVERT: An 95 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: An 99 LEU cc_start: 0.8447 (tt) cc_final: 0.8084 (tp) REVERT: An 102 ASP cc_start: 0.8725 (t0) cc_final: 0.8346 (t0) REVERT: An 135 MET cc_start: 0.9053 (mmm) cc_final: 0.8772 (mmm) REVERT: An 173 MET cc_start: 0.7553 (ttp) cc_final: 0.7178 (ttt) REVERT: An 175 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7760 (m110) REVERT: An 177 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7267 (mtmm) REVERT: Ao 91 ASP cc_start: 0.8737 (m-30) cc_final: 0.8480 (m-30) REVERT: Ao 153 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7596 (mptp) REVERT: Ao 173 MET cc_start: 0.7743 (ttp) cc_final: 0.7414 (ttt) REVERT: Ap 60 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7580 (mptt) REVERT: Ap 116 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (ttp) REVERT: Ap 173 MET cc_start: 0.7753 (ttp) cc_final: 0.7447 (ttt) REVERT: Aq 54 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: Aq 91 ASP cc_start: 0.8701 (m-30) cc_final: 0.8257 (m-30) REVERT: Aq 153 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.7562 (mptp) REVERT: Aq 160 MET cc_start: 0.9246 (mmt) cc_final: 0.8862 (mmt) REVERT: Aq 181 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6837 (mtm) REVERT: Ar 91 ASP cc_start: 0.8795 (m-30) cc_final: 0.8570 (m-30) REVERT: Ar 99 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8284 (tp) REVERT: Ar 135 MET cc_start: 0.9078 (mmm) cc_final: 0.8509 (mmm) REVERT: Ar 168 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7513 (mt-10) REVERT: Ar 173 MET cc_start: 0.7710 (ttp) cc_final: 0.7370 (ttt) REVERT: As 153 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7432 (mptp) outliers start: 122 outliers final: 42 residues processed: 802 average time/residue: 1.6079 time to fit residues: 1429.2096 Evaluate side-chains 846 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 780 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ae residue 54 MET Chi-restraints excluded: chain Ae residue 95 GLU Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 175 ASN Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 54 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain An residue 177 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 54 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 175 ASN Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 139 GLU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 113 ASN ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ad 175 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 113 ASN Af 113 ASN Ag 113 ASN Ag 175 ASN Ah 113 ASN Ah 175 ASN Ai 175 ASN Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN Aq 113 ASN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22914 Z= 0.394 Angle : 0.610 5.837 31103 Z= 0.309 Chirality : 0.044 0.188 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.482 16.400 3040 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.18 % Allowed : 24.09 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.35 (0.16), residues: 2755 helix: 1.29 (0.15), residues: 988 sheet: 1.23 (0.33), residues: 228 loop : -1.58 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAf 132 HIS 0.002 0.001 HISAj 162 PHE 0.015 0.002 PHEAi 163 TYR 0.019 0.002 TYRAr 180 ARG 0.007 0.001 ARGAp 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 784 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8705 (m-30) cc_final: 0.8466 (m-30) REVERT: Aa 160 MET cc_start: 0.9111 (mmp) cc_final: 0.8856 (mmt) REVERT: Aa 177 LYS cc_start: 0.8129 (mtpm) cc_final: 0.7641 (mptt) REVERT: Ab 76 GLN cc_start: 0.8496 (mt0) cc_final: 0.8042 (mt0) REVERT: Ab 99 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8258 (tp) REVERT: Ab 113 ASN cc_start: 0.9020 (m110) cc_final: 0.8816 (m-40) REVERT: Ab 121 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: Ab 173 MET cc_start: 0.7719 (ttp) cc_final: 0.7453 (ttp) REVERT: Ac 76 GLN cc_start: 0.8485 (mt0) cc_final: 0.8065 (mt0) REVERT: Ac 88 SER cc_start: 0.8799 (p) cc_final: 0.8502 (p) REVERT: Ac 139 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: Ac 173 MET cc_start: 0.7631 (ttp) cc_final: 0.7359 (ttp) REVERT: Ad 76 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8027 (mm110) REVERT: Ad 95 GLU cc_start: 0.8053 (mp0) cc_final: 0.7697 (mp0) REVERT: Ad 173 MET cc_start: 0.7871 (ttp) cc_final: 0.7612 (ttp) REVERT: Ae 56 MET cc_start: 0.8816 (mmp) cc_final: 0.8500 (mmt) REVERT: Ae 173 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7791 (ttp) REVERT: Af 46 ARG cc_start: 0.9233 (mpt180) cc_final: 0.9013 (mpt180) REVERT: Af 69 HIS cc_start: 0.8144 (m-70) cc_final: 0.7020 (t70) REVERT: Af 95 GLU cc_start: 0.8163 (mp0) cc_final: 0.7844 (mp0) REVERT: Ag 102 ASP cc_start: 0.8743 (t0) cc_final: 0.8407 (t0) REVERT: Ag 116 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8928 (tmm) REVERT: Ag 168 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7482 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7661 (mptt) REVERT: Ag 181 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6852 (mtm) REVERT: Ah 76 GLN cc_start: 0.8542 (mt0) cc_final: 0.8147 (mt0) REVERT: Ah 91 ASP cc_start: 0.8768 (m-30) cc_final: 0.8539 (m-30) REVERT: Ah 173 MET cc_start: 0.7761 (ttp) cc_final: 0.7389 (ttt) REVERT: Ah 181 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6885 (mtm) REVERT: Ai 99 LEU cc_start: 0.8621 (tt) cc_final: 0.8293 (tp) REVERT: Ai 108 MET cc_start: 0.9037 (tpt) cc_final: 0.8793 (tpt) REVERT: Ai 121 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7600 (tp30) REVERT: Ai 153 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7100 (mptp) REVERT: Ai 168 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7431 (mt-10) REVERT: Ai 173 MET cc_start: 0.7915 (ttp) cc_final: 0.7568 (ttt) REVERT: Ai 177 LYS cc_start: 0.8232 (mtpm) cc_final: 0.7856 (mptt) REVERT: Aj 168 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7633 (mt-10) REVERT: Aj 172 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7166 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7845 (mptt) REVERT: Ak 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8204 (tp) REVERT: Ak 181 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6756 (mtm) REVERT: Al 172 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6661 (mt-10) REVERT: Am 139 GLU cc_start: 0.7748 (tt0) cc_final: 0.7474 (tt0) REVERT: Am 168 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7603 (mt-10) REVERT: Am 177 LYS cc_start: 0.8122 (mtpm) cc_final: 0.7805 (mtmm) REVERT: An 67 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8626 (mp) REVERT: An 95 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: An 99 LEU cc_start: 0.8475 (tt) cc_final: 0.8101 (tp) REVERT: An 102 ASP cc_start: 0.8720 (t0) cc_final: 0.8300 (t0) REVERT: An 121 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7486 (tp30) REVERT: An 135 MET cc_start: 0.9037 (mmm) cc_final: 0.8791 (mmm) REVERT: An 173 MET cc_start: 0.7588 (ttp) cc_final: 0.7272 (ttt) REVERT: An 175 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7651 (m110) REVERT: Ao 67 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8614 (mp) REVERT: Ao 91 ASP cc_start: 0.8742 (m-30) cc_final: 0.8487 (m-30) REVERT: Ao 153 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7591 (mptp) REVERT: Ao 173 MET cc_start: 0.7753 (ttp) cc_final: 0.7426 (ttt) REVERT: Ap 60 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7624 (mptt) REVERT: Ap 116 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (ttp) REVERT: Ap 173 MET cc_start: 0.7836 (ttp) cc_final: 0.7538 (ttt) REVERT: Aq 153 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.7558 (mptp) REVERT: Ar 91 ASP cc_start: 0.8798 (m-30) cc_final: 0.8569 (m-30) REVERT: Ar 99 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8280 (tp) REVERT: Ar 135 MET cc_start: 0.9065 (mmm) cc_final: 0.8614 (mmm) REVERT: Ar 168 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7494 (mt-10) REVERT: Ar 173 MET cc_start: 0.7806 (ttp) cc_final: 0.7487 (ttt) REVERT: As 153 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7442 (mptp) outliers start: 128 outliers final: 46 residues processed: 812 average time/residue: 1.6497 time to fit residues: 1483.9095 Evaluate side-chains 851 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 784 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 175 ASN Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ae residue 54 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 175 ASN Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 60 LYS Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 54 MET Chi-restraints excluded: chain Al residue 58 LYS Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain Ao residue 67 LEU Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Ar residue 60 LYS Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 177 optimal weight: 0.0770 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 151 ASN ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ad 175 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN Ag 175 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 175 ASN Ai 151 ASN Aj 113 ASN ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 175 ASN Aq 113 ASN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22914 Z= 0.262 Angle : 0.552 6.378 31103 Z= 0.278 Chirality : 0.041 0.175 3420 Planarity : 0.005 0.042 4009 Dihedral : 4.222 16.322 3040 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.06 % Allowed : 24.41 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.03 (0.16), residues: 2755 helix: 1.60 (0.16), residues: 988 sheet: 1.17 (0.33), residues: 228 loop : -1.37 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.000 HISAa 69 PHE 0.013 0.002 PHEAb 163 TYR 0.017 0.001 TYRAl 180 ARG 0.007 0.001 ARGAe 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 764 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8680 (m-30) cc_final: 0.8458 (m-30) REVERT: Aa 160 MET cc_start: 0.9112 (mmp) cc_final: 0.8765 (mmt) REVERT: Aa 173 MET cc_start: 0.7820 (ttp) cc_final: 0.7413 (ttt) REVERT: Aa 177 LYS cc_start: 0.8108 (mtpm) cc_final: 0.7703 (mptt) REVERT: Ab 76 GLN cc_start: 0.8452 (mt0) cc_final: 0.8008 (mt0) REVERT: Ab 99 LEU cc_start: 0.8590 (tt) cc_final: 0.8267 (tp) REVERT: Ab 108 MET cc_start: 0.9066 (tpt) cc_final: 0.8809 (mmp) REVERT: Ab 113 ASN cc_start: 0.8864 (m110) cc_final: 0.8620 (m110) REVERT: Ab 121 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: Ab 173 MET cc_start: 0.7639 (ttp) cc_final: 0.7374 (ttp) REVERT: Ac 99 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8199 (tp) REVERT: Ac 108 MET cc_start: 0.9053 (tpt) cc_final: 0.8810 (mmt) REVERT: Ac 139 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: Ac 142 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7952 (mp0) REVERT: Ac 173 MET cc_start: 0.7590 (ttp) cc_final: 0.7308 (ttp) REVERT: Ac 177 LYS cc_start: 0.8091 (mtpm) cc_final: 0.7623 (mptt) REVERT: Ad 76 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8031 (mm110) REVERT: Ad 91 ASP cc_start: 0.8671 (m-30) cc_final: 0.8408 (m-30) REVERT: Ad 95 GLU cc_start: 0.8041 (mp0) cc_final: 0.7748 (mp0) REVERT: Ad 173 MET cc_start: 0.7806 (ttp) cc_final: 0.7557 (ttp) REVERT: Ae 56 MET cc_start: 0.8802 (mmp) cc_final: 0.8474 (mmt) REVERT: Ae 134 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8806 (ttt) REVERT: Ae 173 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (ttp) REVERT: Af 46 ARG cc_start: 0.9233 (mpt180) cc_final: 0.8996 (mpt180) REVERT: Af 69 HIS cc_start: 0.8114 (m-70) cc_final: 0.6980 (t70) REVERT: Ag 102 ASP cc_start: 0.8718 (t0) cc_final: 0.8385 (t0) REVERT: Ag 116 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8924 (tmm) REVERT: Ag 168 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7378 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7786 (m110) REVERT: Ag 177 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7605 (mptt) REVERT: Ag 181 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6873 (mtm) REVERT: Ah 76 GLN cc_start: 0.8514 (mt0) cc_final: 0.8115 (mt0) REVERT: Ah 91 ASP cc_start: 0.8723 (m-30) cc_final: 0.8494 (m-30) REVERT: Ah 173 MET cc_start: 0.7710 (ttp) cc_final: 0.7309 (ttt) REVERT: Ah 177 LYS cc_start: 0.8046 (mtpm) cc_final: 0.7576 (mptt) REVERT: Ah 181 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6927 (mtm) REVERT: Ai 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8228 (tp) REVERT: Ai 108 MET cc_start: 0.9082 (tpt) cc_final: 0.8862 (tpt) REVERT: Ai 121 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7273 (tp30) REVERT: Ai 153 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7058 (mptp) REVERT: Ai 168 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7418 (mt-10) REVERT: Ai 173 MET cc_start: 0.7841 (ttp) cc_final: 0.7496 (ttt) REVERT: Ai 177 LYS cc_start: 0.8214 (mtpm) cc_final: 0.7874 (mptt) REVERT: Aj 172 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7142 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7840 (mptt) REVERT: Al 139 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: Al 172 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6648 (mt-10) REVERT: Al 177 LYS cc_start: 0.8108 (mtpm) cc_final: 0.7614 (mppt) REVERT: Am 139 GLU cc_start: 0.7796 (tt0) cc_final: 0.7492 (tt0) REVERT: Am 168 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7585 (mt-10) REVERT: Am 177 LYS cc_start: 0.8100 (mtpm) cc_final: 0.7605 (mptt) REVERT: An 67 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8593 (mp) REVERT: An 91 ASP cc_start: 0.8549 (m-30) cc_final: 0.8169 (m-30) REVERT: An 95 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: An 99 LEU cc_start: 0.8480 (tt) cc_final: 0.8115 (tp) REVERT: An 121 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7572 (tp30) REVERT: An 135 MET cc_start: 0.9049 (mmm) cc_final: 0.8757 (mmm) REVERT: An 153 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8259 (mmpt) REVERT: An 173 MET cc_start: 0.7548 (ttp) cc_final: 0.7217 (ttt) REVERT: Ao 60 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8048 (mptt) REVERT: Ao 91 ASP cc_start: 0.8729 (m-30) cc_final: 0.8442 (m-30) REVERT: Ao 173 MET cc_start: 0.7667 (ttp) cc_final: 0.7347 (ttt) REVERT: Ap 60 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7498 (mptt) REVERT: Ap 116 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8896 (ttp) REVERT: Ap 173 MET cc_start: 0.7660 (ttp) cc_final: 0.7374 (ttt) REVERT: Aq 153 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7494 (mptp) REVERT: Aq 177 LYS cc_start: 0.8064 (mtpm) cc_final: 0.7735 (mptt) REVERT: Ar 91 ASP cc_start: 0.8781 (m-30) cc_final: 0.8555 (m-30) REVERT: Ar 99 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8275 (tp) REVERT: Ar 168 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7470 (mt-10) REVERT: Ar 173 MET cc_start: 0.7721 (ttp) cc_final: 0.7321 (ttt) REVERT: As 121 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7412 (tp30) outliers start: 125 outliers final: 49 residues processed: 811 average time/residue: 1.5726 time to fit residues: 1416.4843 Evaluate side-chains 834 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 763 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ae residue 54 MET Chi-restraints excluded: chain Ae residue 67 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 134 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 175 ASN Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 175 ASN Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Al residue 58 LYS Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Al residue 139 GLU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 95 GLU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 121 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 175 ASN Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ad 175 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN Ag 175 ASN Ah 113 ASN Ah 175 ASN Ai 175 ASN Aj 113 ASN ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 175 ASN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22914 Z= 0.209 Angle : 0.524 5.697 31103 Z= 0.263 Chirality : 0.040 0.160 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.019 16.364 3040 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.82 % Allowed : 24.45 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2755 helix: 1.82 (0.16), residues: 988 sheet: 1.25 (0.33), residues: 228 loop : -1.23 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAh 132 HIS 0.002 0.000 HISAc 69 PHE 0.011 0.002 PHEAi 163 TYR 0.015 0.001 TYRAl 180 ARG 0.007 0.000 ARGAe 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 754 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8662 (m-30) cc_final: 0.8432 (m-30) REVERT: Aa 160 MET cc_start: 0.9131 (mmp) cc_final: 0.8765 (mmt) REVERT: Aa 173 MET cc_start: 0.7710 (ttp) cc_final: 0.7316 (ttt) REVERT: Aa 177 LYS cc_start: 0.8074 (mtpm) cc_final: 0.7577 (mptt) REVERT: Ab 76 GLN cc_start: 0.8438 (mt0) cc_final: 0.7952 (mt0) REVERT: Ab 99 LEU cc_start: 0.8605 (tt) cc_final: 0.8259 (tp) REVERT: Ab 121 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: Ab 173 MET cc_start: 0.7648 (ttp) cc_final: 0.7371 (ttp) REVERT: Ab 175 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: Ac 99 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8195 (tp) REVERT: Ac 108 MET cc_start: 0.9051 (tpt) cc_final: 0.8793 (mmp) REVERT: Ac 139 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: Ac 142 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8015 (mp0) REVERT: Ac 173 MET cc_start: 0.7547 (ttp) cc_final: 0.7284 (ttp) REVERT: Ac 177 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7562 (mptt) REVERT: Ad 95 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: Ad 160 MET cc_start: 0.9288 (mmp) cc_final: 0.8821 (mmt) REVERT: Ae 134 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8818 (ttt) REVERT: Af 46 ARG cc_start: 0.9214 (mpt180) cc_final: 0.8960 (mpt180) REVERT: Af 69 HIS cc_start: 0.8127 (m-70) cc_final: 0.7016 (t70) REVERT: Ag 116 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8935 (tmm) REVERT: Ag 168 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7464 (mt-10) REVERT: Ah 76 GLN cc_start: 0.8499 (mt0) cc_final: 0.8068 (mt0) REVERT: Ah 91 ASP cc_start: 0.8689 (m-30) cc_final: 0.8463 (m-30) REVERT: Ah 173 MET cc_start: 0.7688 (ttp) cc_final: 0.7316 (ttt) REVERT: Ah 177 LYS cc_start: 0.8028 (mtpm) cc_final: 0.7631 (mptt) REVERT: Ah 181 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6884 (mtm) REVERT: Ai 108 MET cc_start: 0.9145 (tpt) cc_final: 0.8852 (tpt) REVERT: Ai 121 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7293 (tp30) REVERT: Ai 153 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7059 (mptp) REVERT: Ai 168 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7411 (mt-10) REVERT: Ai 173 MET cc_start: 0.7824 (ttp) cc_final: 0.7459 (ttt) REVERT: Ai 177 LYS cc_start: 0.8175 (mtpm) cc_final: 0.7844 (mptt) REVERT: Al 172 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6643 (mt-10) REVERT: Al 177 LYS cc_start: 0.8086 (mtpm) cc_final: 0.7566 (mptt) REVERT: Am 99 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8296 (tp) REVERT: Am 139 GLU cc_start: 0.7798 (tt0) cc_final: 0.7503 (tt0) REVERT: Am 168 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7544 (mt-10) REVERT: Am 177 LYS cc_start: 0.8024 (mtpm) cc_final: 0.7532 (mptt) REVERT: An 67 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8533 (mp) REVERT: An 95 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: An 99 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8163 (tp) REVERT: An 121 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7621 (tp30) REVERT: An 135 MET cc_start: 0.9071 (mmm) cc_final: 0.8762 (mmm) REVERT: An 153 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8555 (mmtm) REVERT: An 173 MET cc_start: 0.7489 (ttp) cc_final: 0.7256 (ttt) REVERT: Ao 60 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8300 (mptt) REVERT: Ao 91 ASP cc_start: 0.8758 (m-30) cc_final: 0.8542 (m-30) REVERT: Ao 121 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7369 (tm-30) REVERT: Ao 173 MET cc_start: 0.7625 (ttp) cc_final: 0.7244 (ttt) REVERT: Ap 116 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8843 (ttp) REVERT: Ap 173 MET cc_start: 0.7628 (ttp) cc_final: 0.7352 (ttt) REVERT: Aq 153 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7477 (mptp) REVERT: Aq 177 LYS cc_start: 0.8066 (mtpm) cc_final: 0.7692 (mptt) REVERT: Ar 91 ASP cc_start: 0.8747 (m-30) cc_final: 0.8528 (m-30) REVERT: Ar 99 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (tp) REVERT: Ar 168 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7445 (mt-10) REVERT: Ar 173 MET cc_start: 0.7648 (ttp) cc_final: 0.7298 (ttt) outliers start: 119 outliers final: 54 residues processed: 796 average time/residue: 1.6109 time to fit residues: 1423.1182 Evaluate side-chains 823 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 751 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 175 ASN Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 134 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 95 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain Am residue 175 ASN Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 175 ASN Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN Ag 175 ASN Ah 113 ASN Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 175 ASN ** Ap 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22914 Z= 0.280 Angle : 0.559 6.550 31103 Z= 0.280 Chirality : 0.042 0.167 3420 Planarity : 0.005 0.043 4009 Dihedral : 4.149 16.163 3040 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.86 % Allowed : 23.93 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.17 (0.16), residues: 2755 helix: 1.73 (0.16), residues: 988 sheet: 1.17 (0.32), residues: 228 loop : -1.21 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 132 HIS 0.002 0.000 HISAn 69 PHE 0.013 0.002 PHEAi 163 TYR 0.018 0.001 TYRAh 180 ARG 0.007 0.001 ARGAn 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 758 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8667 (m-30) cc_final: 0.8425 (m-30) REVERT: Aa 160 MET cc_start: 0.9119 (mmp) cc_final: 0.8808 (mmt) REVERT: Aa 173 MET cc_start: 0.7777 (ttp) cc_final: 0.7403 (ttt) REVERT: Aa 177 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7607 (mptt) REVERT: Ab 76 GLN cc_start: 0.8451 (mt0) cc_final: 0.7978 (mt0) REVERT: Ab 99 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8255 (tp) REVERT: Ab 113 ASN cc_start: 0.8868 (m110) cc_final: 0.8651 (m110) REVERT: Ab 173 MET cc_start: 0.7650 (ttp) cc_final: 0.7387 (ttp) REVERT: Ac 99 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8193 (tp) REVERT: Ac 108 MET cc_start: 0.9047 (tpt) cc_final: 0.8804 (mmp) REVERT: Ac 139 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: Ac 173 MET cc_start: 0.7604 (ttp) cc_final: 0.7332 (ttp) REVERT: Ac 177 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7556 (mptt) REVERT: Ad 76 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8069 (mm110) REVERT: Ad 91 ASP cc_start: 0.8667 (m-30) cc_final: 0.8374 (m-30) REVERT: Ad 95 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: Ad 160 MET cc_start: 0.9305 (mmp) cc_final: 0.8793 (mmt) REVERT: Ae 173 MET cc_start: 0.7996 (ttp) cc_final: 0.7736 (ttp) REVERT: Af 46 ARG cc_start: 0.9210 (mpt180) cc_final: 0.8947 (mpt180) REVERT: Af 69 HIS cc_start: 0.8167 (m-70) cc_final: 0.7040 (t70) REVERT: Ag 116 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8916 (tmm) REVERT: Ag 168 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7409 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7526 (mptt) REVERT: Ah 76 GLN cc_start: 0.8516 (mt0) cc_final: 0.8091 (mt0) REVERT: Ah 91 ASP cc_start: 0.8711 (m-30) cc_final: 0.8436 (m-30) REVERT: Ah 173 MET cc_start: 0.7697 (ttp) cc_final: 0.7344 (ttt) REVERT: Ah 177 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7721 (mptt) REVERT: Ah 181 MET cc_start: 0.7220 (mmt) cc_final: 0.7013 (mtt) REVERT: Ai 99 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8236 (tp) REVERT: Ai 108 MET cc_start: 0.9081 (tpt) cc_final: 0.8748 (tpt) REVERT: Ai 121 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7301 (tp30) REVERT: Ai 153 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7062 (mptp) REVERT: Ai 168 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7431 (mt-10) REVERT: Ai 173 MET cc_start: 0.7860 (ttp) cc_final: 0.7509 (ttt) REVERT: Ai 177 LYS cc_start: 0.8185 (mtpm) cc_final: 0.7827 (mptt) REVERT: Aj 172 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7176 (mm-30) REVERT: Ak 99 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8186 (tp) REVERT: Al 172 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6605 (mt-10) REVERT: Al 177 LYS cc_start: 0.8035 (mtpm) cc_final: 0.7612 (mppt) REVERT: Am 99 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8304 (tp) REVERT: Am 139 GLU cc_start: 0.7773 (tt0) cc_final: 0.7458 (tt0) REVERT: Am 168 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7612 (mt-10) REVERT: Am 177 LYS cc_start: 0.8032 (mtpm) cc_final: 0.7539 (mptt) REVERT: An 67 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (mp) REVERT: An 99 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8136 (tp) REVERT: An 121 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7553 (tp30) REVERT: An 153 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8567 (mmtm) REVERT: An 173 MET cc_start: 0.7609 (ttp) cc_final: 0.7300 (ttt) REVERT: An 177 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7634 (mptt) REVERT: Ao 60 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8011 (mptt) REVERT: Ao 91 ASP cc_start: 0.8803 (m-30) cc_final: 0.8586 (m-30) REVERT: Ao 99 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8130 (tp) REVERT: Ao 153 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: Ao 173 MET cc_start: 0.7592 (ttp) cc_final: 0.7250 (ttt) REVERT: Ap 60 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7478 (mptt) REVERT: Ap 116 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8891 (ttp) REVERT: Ap 173 MET cc_start: 0.7653 (ttp) cc_final: 0.7377 (ttt) REVERT: Aq 67 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8185 (mp) REVERT: Aq 99 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8230 (tp) REVERT: Aq 153 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7486 (mptp) REVERT: Aq 177 LYS cc_start: 0.8030 (mtpm) cc_final: 0.7669 (mptt) REVERT: Ar 91 ASP cc_start: 0.8778 (m-30) cc_final: 0.8542 (m-30) REVERT: Ar 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (tp) REVERT: Ar 173 MET cc_start: 0.7697 (ttp) cc_final: 0.7420 (ttt) REVERT: As 121 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7662 (tm-30) REVERT: As 153 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7401 (mptp) outliers start: 120 outliers final: 59 residues processed: 801 average time/residue: 1.5924 time to fit residues: 1417.7878 Evaluate side-chains 832 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 750 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 67 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 175 ASN Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN ** Ak 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN Am 175 ASN ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN Ao 175 ASN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22914 Z= 0.295 Angle : 0.571 6.058 31103 Z= 0.287 Chirality : 0.043 0.188 3420 Planarity : 0.005 0.042 4009 Dihedral : 4.199 16.168 3040 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.57 % Allowed : 24.70 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2755 helix: 1.67 (0.16), residues: 988 sheet: 1.08 (0.32), residues: 228 loop : -1.18 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.002 0.001 HISAn 69 PHE 0.013 0.002 PHEAi 163 TYR 0.019 0.001 TYRAh 180 ARG 0.008 0.001 ARGAe 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 738 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8695 (m-30) cc_final: 0.8458 (m-30) REVERT: Aa 160 MET cc_start: 0.9130 (mmp) cc_final: 0.8816 (mmt) REVERT: Aa 173 MET cc_start: 0.7759 (ttp) cc_final: 0.7327 (ttt) REVERT: Aa 177 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7710 (mptt) REVERT: Ab 76 GLN cc_start: 0.8452 (mt0) cc_final: 0.7995 (mt0) REVERT: Ab 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8260 (tp) REVERT: Ab 113 ASN cc_start: 0.8904 (m110) cc_final: 0.8682 (m110) REVERT: Ab 173 MET cc_start: 0.7637 (ttp) cc_final: 0.7367 (ttp) REVERT: Ac 99 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (tp) REVERT: Ac 108 MET cc_start: 0.9037 (tpt) cc_final: 0.8809 (mmp) REVERT: Ac 139 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: Ac 142 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7969 (mp0) REVERT: Ac 173 MET cc_start: 0.7584 (ttp) cc_final: 0.7308 (ttp) REVERT: Ac 177 LYS cc_start: 0.8055 (mtpm) cc_final: 0.7570 (mptt) REVERT: Ad 76 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: Ad 91 ASP cc_start: 0.8686 (m-30) cc_final: 0.8390 (m-30) REVERT: Ad 95 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: Ad 160 MET cc_start: 0.9288 (mmp) cc_final: 0.8757 (mmt) REVERT: Ae 173 MET cc_start: 0.7986 (ttp) cc_final: 0.7716 (ttp) REVERT: Af 69 HIS cc_start: 0.8190 (m-70) cc_final: 0.7057 (t70) REVERT: Ag 102 ASP cc_start: 0.8712 (t0) cc_final: 0.8346 (t0) REVERT: Ag 116 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8895 (tmm) REVERT: Ag 168 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7418 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8118 (mtpm) cc_final: 0.7559 (mptt) REVERT: Ah 48 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8161 (mtmm) REVERT: Ah 76 GLN cc_start: 0.8525 (mt0) cc_final: 0.8096 (mt0) REVERT: Ah 91 ASP cc_start: 0.8716 (m-30) cc_final: 0.8442 (m-30) REVERT: Ah 99 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8247 (tp) REVERT: Ah 173 MET cc_start: 0.7761 (ttp) cc_final: 0.7398 (ttt) REVERT: Ah 177 LYS cc_start: 0.8086 (mtpm) cc_final: 0.7744 (mptt) REVERT: Ai 99 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8236 (tp) REVERT: Ai 108 MET cc_start: 0.9070 (tpt) cc_final: 0.8857 (tpt) REVERT: Ai 121 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7307 (tp30) REVERT: Ai 153 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7047 (mptp) REVERT: Ai 168 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7431 (mt-10) REVERT: Ai 173 MET cc_start: 0.7843 (ttp) cc_final: 0.7497 (ttt) REVERT: Ai 177 LYS cc_start: 0.8192 (mtpm) cc_final: 0.7812 (mptt) REVERT: Aj 172 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7199 (mm-30) REVERT: Ak 99 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8191 (tp) REVERT: Al 172 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6603 (mt-10) REVERT: Al 177 LYS cc_start: 0.8066 (mtpm) cc_final: 0.7675 (mptt) REVERT: Am 99 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8313 (tp) REVERT: Am 139 GLU cc_start: 0.7728 (tt0) cc_final: 0.7387 (tt0) REVERT: Am 168 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7602 (mt-10) REVERT: Am 177 LYS cc_start: 0.8042 (mtpm) cc_final: 0.7523 (mptt) REVERT: An 67 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8481 (mp) REVERT: An 95 GLU cc_start: 0.8127 (mp0) cc_final: 0.7837 (mp0) REVERT: An 99 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8122 (tp) REVERT: An 102 ASP cc_start: 0.8678 (t0) cc_final: 0.8331 (t0) REVERT: An 121 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7549 (tp30) REVERT: An 153 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8569 (mmtm) REVERT: An 173 MET cc_start: 0.7640 (ttp) cc_final: 0.7306 (ttt) REVERT: An 177 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7616 (mptt) REVERT: Ao 60 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (mptt) REVERT: Ao 91 ASP cc_start: 0.8769 (m-30) cc_final: 0.8544 (m-30) REVERT: Ao 99 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8128 (tp) REVERT: Ao 153 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: Ao 173 MET cc_start: 0.7617 (ttp) cc_final: 0.7277 (ttt) REVERT: Ap 60 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7471 (mptt) REVERT: Ap 116 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8929 (ttp) REVERT: Ap 173 MET cc_start: 0.7670 (ttp) cc_final: 0.7398 (ttt) REVERT: Aq 67 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8224 (mp) REVERT: Aq 99 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8235 (tp) REVERT: Aq 153 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7512 (mptp) REVERT: Aq 177 LYS cc_start: 0.8110 (mtpm) cc_final: 0.7737 (mptt) REVERT: Ar 91 ASP cc_start: 0.8781 (m-30) cc_final: 0.8542 (m-30) REVERT: Ar 99 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8278 (tp) REVERT: Ar 173 MET cc_start: 0.7699 (ttp) cc_final: 0.7428 (ttt) REVERT: As 153 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7397 (mptp) outliers start: 113 outliers final: 57 residues processed: 778 average time/residue: 1.5900 time to fit residues: 1374.2520 Evaluate side-chains 819 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 737 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 103 ILE Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 67 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 224 optimal weight: 0.0020 chunk 238 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 175 ASN ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 175 ASN ** Ap 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22914 Z= 0.264 Angle : 0.562 6.363 31103 Z= 0.282 Chirality : 0.042 0.175 3420 Planarity : 0.005 0.045 4009 Dihedral : 4.148 16.229 3040 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.41 % Allowed : 25.18 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.20 (0.16), residues: 2755 helix: 1.68 (0.16), residues: 988 sheet: 1.09 (0.32), residues: 228 loop : -1.11 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.005 0.001 HISAc 69 PHE 0.014 0.002 PHEAb 163 TYR 0.018 0.001 TYRAh 180 ARG 0.008 0.001 ARGAe 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 735 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8689 (m-30) cc_final: 0.8448 (m-30) REVERT: Aa 160 MET cc_start: 0.9113 (mmp) cc_final: 0.8714 (mmt) REVERT: Aa 168 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7496 (mt-10) REVERT: Aa 173 MET cc_start: 0.7785 (ttp) cc_final: 0.7407 (ttt) REVERT: Aa 177 LYS cc_start: 0.8066 (mtpm) cc_final: 0.7620 (mptt) REVERT: Ab 76 GLN cc_start: 0.8449 (mt0) cc_final: 0.7985 (mt0) REVERT: Ab 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8262 (tp) REVERT: Ab 113 ASN cc_start: 0.8852 (m110) cc_final: 0.8648 (m110) REVERT: Ab 173 MET cc_start: 0.7615 (ttp) cc_final: 0.7360 (ttp) REVERT: Ac 99 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8191 (tp) REVERT: Ac 108 MET cc_start: 0.9041 (tpt) cc_final: 0.8805 (mmp) REVERT: Ac 139 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: Ac 142 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7963 (mp0) REVERT: Ac 173 MET cc_start: 0.7593 (ttp) cc_final: 0.7328 (ttp) REVERT: Ac 177 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7554 (mptt) REVERT: Ad 76 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8060 (mm110) REVERT: Ad 91 ASP cc_start: 0.8674 (m-30) cc_final: 0.8362 (m-30) REVERT: Ad 95 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: Ad 121 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7520 (tm-30) REVERT: Ad 160 MET cc_start: 0.9301 (mmp) cc_final: 0.8770 (mmt) REVERT: Ae 173 MET cc_start: 0.7975 (ttp) cc_final: 0.7691 (ttp) REVERT: Af 69 HIS cc_start: 0.8188 (m-70) cc_final: 0.7055 (t70) REVERT: Ag 102 ASP cc_start: 0.8711 (t0) cc_final: 0.8345 (t0) REVERT: Ag 116 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8934 (tmm) REVERT: Ag 168 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7438 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8115 (mtpm) cc_final: 0.7556 (mptt) REVERT: Ah 48 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8157 (mtmm) REVERT: Ah 76 GLN cc_start: 0.8519 (mt0) cc_final: 0.8085 (mt0) REVERT: Ah 91 ASP cc_start: 0.8709 (m-30) cc_final: 0.8434 (m-30) REVERT: Ah 99 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (tp) REVERT: Ah 173 MET cc_start: 0.7726 (ttp) cc_final: 0.7368 (ttt) REVERT: Ah 177 LYS cc_start: 0.8083 (mtpm) cc_final: 0.7738 (mptt) REVERT: Ai 99 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8233 (tp) REVERT: Ai 108 MET cc_start: 0.9094 (tpt) cc_final: 0.8774 (tpt) REVERT: Ai 121 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7315 (tp30) REVERT: Ai 153 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7017 (mptp) REVERT: Ai 168 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7425 (mt-10) REVERT: Ai 173 MET cc_start: 0.7829 (ttp) cc_final: 0.7507 (ttt) REVERT: Ai 177 LYS cc_start: 0.8169 (mtpm) cc_final: 0.7761 (mptt) REVERT: Aj 172 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7180 (mm-30) REVERT: Ak 99 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8182 (tp) REVERT: Al 172 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6594 (mt-10) REVERT: Al 177 LYS cc_start: 0.8056 (mtpm) cc_final: 0.7627 (mppt) REVERT: Am 99 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8313 (tp) REVERT: Am 113 ASN cc_start: 0.8681 (m-40) cc_final: 0.8465 (m-40) REVERT: Am 139 GLU cc_start: 0.7732 (tt0) cc_final: 0.7386 (tt0) REVERT: Am 168 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7605 (mt-10) REVERT: Am 177 LYS cc_start: 0.8021 (mtpm) cc_final: 0.7509 (mptt) REVERT: An 95 GLU cc_start: 0.8117 (mp0) cc_final: 0.7824 (mp0) REVERT: An 99 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8124 (tp) REVERT: An 102 ASP cc_start: 0.8689 (t0) cc_final: 0.8329 (t0) REVERT: An 121 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7546 (tp30) REVERT: An 153 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8567 (mmtm) REVERT: An 173 MET cc_start: 0.7603 (ttp) cc_final: 0.7277 (ttt) REVERT: An 177 LYS cc_start: 0.8135 (mtpm) cc_final: 0.7628 (mptt) REVERT: Ao 91 ASP cc_start: 0.8760 (m-30) cc_final: 0.8537 (m-30) REVERT: Ao 99 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8120 (tp) REVERT: Ao 153 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7474 (mptp) REVERT: Ao 173 MET cc_start: 0.7585 (ttp) cc_final: 0.7249 (ttt) REVERT: Ap 60 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7413 (mptt) REVERT: Ap 116 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8900 (ttp) REVERT: Ap 173 MET cc_start: 0.7646 (ttp) cc_final: 0.7375 (ttt) REVERT: Aq 67 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8268 (mp) REVERT: Aq 99 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8102 (mt) REVERT: Aq 153 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7513 (mptp) REVERT: Aq 177 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7728 (mptt) REVERT: Ar 91 ASP cc_start: 0.8779 (m-30) cc_final: 0.8547 (m-30) REVERT: Ar 99 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8279 (tp) REVERT: Ar 173 MET cc_start: 0.7678 (ttp) cc_final: 0.7412 (ttt) REVERT: As 121 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7671 (tm-30) REVERT: As 153 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7395 (mptp) outliers start: 109 outliers final: 63 residues processed: 770 average time/residue: 1.6109 time to fit residues: 1381.1089 Evaluate side-chains 820 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 734 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 103 ILE Chi-restraints excluded: chain Aa residue 175 ASN Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 181 MET Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 181 MET Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 67 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN Ah 113 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN Ak 175 ASN ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 69 HIS An 175 ASN As 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22914 Z= 0.290 Angle : 0.575 7.138 31103 Z= 0.290 Chirality : 0.043 0.177 3420 Planarity : 0.005 0.043 4009 Dihedral : 4.212 16.370 3040 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.13 % Allowed : 25.34 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.17 (0.16), residues: 2755 helix: 1.59 (0.16), residues: 988 sheet: 1.07 (0.32), residues: 228 loop : -1.08 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.005 0.001 HISAc 69 PHE 0.013 0.002 PHEAi 163 TYR 0.017 0.001 TYRAc 180 ARG 0.008 0.001 ARGAe 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 739 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8673 (m-30) cc_final: 0.8428 (m-30) REVERT: Aa 160 MET cc_start: 0.9131 (mmp) cc_final: 0.8816 (mmt) REVERT: Aa 168 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7497 (mt-10) REVERT: Aa 173 MET cc_start: 0.7809 (ttp) cc_final: 0.7426 (ttt) REVERT: Aa 177 LYS cc_start: 0.8056 (mtpm) cc_final: 0.7602 (mptt) REVERT: Ab 76 GLN cc_start: 0.8458 (mt0) cc_final: 0.8001 (mt0) REVERT: Ab 99 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ab 113 ASN cc_start: 0.8893 (m110) cc_final: 0.8661 (m110) REVERT: Ab 173 MET cc_start: 0.7611 (ttp) cc_final: 0.7354 (ttp) REVERT: Ac 99 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8191 (tp) REVERT: Ac 108 MET cc_start: 0.9050 (tpt) cc_final: 0.8815 (mmp) REVERT: Ac 139 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: Ac 173 MET cc_start: 0.7618 (ttp) cc_final: 0.7348 (ttp) REVERT: Ac 177 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7572 (mptt) REVERT: Ad 76 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8063 (mm110) REVERT: Ad 95 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: Ad 121 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7552 (tm-30) REVERT: Ad 160 MET cc_start: 0.9287 (mmp) cc_final: 0.8747 (mmt) REVERT: Ae 99 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8159 (tp) REVERT: Ae 173 MET cc_start: 0.7981 (ttp) cc_final: 0.7709 (ttp) REVERT: Af 69 HIS cc_start: 0.8185 (m-70) cc_final: 0.7055 (t70) REVERT: Ag 102 ASP cc_start: 0.8726 (t0) cc_final: 0.8361 (t0) REVERT: Ag 116 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8914 (tmm) REVERT: Ag 168 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7436 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8126 (mtpm) cc_final: 0.7565 (mptt) REVERT: Ah 48 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (mtmm) REVERT: Ah 76 GLN cc_start: 0.8522 (mt0) cc_final: 0.8094 (mt0) REVERT: Ah 91 ASP cc_start: 0.8717 (m-30) cc_final: 0.8497 (m-30) REVERT: Ah 99 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8234 (tp) REVERT: Ah 173 MET cc_start: 0.7740 (ttp) cc_final: 0.7382 (ttt) REVERT: Ah 177 LYS cc_start: 0.8062 (mtpm) cc_final: 0.7726 (mptt) REVERT: Ai 69 HIS cc_start: 0.8024 (m-70) cc_final: 0.6788 (t-90) REVERT: Ai 99 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (tp) REVERT: Ai 108 MET cc_start: 0.9071 (tpt) cc_final: 0.8851 (tpt) REVERT: Ai 121 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7308 (tp30) REVERT: Ai 153 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.6998 (mptp) REVERT: Ai 168 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7436 (mt-10) REVERT: Ai 173 MET cc_start: 0.7840 (ttp) cc_final: 0.7517 (ttt) REVERT: Ai 177 LYS cc_start: 0.8164 (mtpm) cc_final: 0.7774 (mptt) REVERT: Aj 69 HIS cc_start: 0.8110 (m90) cc_final: 0.7801 (m-70) REVERT: Aj 172 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7182 (mm-30) REVERT: Ak 99 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8188 (tp) REVERT: Al 172 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6596 (mt-10) REVERT: Al 177 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7544 (mptt) REVERT: Am 99 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8314 (tp) REVERT: Am 139 GLU cc_start: 0.7737 (tt0) cc_final: 0.7393 (tt0) REVERT: Am 168 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7612 (mt-10) REVERT: Am 177 LYS cc_start: 0.8062 (mtpm) cc_final: 0.7540 (mptt) REVERT: An 95 GLU cc_start: 0.8120 (mp0) cc_final: 0.7815 (mp0) REVERT: An 99 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8126 (tp) REVERT: An 102 ASP cc_start: 0.8694 (t0) cc_final: 0.8333 (t0) REVERT: An 121 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7559 (tp30) REVERT: An 153 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8568 (mmtm) REVERT: An 173 MET cc_start: 0.7616 (ttp) cc_final: 0.7310 (ttt) REVERT: An 177 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7633 (mptt) REVERT: Ao 91 ASP cc_start: 0.8764 (m-30) cc_final: 0.8543 (m-30) REVERT: Ao 99 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8159 (tp) REVERT: Ao 153 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7472 (mptp) REVERT: Ao 173 MET cc_start: 0.7612 (ttp) cc_final: 0.7275 (ttt) REVERT: Ap 60 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7408 (mptt) REVERT: Ap 116 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8914 (ttp) REVERT: Ap 173 MET cc_start: 0.7658 (ttp) cc_final: 0.7392 (ttt) REVERT: Aq 67 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8286 (mp) REVERT: Aq 99 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8235 (tp) REVERT: Aq 153 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.7520 (mptp) REVERT: Aq 177 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7726 (mptt) REVERT: Ar 91 ASP cc_start: 0.8776 (m-30) cc_final: 0.8535 (m-30) REVERT: Ar 99 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8267 (tp) REVERT: Ar 173 MET cc_start: 0.7692 (ttp) cc_final: 0.7424 (ttt) REVERT: As 121 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7671 (tm-30) REVERT: As 153 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7396 (mptp) outliers start: 102 outliers final: 64 residues processed: 780 average time/residue: 1.5868 time to fit residues: 1372.9447 Evaluate side-chains 827 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 739 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 103 ILE Chi-restraints excluded: chain Aa residue 175 ASN Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 181 MET Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 76 GLN Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 175 ASN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 175 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 181 MET Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 103 ILE Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 187 VAL Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.0980 chunk 185 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 175 ASN ** Al 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 175 ASN An 175 ASN ** Ap 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135903 restraints weight = 24241.391| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.00 r_work: 0.3372 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22914 Z= 0.209 Angle : 0.541 7.020 31103 Z= 0.272 Chirality : 0.041 0.168 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.009 16.911 3040 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.85 % Allowed : 25.87 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.37 (0.16), residues: 2755 helix: 1.30 (0.15), residues: 1102 sheet: 2.26 (0.32), residues: 190 loop : -0.89 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAf 132 HIS 0.005 0.000 HISAc 69 PHE 0.011 0.002 PHEAi 163 TYR 0.015 0.001 TYRAc 180 ARG 0.008 0.000 ARGAe 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16902.17 seconds wall clock time: 294 minutes 11.11 seconds (17651.11 seconds total)