Starting phenix.real_space_refine on Sat Feb 7 08:33:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.map" model { file = "/net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e39_47475/02_2026/9e39_47475.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 216 5.16 5 C 19590 2.51 5 N 5500 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31231 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "B" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "C" Number of atoms: 1739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1713 Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "E" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "F" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "G" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "H" Number of atoms: 1739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1713 Chain: "I" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "J" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "K" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "L" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "M" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "N" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "O" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "P" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1725 Chain: "Q" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "R" Number of atoms: 1730 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1723 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'2I4': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 38 residue: pdb=" N ALYS A 30 " occ=0.42 ... (16 atoms not shown) pdb=" NZ BLYS A 30 " occ=0.58 residue: pdb=" N AGLN A 176 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN A 176 " occ=0.46 residue: pdb=" N ALYS B 30 " occ=0.59 ... (16 atoms not shown) pdb=" NZ BLYS B 30 " occ=0.41 residue: pdb=" N AARG B 229 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 229 " occ=0.57 residue: pdb=" N ALYS C 30 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 30 " occ=0.50 residue: pdb=" N AGLN C 176 " occ=0.56 ... (16 atoms not shown) pdb=" NE2BGLN C 176 " occ=0.44 residue: pdb=" N AARG C 229 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG C 229 " occ=0.49 residue: pdb=" N ALYS D 30 " occ=0.34 ... (16 atoms not shown) pdb=" NZ BLYS D 30 " occ=0.66 residue: pdb=" N AGLN D 176 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN D 176 " occ=0.49 residue: pdb=" N AGLN E 176 " occ=0.52 ... (16 atoms not shown) pdb=" NE2BGLN E 176 " occ=0.48 residue: pdb=" N AARG E 229 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG E 229 " occ=0.43 residue: pdb=" N ALYS F 30 " occ=0.49 ... (16 atoms not shown) pdb=" NZ BLYS F 30 " occ=0.51 ... (remaining 26 not shown) Time building chain proxies: 12.73, per 1000 atoms: 0.41 Number of scatterers: 31231 At special positions: 0 Unit cell: (171.288, 167.719, 107.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 P 6 15.00 O 5919 8.00 N 5500 7.00 C 19590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 2.2 seconds 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7492 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.629A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.729A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.883A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.778A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.669A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.855A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 223 through 242 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.633A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.540A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.713A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.863A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 223 through 242 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.742A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.888A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.839A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.767A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 223 through 242 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.631A pdb=" N SER E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.944A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 174 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.653A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 4.006A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 223 through 242 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 removed outlier: 3.548A pdb=" N MET F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 174 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.753A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.910A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 223 through 242 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.813A pdb=" N MET G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.735A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 removed outlier: 3.656A pdb=" N ALA G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.706A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.857A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'G' and resid 223 through 242 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 35 through 44 removed outlier: 3.625A pdb=" N MET H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 149 through 153 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.769A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 4.078A pdb=" N ILE H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'H' and resid 223 through 242 removed outlier: 3.628A pdb=" N ALA H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 removed outlier: 3.775A pdb=" N MET I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 59 removed outlier: 4.095A pdb=" N VAL I 59 " --> pdb=" O MET I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.912A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.885A pdb=" N ILE I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 removed outlier: 3.636A pdb=" N CYS I 218 " --> pdb=" O MET I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 242 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 35 through 44 removed outlier: 3.614A pdb=" N MET J 39 " --> pdb=" O GLU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.941A pdb=" N VAL J 59 " --> pdb=" O MET J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 84 Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.799A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.854A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'J' and resid 223 through 242 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 removed outlier: 3.633A pdb=" N MET K 39 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 145 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 175 Processing helix chain 'K' and resid 178 through 190 removed outlier: 3.587A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 205 removed outlier: 3.875A pdb=" N ILE K 201 " --> pdb=" O ASP K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'K' and resid 223 through 242 Processing helix chain 'L' and resid 16 through 31 Processing helix chain 'L' and resid 35 through 45 removed outlier: 3.583A pdb=" N MET L 39 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 59 removed outlier: 3.802A pdb=" N VAL L 59 " --> pdb=" O MET L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 119 Processing helix chain 'L' and resid 125 through 145 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.877A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.772A pdb=" N ILE L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'L' and resid 223 through 242 removed outlier: 3.558A pdb=" N ALA L 242 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 31 Processing helix chain 'M' and resid 35 through 44 removed outlier: 3.737A pdb=" N MET M 39 " --> pdb=" O GLU M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 58 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 100 through 105 removed outlier: 3.717A pdb=" N ALA M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 119 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 175 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.796A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.803A pdb=" N ILE M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'M' and resid 223 through 242 Processing helix chain 'N' and resid 16 through 31 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 48 through 59 removed outlier: 4.058A pdb=" N VAL N 59 " --> pdb=" O MET N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 84 Processing helix chain 'N' and resid 100 through 105 Processing helix chain 'N' and resid 110 through 120 Processing helix chain 'N' and resid 125 through 145 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 190 removed outlier: 3.509A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 205 removed outlier: 3.824A pdb=" N ILE N 201 " --> pdb=" O ASP N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'N' and resid 223 through 242 Processing helix chain 'O' and resid 16 through 31 Processing helix chain 'O' and resid 35 through 44 removed outlier: 3.609A pdb=" N MET O 39 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER O 44 " --> pdb=" O PHE O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 58 Processing helix chain 'O' and resid 62 through 84 Processing helix chain 'O' and resid 100 through 105 Processing helix chain 'O' and resid 110 through 120 Processing helix chain 'O' and resid 125 through 145 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 175 Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.780A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.791A pdb=" N ILE O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 223 through 242 Processing helix chain 'P' and resid 16 through 31 Processing helix chain 'P' and resid 35 through 44 removed outlier: 3.604A pdb=" N MET P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 59 removed outlier: 3.691A pdb=" N VAL P 59 " --> pdb=" O MET P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 84 Processing helix chain 'P' and resid 100 through 105 Processing helix chain 'P' and resid 110 through 120 Processing helix chain 'P' and resid 125 through 145 Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 160 through 175 Processing helix chain 'P' and resid 178 through 193 removed outlier: 3.757A pdb=" N LEU P 190 " --> pdb=" O THR P 186 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 206 removed outlier: 3.791A pdb=" N ILE P 201 " --> pdb=" O ASP P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 219 Processing helix chain 'P' and resid 223 through 242 Processing helix chain 'Q' and resid 16 through 31 Processing helix chain 'Q' and resid 35 through 44 removed outlier: 3.501A pdb=" N MET Q 39 " --> pdb=" O GLU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 58 Processing helix chain 'Q' and resid 62 through 84 Processing helix chain 'Q' and resid 100 through 106 Processing helix chain 'Q' and resid 110 through 120 Processing helix chain 'Q' and resid 125 through 145 Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'Q' and resid 160 through 175 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 3.681A pdb=" N LEU Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN Q 192 " --> pdb=" O THR Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 205 removed outlier: 3.980A pdb=" N ILE Q 201 " --> pdb=" O ASP Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 219 Processing helix chain 'Q' and resid 223 through 242 Processing helix chain 'R' and resid 16 through 31 Processing helix chain 'R' and resid 35 through 45 Processing helix chain 'R' and resid 48 through 58 Processing helix chain 'R' and resid 62 through 84 Processing helix chain 'R' and resid 100 through 105 Processing helix chain 'R' and resid 110 through 120 Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 149 through 153 Processing helix chain 'R' and resid 160 through 175 Processing helix chain 'R' and resid 178 through 193 removed outlier: 3.928A pdb=" N LEU R 190 " --> pdb=" O THR R 186 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL R 191 " --> pdb=" O GLU R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 205 removed outlier: 3.739A pdb=" N ILE R 201 " --> pdb=" O ASP R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 218 removed outlier: 3.647A pdb=" N CYS R 218 " --> pdb=" O MET R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 242 2182 hydrogen bonds defined for protein. 6462 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: 5.28 Time building geometry restraints manager: 3.68 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: 10517 1.34 - 1.46: 6221 1.46 - 1.58: 14755 1.58 - 1.70: 7 1.70 - 1.82: 396 Bond restraints: 31896 Sorted by residual: bond pdb=" N ILE H 153 " pdb=" CA ILE H 153 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 9.84e+00 bond pdb=" N ILE C 37 " pdb=" CA ILE C 37 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.79e+00 bond pdb=" N ILE R 37 " pdb=" CA ILE R 37 " ideal model delta sigma weight residual 1.463 1.498 -0.035 1.20e-02 6.94e+03 8.38e+00 bond pdb=" N VAL H 221 " pdb=" CA VAL H 221 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" N ILE D 37 " pdb=" CA ILE D 37 " ideal model delta sigma weight residual 1.463 1.496 -0.033 1.20e-02 6.94e+03 7.56e+00 ... (remaining 31891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 42641 2.32 - 4.64: 619 4.64 - 6.96: 79 6.96 - 9.28: 15 9.28 - 11.60: 6 Bond angle restraints: 43360 Sorted by residual: angle pdb=" CB MET H 235 " pdb=" CG MET H 235 " pdb=" SD MET H 235 " ideal model delta sigma weight residual 112.70 124.30 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA GLN L 237 " pdb=" CB GLN L 237 " pdb=" CG GLN L 237 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " pdb=" CG GLN B 237 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA GLN I 237 " pdb=" CB GLN I 237 " pdb=" CG GLN I 237 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CB GLN L 237 " pdb=" CG GLN L 237 " pdb=" CD GLN L 237 " ideal model delta sigma weight residual 112.60 118.81 -6.21 1.70e+00 3.46e-01 1.33e+01 ... (remaining 43355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.64: 17944 26.64 - 53.28: 1590 53.28 - 79.92: 170 79.92 - 106.55: 29 106.55 - 133.19: 5 Dihedral angle restraints: 19738 sinusoidal: 8174 harmonic: 11564 Sorted by residual: dihedral pdb=" O11 IHP J 401 " pdb=" C1 IHP J 401 " pdb=" C2 IHP J 401 " pdb=" O12 IHP J 401 " ideal model delta sinusoidal sigma weight residual -64.01 69.18 -133.19 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C6 IHP J 401 " pdb=" C1 IHP J 401 " pdb=" C2 IHP J 401 " pdb=" O12 IHP J 401 " ideal model delta sinusoidal sigma weight residual 61.05 -166.22 -132.73 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" C3 IHP J 401 " pdb=" C1 IHP J 401 " pdb=" C2 IHP J 401 " pdb=" O11 IHP J 401 " ideal model delta sinusoidal sigma weight residual 184.60 60.93 123.67 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 19735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4550 0.079 - 0.157: 285 0.157 - 0.236: 4 0.236 - 0.314: 2 0.314 - 0.393: 1 Chirality restraints: 4842 Sorted by residual: chirality pdb=" C2 IHP J 401 " pdb=" C1 IHP J 401 " pdb=" C3 IHP J 401 " pdb=" O12 IHP J 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.13 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C3 IHP J 401 " pdb=" C2 IHP J 401 " pdb=" C4 IHP J 401 " pdb=" O13 IHP J 401 " both_signs ideal model delta sigma weight residual False -2.34 -2.06 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C18 2I4 D 301 " pdb=" C13 2I4 D 301 " pdb=" C17 2I4 D 301 " pdb=" C19 2I4 D 301 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4839 not shown) Planarity restraints: 5666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 44 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C SER N 44 " -0.041 2.00e-02 2.50e+03 pdb=" O SER N 44 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU N 45 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 48 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO C 49 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 195 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 196 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " 0.030 5.00e-02 4.00e+02 ... (remaining 5663 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4646 2.75 - 3.29: 31522 3.29 - 3.83: 54168 3.83 - 4.36: 59223 4.36 - 4.90: 104408 Nonbonded interactions: 253967 Sorted by model distance: nonbonded pdb=" OD1 ASN G 53 " pdb=" OH TYR G 130 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN E 53 " pdb=" OH TYR E 130 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 16 " pdb=" OG1 THR B 19 " model vdw 2.223 3.040 nonbonded pdb=" O THR N 54 " pdb=" OG1 THR N 58 " model vdw 2.224 3.040 nonbonded pdb=" O PHE N 40 " pdb=" OG SER N 44 " model vdw 2.230 3.040 ... (remaining 253962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'B' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'C' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'D' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'E' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'F' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'G' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'H' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'I' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'J' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'K' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'L' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'M' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'N' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'O' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'P' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'Q' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) selection = (chain 'R' and (resid 12 through 29 or resid 31 through 175 or resid 177 through \ 228 or resid 230 through 242)) } 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=0.16 max=1.00 mean=0.99 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: 7.020 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 33.010 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.003 0.052 31896 Z= 0.165 Angle : 0.622 11.605 43360 Z= 0.316 Chirality : 0.039 0.393 4842 Planarity : 0.005 0.055 5666 Dihedral : 18.367 133.193 12246 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.54 % Favored : 98.43 % Rotamer: Outliers : 2.76 % Allowed : 30.97 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.13), residues: 4002 helix: 2.37 (0.10), residues: 3046 sheet: None (None), residues: 0 loop : -0.19 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 143 TYR 0.026 0.002 TYR B 145 PHE 0.013 0.001 PHE B 32 TRP 0.014 0.001 TRP L 23 HIS 0.002 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00317 (31896) covalent geometry : angle 0.62196 (43360) hydrogen bonds : bond 0.11322 ( 2182) hydrogen bonds : angle 4.65319 ( 6462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1163 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8551 (m110) cc_final: 0.7782 (t0) REVERT: A 70 LYS cc_start: 0.8532 (mtpm) cc_final: 0.8227 (ttmt) REVERT: A 108 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 112 GLN cc_start: 0.8428 (tp40) cc_final: 0.8093 (tt0) REVERT: A 120 ASN cc_start: 0.8558 (t0) cc_final: 0.8132 (t0) REVERT: A 212 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7222 (mp0) REVERT: B 18 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.8053 (mtp85) REVERT: B 25 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8052 (tppp) REVERT: B 67 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8314 (tp-100) REVERT: B 70 LYS cc_start: 0.8753 (tttm) cc_final: 0.8408 (ttpt) REVERT: B 173 ARG cc_start: 0.8538 (mtt90) cc_final: 0.7929 (ttt180) REVERT: C 21 ASN cc_start: 0.8316 (m110) cc_final: 0.7640 (t0) REVERT: C 26 VAL cc_start: 0.8663 (p) cc_final: 0.8452 (p) REVERT: C 41 SER cc_start: 0.8124 (t) cc_final: 0.7851 (p) REVERT: C 63 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7557 (tp40) REVERT: C 74 ASN cc_start: 0.9021 (m-40) cc_final: 0.8544 (m110) REVERT: C 82 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8355 (ttp80) REVERT: C 159 GLU cc_start: 0.8992 (tt0) cc_final: 0.8677 (tt0) REVERT: C 170 LYS cc_start: 0.8532 (tttm) cc_final: 0.8315 (ttmp) REVERT: C 183 ASN cc_start: 0.8405 (m-40) cc_final: 0.8032 (m-40) REVERT: D 25 LYS cc_start: 0.8127 (mttp) cc_final: 0.7758 (mmmm) REVERT: D 41 SER cc_start: 0.7728 (t) cc_final: 0.7369 (m) REVERT: D 67 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8092 (tp-100) REVERT: D 70 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8046 (ttmt) REVERT: D 119 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8647 (p) REVERT: D 120 ASN cc_start: 0.8436 (t0) cc_final: 0.7983 (t0) REVERT: D 170 LYS cc_start: 0.8100 (tttm) cc_final: 0.7742 (ttmp) REVERT: D 180 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: D 213 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7833 (mt-10) REVERT: E 29 GLU cc_start: 0.8748 (tt0) cc_final: 0.7844 (tp30) REVERT: E 63 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7947 (mp10) REVERT: E 70 LYS cc_start: 0.8535 (tttt) cc_final: 0.8207 (ttmm) REVERT: E 71 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7947 (mm-30) REVERT: E 74 ASN cc_start: 0.9096 (m110) cc_final: 0.8463 (m110) REVERT: E 154 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8779 (mtp85) REVERT: E 183 ASN cc_start: 0.8578 (m-40) cc_final: 0.8290 (m110) REVERT: F 25 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7833 (tppp) REVERT: F 57 ASN cc_start: 0.8184 (m-40) cc_final: 0.7969 (m-40) REVERT: F 79 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6210 (mt-10) REVERT: F 128 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7618 (mm-30) REVERT: F 180 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8370 (mp0) REVERT: F 237 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: G 51 ASP cc_start: 0.7949 (m-30) cc_final: 0.7595 (m-30) REVERT: G 100 ARG cc_start: 0.7053 (mmp80) cc_final: 0.6550 (mmp80) REVERT: G 120 ASN cc_start: 0.8320 (t0) cc_final: 0.7893 (t0) REVERT: G 166 ASP cc_start: 0.8337 (m-30) cc_final: 0.7992 (m-30) REVERT: H 21 ASN cc_start: 0.8142 (m-40) cc_final: 0.7623 (t0) REVERT: H 29 GLU cc_start: 0.8676 (tt0) cc_final: 0.7793 (tp30) REVERT: H 74 ASN cc_start: 0.8891 (m110) cc_final: 0.8466 (m-40) REVERT: H 170 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7947 (ttmm) REVERT: H 195 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8170 (p0) REVERT: I 112 GLN cc_start: 0.8922 (mt0) cc_final: 0.8720 (mp10) REVERT: I 113 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7823 (mt-10) REVERT: I 158 LYS cc_start: 0.9260 (mttp) cc_final: 0.8911 (mmtm) REVERT: I 173 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7662 (ttp-170) REVERT: I 179 GLN cc_start: 0.8219 (mm110) cc_final: 0.7964 (mm-40) REVERT: J 67 GLN cc_start: 0.8369 (tp40) cc_final: 0.8108 (tp-100) REVERT: J 70 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8240 (ttmt) REVERT: J 71 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8148 (mt-10) REVERT: J 120 ASN cc_start: 0.8283 (t0) cc_final: 0.7912 (t0) REVERT: K 29 GLU cc_start: 0.8854 (tt0) cc_final: 0.7849 (tp30) REVERT: K 63 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7963 (mp10) REVERT: K 100 ARG cc_start: 0.6628 (mtp85) cc_final: 0.6256 (mtp85) REVERT: K 108 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8535 (p) REVERT: K 158 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6918 (mttt) REVERT: K 159 GLU cc_start: 0.8975 (tt0) cc_final: 0.8391 (mt-10) REVERT: K 183 ASN cc_start: 0.8523 (m110) cc_final: 0.8232 (m-40) REVERT: L 25 LYS cc_start: 0.8496 (tppp) cc_final: 0.8116 (mmmm) REVERT: L 70 LYS cc_start: 0.8544 (tttm) cc_final: 0.8175 (ttpt) REVERT: L 97 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5265 (ptm-80) REVERT: L 102 SER cc_start: 0.7683 (p) cc_final: 0.7448 (p) REVERT: L 112 GLN cc_start: 0.8724 (mt0) cc_final: 0.8510 (mm-40) REVERT: L 173 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7719 (ttt180) REVERT: M 45 GLU cc_start: 0.5913 (pp20) cc_final: 0.5549 (tt0) REVERT: M 63 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8092 (mp10) REVERT: M 70 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7955 (ttmt) REVERT: M 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.8080 (m-30) REVERT: M 100 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6683 (tpm-80) REVERT: M 108 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7898 (p) REVERT: M 120 ASN cc_start: 0.8373 (t0) cc_final: 0.7926 (t0) REVERT: N 21 ASN cc_start: 0.7961 (t0) cc_final: 0.7755 (t0) REVERT: N 74 ASN cc_start: 0.8911 (m-40) cc_final: 0.8510 (m110) REVERT: N 159 GLU cc_start: 0.8722 (tt0) cc_final: 0.8498 (tt0) REVERT: N 233 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7444 (tm-30) REVERT: O 25 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7675 (tppp) REVERT: O 29 GLU cc_start: 0.8230 (tt0) cc_final: 0.7631 (OUTLIER) REVERT: P 79 GLU cc_start: 0.7697 (tp30) cc_final: 0.7265 (mm-30) REVERT: P 112 GLN cc_start: 0.8462 (mm110) cc_final: 0.7986 (mp-120) REVERT: P 120 ASN cc_start: 0.8109 (t0) cc_final: 0.7809 (t0) REVERT: P 145 TYR cc_start: 0.8515 (t80) cc_final: 0.8189 (t80) REVERT: Q 25 LYS cc_start: 0.7558 (mttp) cc_final: 0.7124 (tttp) REVERT: Q 29 GLU cc_start: 0.8654 (tt0) cc_final: 0.7773 (tp30) REVERT: Q 63 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7308 (tm-30) REVERT: Q 74 ASN cc_start: 0.8862 (m110) cc_final: 0.8418 (m-40) REVERT: Q 100 ARG cc_start: 0.6480 (mmt180) cc_final: 0.6133 (mmm160) REVERT: Q 144 MET cc_start: 0.8299 (ppp) cc_final: 0.8013 (pp-130) REVERT: Q 159 GLU cc_start: 0.8897 (tt0) cc_final: 0.8636 (tt0) REVERT: Q 170 LYS cc_start: 0.8203 (ttpp) cc_final: 0.8000 (ttmm) REVERT: Q 199 LYS cc_start: 0.7561 (tttt) cc_final: 0.7326 (tttt) REVERT: R 25 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7961 (tppp) REVERT: R 29 GLU cc_start: 0.8295 (tt0) cc_final: 0.7694 (tp30) REVERT: R 70 LYS cc_start: 0.8465 (tttm) cc_final: 0.8034 (ttpt) REVERT: R 113 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7880 (pt0) REVERT: R 237 GLN cc_start: 0.8308 (tt0) cc_final: 0.8044 (tm-30) outliers start: 72 outliers final: 37 residues processed: 1199 average time/residue: 0.7832 time to fit residues: 1072.5789 Evaluate side-chains 1145 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1098 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 ARG Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain R residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 237 GLN B 183 ASN B 192 GLN C 179 GLN C 183 ASN E 57 ASN F 67 GLN G 74 ASN G 237 GLN H 219 GLN I 67 GLN J 21 ASN J 237 GLN L 63 GLN L 67 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN M 74 ASN N 67 GLN O 183 ASN P 74 ASN P 237 GLN Q 50 GLN Q 67 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.093656 restraints weight = 211861.299| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 5.73 r_work: 0.2822 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31896 Z= 0.188 Angle : 0.601 9.935 43360 Z= 0.296 Chirality : 0.041 0.282 4842 Planarity : 0.005 0.054 5666 Dihedral : 7.342 117.952 4510 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Rotamer: Outliers : 3.95 % Allowed : 27.88 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.13), residues: 4002 helix: 2.34 (0.09), residues: 3064 sheet: None (None), residues: 0 loop : -0.24 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 100 TYR 0.023 0.002 TYR M 130 PHE 0.016 0.002 PHE L 40 TRP 0.008 0.001 TRP B 23 HIS 0.003 0.001 HIS O 84 Details of bonding type rmsd covalent geometry : bond 0.00461 (31896) covalent geometry : angle 0.60063 (43360) hydrogen bonds : bond 0.03998 ( 2182) hydrogen bonds : angle 3.93291 ( 6462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1128 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8740 (mtpm) cc_final: 0.8501 (ttmt) REVERT: A 108 THR cc_start: 0.8591 (m) cc_final: 0.8168 (p) REVERT: A 112 GLN cc_start: 0.8523 (tp40) cc_final: 0.8243 (tt0) REVERT: A 120 ASN cc_start: 0.8600 (t0) cc_final: 0.8190 (t0) REVERT: A 128 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 143 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7993 (mtm110) REVERT: A 212 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7548 (mp0) REVERT: B 18 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.8094 (mtp85) REVERT: B 25 LYS cc_start: 0.8324 (mmmm) cc_final: 0.8005 (tppp) REVERT: B 67 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8257 (tp-100) REVERT: B 70 LYS cc_start: 0.8673 (tttm) cc_final: 0.8279 (ttpt) REVERT: B 173 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7832 (ttt180) REVERT: B 203 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8059 (mptm) REVERT: C 18 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7593 (mtp180) REVERT: C 21 ASN cc_start: 0.8300 (m110) cc_final: 0.7785 (t0) REVERT: C 25 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7944 (tmtt) REVERT: C 63 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7626 (tp-100) REVERT: C 97 ARG cc_start: 0.5964 (ptm-80) cc_final: 0.5594 (ptt-90) REVERT: C 159 GLU cc_start: 0.9051 (tt0) cc_final: 0.8692 (tt0) REVERT: C 170 LYS cc_start: 0.8638 (tttm) cc_final: 0.8377 (ttmp) REVERT: C 183 ASN cc_start: 0.8557 (m110) cc_final: 0.8095 (m-40) REVERT: D 67 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8292 (tp-100) REVERT: D 70 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8296 (ttmt) REVERT: D 119 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8931 (p) REVERT: D 120 ASN cc_start: 0.8601 (t0) cc_final: 0.8148 (t0) REVERT: D 170 LYS cc_start: 0.8652 (tttm) cc_final: 0.8318 (ttmp) REVERT: D 175 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: D 213 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8275 (mt-10) REVERT: E 20 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7761 (tt) REVERT: E 29 GLU cc_start: 0.8853 (tt0) cc_final: 0.7948 (tp30) REVERT: E 71 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8037 (mt-10) REVERT: E 100 ARG cc_start: 0.6539 (mmt180) cc_final: 0.6045 (mtp85) REVERT: E 112 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: E 118 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.4587 (mpt) REVERT: E 183 ASN cc_start: 0.8709 (m-40) cc_final: 0.8434 (m110) REVERT: F 25 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7895 (tppp) REVERT: F 57 ASN cc_start: 0.8044 (m-40) cc_final: 0.7836 (m-40) REVERT: F 75 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10) REVERT: F 79 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: F 128 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7982 (mm-30) REVERT: F 173 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5552 (ttt180) REVERT: F 180 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8545 (mp0) REVERT: F 237 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: G 51 ASP cc_start: 0.8524 (m-30) cc_final: 0.8241 (m-30) REVERT: G 120 ASN cc_start: 0.8438 (t0) cc_final: 0.7932 (t0) REVERT: G 166 ASP cc_start: 0.8864 (m-30) cc_final: 0.8611 (m-30) REVERT: H 29 GLU cc_start: 0.8803 (tt0) cc_final: 0.7915 (tp30) REVERT: H 41 SER cc_start: 0.8533 (t) cc_final: 0.8257 (p) REVERT: H 45 GLU cc_start: 0.8169 (tt0) cc_final: 0.7759 (tt0) REVERT: H 74 ASN cc_start: 0.9022 (m110) cc_final: 0.8550 (m110) REVERT: H 170 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8214 (ttmm) REVERT: H 195 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8651 (p0) REVERT: I 70 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8300 (ttmt) REVERT: I 112 GLN cc_start: 0.8928 (mt0) cc_final: 0.8703 (mp10) REVERT: I 173 ARG cc_start: 0.8472 (mtt90) cc_final: 0.7697 (ttt180) REVERT: I 179 GLN cc_start: 0.8096 (mm110) cc_final: 0.7894 (mm-40) REVERT: J 71 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8407 (mt-10) REVERT: J 100 ARG cc_start: 0.7120 (mmp80) cc_final: 0.6859 (mmp80) REVERT: J 120 ASN cc_start: 0.8527 (t0) cc_final: 0.8206 (t0) REVERT: J 143 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7869 (mtm110) REVERT: K 29 GLU cc_start: 0.8856 (tt0) cc_final: 0.7862 (tp30) REVERT: K 100 ARG cc_start: 0.6685 (mtp85) cc_final: 0.6355 (mtp85) REVERT: K 108 THR cc_start: 0.8794 (m) cc_final: 0.8441 (p) REVERT: K 159 GLU cc_start: 0.8921 (tt0) cc_final: 0.8399 (mt-10) REVERT: K 183 ASN cc_start: 0.8443 (m110) cc_final: 0.8202 (m-40) REVERT: L 25 LYS cc_start: 0.8446 (tppp) cc_final: 0.8079 (mmmm) REVERT: L 102 SER cc_start: 0.7907 (p) cc_final: 0.7699 (p) REVERT: L 112 GLN cc_start: 0.8711 (mt0) cc_final: 0.8496 (mm-40) REVERT: L 173 ARG cc_start: 0.8459 (mtt90) cc_final: 0.7726 (ttt180) REVERT: L 203 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8200 (mptm) REVERT: M 21 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8245 (m110) REVERT: M 63 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8226 (mp10) REVERT: M 70 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8326 (ttmt) REVERT: M 79 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: M 81 ASP cc_start: 0.8588 (m-30) cc_final: 0.8346 (m-30) REVERT: M 108 THR cc_start: 0.8380 (m) cc_final: 0.7929 (p) REVERT: M 120 ASN cc_start: 0.8504 (t0) cc_final: 0.8042 (t0) REVERT: M 145 TYR cc_start: 0.8679 (t80) cc_final: 0.8283 (t80) REVERT: N 67 GLN cc_start: 0.8503 (tp40) cc_final: 0.8217 (tp40) REVERT: N 70 LYS cc_start: 0.8540 (tttt) cc_final: 0.8303 (ttmm) REVERT: N 74 ASN cc_start: 0.8991 (m-40) cc_final: 0.8588 (m110) REVERT: O 25 LYS cc_start: 0.8173 (mmmm) cc_final: 0.7846 (tppp) REVERT: O 29 GLU cc_start: 0.8588 (tt0) cc_final: 0.7961 (tp30) REVERT: O 199 LYS cc_start: 0.7435 (tptm) cc_final: 0.7075 (tptm) REVERT: O 203 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8045 (mptm) REVERT: P 81 ASP cc_start: 0.8409 (m-30) cc_final: 0.8091 (m-30) REVERT: P 100 ARG cc_start: 0.7056 (mmp80) cc_final: 0.6673 (ttm-80) REVERT: P 112 GLN cc_start: 0.8658 (mm110) cc_final: 0.8154 (mp10) REVERT: P 120 ASN cc_start: 0.8299 (t0) cc_final: 0.7873 (t0) REVERT: P 231 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8496 (tt) REVERT: Q 25 LYS cc_start: 0.7815 (mttp) cc_final: 0.7351 (tttp) REVERT: Q 29 GLU cc_start: 0.8792 (tt0) cc_final: 0.7931 (tp30) REVERT: Q 45 GLU cc_start: 0.8567 (tt0) cc_final: 0.8090 (tt0) REVERT: Q 63 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7605 (tm-30) REVERT: Q 74 ASN cc_start: 0.9050 (m110) cc_final: 0.8546 (m110) REVERT: Q 100 ARG cc_start: 0.6594 (mmt180) cc_final: 0.5695 (mmm160) REVERT: Q 104 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8486 (mp) REVERT: Q 144 MET cc_start: 0.8572 (ppp) cc_final: 0.8154 (pp-130) REVERT: Q 159 GLU cc_start: 0.8922 (tt0) cc_final: 0.8719 (tt0) REVERT: Q 170 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8255 (ttmm) REVERT: Q 199 LYS cc_start: 0.8247 (tttt) cc_final: 0.7967 (tttt) REVERT: R 25 LYS cc_start: 0.8360 (mmmm) cc_final: 0.7992 (tppp) REVERT: R 29 GLU cc_start: 0.8591 (tt0) cc_final: 0.7961 (tp30) REVERT: R 70 LYS cc_start: 0.8676 (tttm) cc_final: 0.8270 (ttpt) REVERT: R 97 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5916 (ptt-90) REVERT: R 113 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7756 (pt0) REVERT: R 237 GLN cc_start: 0.8420 (tt0) cc_final: 0.8151 (tm-30) outliers start: 114 outliers final: 37 residues processed: 1188 average time/residue: 0.8297 time to fit residues: 1125.8290 Evaluate side-chains 1148 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1091 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 149 SER Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 104 ILE Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 97 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 221 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 83 optimal weight: 0.0570 chunk 206 optimal weight: 0.0000 chunk 383 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 351 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 374 optimal weight: 0.1980 chunk 244 optimal weight: 1.9990 overall best weight: 0.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 183 ASN E 57 ASN F 67 GLN G 21 ASN G 74 ASN G 237 GLN I 50 GLN I 63 GLN J 21 ASN J 237 GLN K 74 ASN L 67 GLN L 183 ASN M 67 GLN M 74 ASN N 219 GLN P 74 ASN P 237 GLN Q 67 GLN R 63 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099170 restraints weight = 214728.562| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 5.68 r_work: 0.2905 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 31896 Z= 0.108 Angle : 0.534 10.819 43360 Z= 0.264 Chirality : 0.037 0.239 4842 Planarity : 0.005 0.059 5666 Dihedral : 6.812 116.437 4460 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.30 % Allowed : 28.15 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.13), residues: 4002 helix: 2.49 (0.09), residues: 3064 sheet: None (None), residues: 0 loop : -0.14 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 143 TYR 0.020 0.001 TYR F 145 PHE 0.011 0.001 PHE F 32 TRP 0.016 0.001 TRP M 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00245 (31896) covalent geometry : angle 0.53406 (43360) hydrogen bonds : bond 0.03331 ( 2182) hydrogen bonds : angle 3.70198 ( 6462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1139 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8533 (mmmm) cc_final: 0.7822 (tppp) REVERT: A 70 LYS cc_start: 0.8631 (mtpm) cc_final: 0.8343 (ttmt) REVERT: A 108 THR cc_start: 0.8537 (m) cc_final: 0.8137 (p) REVERT: A 112 GLN cc_start: 0.8472 (tp40) cc_final: 0.8177 (tt0) REVERT: A 120 ASN cc_start: 0.8557 (t0) cc_final: 0.8158 (t0) REVERT: A 128 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 143 ARG cc_start: 0.8263 (ttp80) cc_final: 0.8037 (ttp80) REVERT: A 212 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7418 (mp0) REVERT: B 18 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7989 (mtp85) REVERT: B 25 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7858 (tppp) REVERT: B 29 GLU cc_start: 0.8336 (tt0) cc_final: 0.7894 (tp30) REVERT: B 70 LYS cc_start: 0.8600 (tttm) cc_final: 0.8239 (ttpt) REVERT: B 158 LYS cc_start: 0.9251 (mmtp) cc_final: 0.8987 (mmtp) REVERT: B 173 ARG cc_start: 0.8381 (mtt90) cc_final: 0.7769 (ttt180) REVERT: C 21 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7705 (t0) REVERT: C 26 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8322 (p) REVERT: C 63 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7478 (tp40) REVERT: C 79 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 97 ARG cc_start: 0.6090 (ptm-80) cc_final: 0.5726 (ptt-90) REVERT: C 159 GLU cc_start: 0.8988 (tt0) cc_final: 0.8670 (tt0) REVERT: C 170 LYS cc_start: 0.8498 (tttm) cc_final: 0.8257 (ttmp) REVERT: C 175 GLU cc_start: 0.8198 (tp30) cc_final: 0.7833 (tp30) REVERT: D 25 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8001 (mmmm) REVERT: D 67 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8249 (tp-100) REVERT: D 70 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8176 (ttmt) REVERT: D 119 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8815 (p) REVERT: D 120 ASN cc_start: 0.8532 (t0) cc_final: 0.8091 (t0) REVERT: D 170 LYS cc_start: 0.8489 (tttm) cc_final: 0.8154 (ttmp) REVERT: D 175 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: D 213 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8068 (mt-10) REVERT: E 29 GLU cc_start: 0.8860 (tt0) cc_final: 0.7951 (tp30) REVERT: E 71 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8054 (mm-30) REVERT: E 74 ASN cc_start: 0.9042 (m110) cc_final: 0.8406 (m110) REVERT: E 100 ARG cc_start: 0.6424 (mmt180) cc_final: 0.6039 (mmm160) REVERT: E 166 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: E 183 ASN cc_start: 0.8584 (m-40) cc_final: 0.8317 (m110) REVERT: F 25 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7761 (tppp) REVERT: F 57 ASN cc_start: 0.7996 (m-40) cc_final: 0.7773 (m-40) REVERT: F 63 GLN cc_start: 0.8064 (tp40) cc_final: 0.7696 (mm110) REVERT: F 67 GLN cc_start: 0.8200 (tp40) cc_final: 0.7897 (tp-100) REVERT: F 79 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: F 128 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7852 (mm-30) REVERT: F 180 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8458 (mp0) REVERT: F 237 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: G 21 ASN cc_start: 0.8469 (m-40) cc_final: 0.8238 (m110) REVERT: G 35 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8065 (mt-10) REVERT: G 51 ASP cc_start: 0.8360 (m-30) cc_final: 0.8042 (m-30) REVERT: G 100 ARG cc_start: 0.7213 (mmp80) cc_final: 0.6753 (mmp80) REVERT: G 120 ASN cc_start: 0.8434 (t0) cc_final: 0.7948 (t0) REVERT: G 166 ASP cc_start: 0.8763 (m-30) cc_final: 0.8485 (m-30) REVERT: H 29 GLU cc_start: 0.8748 (tt0) cc_final: 0.7834 (tp30) REVERT: H 41 SER cc_start: 0.8358 (t) cc_final: 0.8083 (p) REVERT: H 74 ASN cc_start: 0.8942 (m110) cc_final: 0.8549 (m-40) REVERT: H 170 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8083 (ttmm) REVERT: H 195 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8506 (p0) REVERT: I 25 LYS cc_start: 0.8249 (tppp) cc_final: 0.7976 (mmmm) REVERT: I 112 GLN cc_start: 0.8862 (mt0) cc_final: 0.8655 (mp10) REVERT: I 158 LYS cc_start: 0.9286 (mttp) cc_final: 0.9067 (mmtm) REVERT: I 173 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7618 (ttp-170) REVERT: J 67 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8032 (tp-100) REVERT: J 70 LYS cc_start: 0.8632 (mtpm) cc_final: 0.8382 (ttmt) REVERT: J 71 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8341 (mt-10) REVERT: J 120 ASN cc_start: 0.8500 (t0) cc_final: 0.8174 (t0) REVERT: J 143 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7806 (mtm110) REVERT: K 29 GLU cc_start: 0.8844 (tt0) cc_final: 0.7834 (tp30) REVERT: K 100 ARG cc_start: 0.6434 (mtp85) cc_final: 0.5994 (mtp85) REVERT: K 108 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8392 (p) REVERT: K 158 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6856 (mttt) REVERT: K 159 GLU cc_start: 0.8829 (tt0) cc_final: 0.8365 (tt0) REVERT: K 183 ASN cc_start: 0.8333 (m110) cc_final: 0.8059 (m-40) REVERT: L 25 LYS cc_start: 0.8356 (tppp) cc_final: 0.7965 (mmmm) REVERT: L 70 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8273 (ttpt) REVERT: L 97 ARG cc_start: 0.5769 (mtm180) cc_final: 0.5451 (ptm-80) REVERT: L 112 GLN cc_start: 0.8627 (mt0) cc_final: 0.8398 (mm-40) REVERT: L 173 ARG cc_start: 0.8376 (mtt90) cc_final: 0.7676 (ttt180) REVERT: M 45 GLU cc_start: 0.6848 (tt0) cc_final: 0.6573 (pt0) REVERT: M 63 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8163 (mp10) REVERT: M 70 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8184 (ttmt) REVERT: M 108 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7920 (p) REVERT: M 120 ASN cc_start: 0.8499 (t0) cc_final: 0.8017 (t0) REVERT: M 145 TYR cc_start: 0.8576 (t80) cc_final: 0.8163 (t80) REVERT: N 44 SER cc_start: 0.8862 (p) cc_final: 0.8656 (p) REVERT: N 74 ASN cc_start: 0.8929 (m-40) cc_final: 0.8509 (m110) REVERT: O 25 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7607 (tppp) REVERT: O 29 GLU cc_start: 0.8526 (tt0) cc_final: 0.7925 (tp30) REVERT: O 104 ILE cc_start: 0.8807 (mt) cc_final: 0.8568 (mp) REVERT: P 112 GLN cc_start: 0.8605 (mm110) cc_final: 0.8110 (mp10) REVERT: P 143 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7967 (mtm110) REVERT: Q 25 LYS cc_start: 0.7726 (mttp) cc_final: 0.7253 (tttm) REVERT: Q 29 GLU cc_start: 0.8757 (tt0) cc_final: 0.7900 (tp30) REVERT: Q 45 GLU cc_start: 0.8438 (tt0) cc_final: 0.7958 (tt0) REVERT: Q 63 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7499 (tm-30) REVERT: Q 74 ASN cc_start: 0.8968 (m110) cc_final: 0.8497 (m-40) REVERT: Q 100 ARG cc_start: 0.6408 (mmt180) cc_final: 0.6074 (mmm160) REVERT: Q 144 MET cc_start: 0.8498 (ppp) cc_final: 0.8121 (pp-130) REVERT: Q 170 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8135 (ttmm) REVERT: Q 199 LYS cc_start: 0.8059 (tttt) cc_final: 0.7783 (tttt) REVERT: R 25 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7828 (tppp) REVERT: R 29 GLU cc_start: 0.8587 (tt0) cc_final: 0.7968 (tp30) REVERT: R 70 LYS cc_start: 0.8564 (tttm) cc_final: 0.8174 (ttpt) REVERT: R 97 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5956 (ptt-90) REVERT: R 104 ILE cc_start: 0.8771 (mt) cc_final: 0.8511 (mp) REVERT: R 113 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7650 (pt0) REVERT: R 155 GLN cc_start: 0.8860 (tt0) cc_final: 0.8522 (tt0) REVERT: R 237 GLN cc_start: 0.8340 (tt0) cc_final: 0.8065 (tm-30) outliers start: 92 outliers final: 33 residues processed: 1193 average time/residue: 0.8176 time to fit residues: 1115.3000 Evaluate side-chains 1122 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1074 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 67 GLN Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 97 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 68 optimal weight: 0.8980 chunk 317 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 128 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 155 GLN D 237 GLN E 57 ASN G 74 ASN J 21 ASN J 155 GLN K 74 ASN L 63 GLN L 67 GLN L 183 ASN M 21 ASN M 67 GLN M 74 ASN N 67 GLN N 179 GLN O 183 ASN P 74 ASN P 237 GLN Q 67 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098155 restraints weight = 218538.224| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 5.78 r_work: 0.2885 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31896 Z= 0.112 Angle : 0.538 10.902 43360 Z= 0.263 Chirality : 0.037 0.252 4842 Planarity : 0.005 0.058 5666 Dihedral : 6.707 114.654 4456 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.53 % Allowed : 28.30 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.13), residues: 4002 helix: 2.54 (0.09), residues: 3064 sheet: None (None), residues: 0 loop : -0.09 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.021 0.002 TYR B 145 PHE 0.011 0.001 PHE D 32 TRP 0.010 0.001 TRP K 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00267 (31896) covalent geometry : angle 0.53773 (43360) hydrogen bonds : bond 0.03308 ( 2182) hydrogen bonds : angle 3.67438 ( 6462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1094 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8532 (mmmm) cc_final: 0.7801 (tppp) REVERT: A 70 LYS cc_start: 0.8634 (mtpm) cc_final: 0.8348 (ttmt) REVERT: A 108 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 112 GLN cc_start: 0.8477 (tp40) cc_final: 0.8185 (tt0) REVERT: A 120 ASN cc_start: 0.8540 (t0) cc_final: 0.8127 (t0) REVERT: A 128 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 18 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7935 (mtp85) REVERT: B 25 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7891 (tppp) REVERT: B 70 LYS cc_start: 0.8571 (tttm) cc_final: 0.8212 (ttpt) REVERT: B 158 LYS cc_start: 0.9234 (mmtp) cc_final: 0.8936 (mmtm) REVERT: B 173 ARG cc_start: 0.8388 (mtt90) cc_final: 0.7742 (ttt180) REVERT: C 21 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7678 (t0) REVERT: C 25 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7661 (tmtt) REVERT: C 63 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7501 (tp40) REVERT: C 79 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: C 159 GLU cc_start: 0.8997 (tt0) cc_final: 0.8675 (tt0) REVERT: C 170 LYS cc_start: 0.8498 (tttm) cc_final: 0.8257 (ttmp) REVERT: C 175 GLU cc_start: 0.8214 (tp30) cc_final: 0.7851 (tp30) REVERT: D 25 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8000 (mmmm) REVERT: D 67 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8319 (tp40) REVERT: D 70 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8193 (ttmt) REVERT: D 119 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8928 (p) REVERT: D 120 ASN cc_start: 0.8513 (t0) cc_final: 0.8070 (t0) REVERT: D 170 LYS cc_start: 0.8508 (tttm) cc_final: 0.8167 (ttmp) REVERT: D 213 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8112 (mt-10) REVERT: E 29 GLU cc_start: 0.8868 (tt0) cc_final: 0.7967 (tp30) REVERT: E 71 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8037 (mt-10) REVERT: E 100 ARG cc_start: 0.6504 (mmt180) cc_final: 0.6093 (mmm160) REVERT: E 166 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: E 175 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: E 183 ASN cc_start: 0.8586 (m-40) cc_final: 0.8314 (m110) REVERT: F 25 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7757 (tppp) REVERT: F 63 GLN cc_start: 0.8171 (tp40) cc_final: 0.7948 (mm-40) REVERT: F 79 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: F 180 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8457 (mp0) REVERT: F 237 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: G 35 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8101 (mt-10) REVERT: G 51 ASP cc_start: 0.8362 (m-30) cc_final: 0.8049 (m-30) REVERT: G 120 ASN cc_start: 0.8427 (t0) cc_final: 0.7919 (t0) REVERT: G 166 ASP cc_start: 0.8772 (m-30) cc_final: 0.8508 (m-30) REVERT: H 29 GLU cc_start: 0.8742 (tt0) cc_final: 0.7823 (tp30) REVERT: H 41 SER cc_start: 0.8363 (t) cc_final: 0.8060 (p) REVERT: H 74 ASN cc_start: 0.8914 (m110) cc_final: 0.8507 (m-40) REVERT: H 170 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8076 (ttmm) REVERT: I 25 LYS cc_start: 0.8251 (tppp) cc_final: 0.7979 (mmmm) REVERT: I 70 LYS cc_start: 0.8662 (mtpm) cc_final: 0.8229 (ttmt) REVERT: I 143 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8089 (mtm110) REVERT: I 173 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7598 (ttt180) REVERT: I 180 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8245 (mp0) REVERT: J 67 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8050 (tp-100) REVERT: J 70 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8383 (ttmt) REVERT: J 71 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8367 (mt-10) REVERT: J 120 ASN cc_start: 0.8525 (t0) cc_final: 0.8161 (t0) REVERT: J 143 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7840 (mtm110) REVERT: K 29 GLU cc_start: 0.8847 (tt0) cc_final: 0.7829 (tp30) REVERT: K 100 ARG cc_start: 0.6448 (mtp85) cc_final: 0.6020 (mtp85) REVERT: K 108 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8407 (p) REVERT: K 158 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6832 (mttt) REVERT: K 159 GLU cc_start: 0.8822 (tt0) cc_final: 0.8348 (tt0) REVERT: K 183 ASN cc_start: 0.8377 (m110) cc_final: 0.8109 (m-40) REVERT: L 25 LYS cc_start: 0.8329 (tppp) cc_final: 0.7945 (mmmm) REVERT: L 97 ARG cc_start: 0.5834 (mtm180) cc_final: 0.5634 (ptm-80) REVERT: L 102 SER cc_start: 0.7771 (p) cc_final: 0.7564 (p) REVERT: L 112 GLN cc_start: 0.8655 (mt0) cc_final: 0.8421 (mm-40) REVERT: L 173 ARG cc_start: 0.8338 (mtt90) cc_final: 0.7625 (ttt180) REVERT: M 21 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7927 (m110) REVERT: M 55 MET cc_start: 0.8978 (mtp) cc_final: 0.8560 (mtp) REVERT: M 63 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8176 (mp10) REVERT: M 70 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8194 (ttmt) REVERT: M 79 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: M 100 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6617 (tpm-80) REVERT: M 108 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7942 (p) REVERT: M 120 ASN cc_start: 0.8506 (t0) cc_final: 0.8030 (t0) REVERT: M 145 TYR cc_start: 0.8595 (t80) cc_final: 0.8197 (t80) REVERT: N 20 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7607 (tt) REVERT: N 44 SER cc_start: 0.8941 (p) cc_final: 0.8734 (p) REVERT: N 67 GLN cc_start: 0.8472 (tp40) cc_final: 0.8179 (tp40) REVERT: N 74 ASN cc_start: 0.8925 (m-40) cc_final: 0.8514 (m110) REVERT: N 128 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7696 (mm-30) REVERT: O 25 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7586 (tppp) REVERT: O 82 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7979 (ttp80) REVERT: O 104 ILE cc_start: 0.8803 (mt) cc_final: 0.8572 (mp) REVERT: P 112 GLN cc_start: 0.8594 (mm110) cc_final: 0.8093 (mp10) REVERT: P 143 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7994 (mtm110) REVERT: Q 25 LYS cc_start: 0.7725 (mttp) cc_final: 0.7224 (tttp) REVERT: Q 29 GLU cc_start: 0.8768 (tt0) cc_final: 0.7915 (OUTLIER) REVERT: Q 45 GLU cc_start: 0.8419 (tt0) cc_final: 0.7890 (tt0) REVERT: Q 63 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7557 (tm-30) REVERT: Q 74 ASN cc_start: 0.8975 (m110) cc_final: 0.8514 (m-40) REVERT: Q 100 ARG cc_start: 0.6430 (mmt180) cc_final: 0.5507 (mmm160) REVERT: Q 104 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8429 (mp) REVERT: Q 144 MET cc_start: 0.8532 (ppp) cc_final: 0.8120 (pp-130) REVERT: Q 170 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8128 (ttmm) REVERT: Q 199 LYS cc_start: 0.8091 (tttt) cc_final: 0.7817 (tttt) REVERT: R 25 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7831 (tppp) REVERT: R 29 GLU cc_start: 0.8578 (tt0) cc_final: 0.7915 (tp30) REVERT: R 70 LYS cc_start: 0.8559 (tttm) cc_final: 0.8177 (ttpt) REVERT: R 104 ILE cc_start: 0.8743 (mt) cc_final: 0.8496 (mp) REVERT: R 113 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7767 (pt0) REVERT: R 237 GLN cc_start: 0.8334 (tt0) cc_final: 0.8060 (tm-30) outliers start: 100 outliers final: 49 residues processed: 1150 average time/residue: 0.8359 time to fit residues: 1097.4771 Evaluate side-chains 1118 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1052 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 104 ILE Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 160 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 150 optimal weight: 0.0370 chunk 22 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 386 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 183 ASN C 74 ASN D 237 GLN E 57 ASN F 67 GLN G 74 ASN G 237 GLN I 63 GLN J 21 ASN K 74 ASN M 67 GLN N 50 GLN P 74 ASN P 120 ASN P 237 GLN R 63 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097708 restraints weight = 219740.500| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 5.76 r_work: 0.2876 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31896 Z= 0.117 Angle : 0.544 11.006 43360 Z= 0.266 Chirality : 0.038 0.274 4842 Planarity : 0.005 0.058 5666 Dihedral : 6.618 111.844 4454 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.36 % Allowed : 28.36 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.13), residues: 4002 helix: 2.55 (0.09), residues: 3064 sheet: None (None), residues: 0 loop : -0.08 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 143 TYR 0.019 0.001 TYR F 145 PHE 0.012 0.001 PHE J 32 TRP 0.010 0.001 TRP M 23 HIS 0.002 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00284 (31896) covalent geometry : angle 0.54410 (43360) hydrogen bonds : bond 0.03308 ( 2182) hydrogen bonds : angle 3.65879 ( 6462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1097 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8507 (mmmm) cc_final: 0.7777 (tppp) REVERT: A 70 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8316 (ttmt) REVERT: A 108 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8118 (p) REVERT: A 112 GLN cc_start: 0.8470 (tp40) cc_final: 0.8171 (tt0) REVERT: A 120 ASN cc_start: 0.8547 (t0) cc_final: 0.8119 (t0) REVERT: A 128 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 144 MET cc_start: 0.8888 (ppp) cc_final: 0.8500 (pp-130) REVERT: A 212 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7473 (mp0) REVERT: B 18 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7977 (mtp85) REVERT: B 25 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7853 (tppp) REVERT: B 29 GLU cc_start: 0.8343 (tt0) cc_final: 0.7888 (tp30) REVERT: B 70 LYS cc_start: 0.8529 (tttm) cc_final: 0.8157 (ttpt) REVERT: B 158 LYS cc_start: 0.9226 (mmtp) cc_final: 0.8864 (mmtm) REVERT: B 173 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7722 (ttt180) REVERT: C 21 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7693 (t0) REVERT: C 25 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7809 (tmtt) REVERT: C 63 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7545 (tp40) REVERT: C 79 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 159 GLU cc_start: 0.8977 (tt0) cc_final: 0.8682 (tt0) REVERT: C 170 LYS cc_start: 0.8477 (tttm) cc_final: 0.8235 (ttmp) REVERT: C 175 GLU cc_start: 0.8188 (tp30) cc_final: 0.7819 (tp30) REVERT: C 235 MET cc_start: 0.8251 (mmm) cc_final: 0.8048 (mmm) REVERT: D 25 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7972 (mmmm) REVERT: D 67 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8190 (tp-100) REVERT: D 70 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8196 (ttmt) REVERT: D 119 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (p) REVERT: D 120 ASN cc_start: 0.8509 (t0) cc_final: 0.8062 (t0) REVERT: D 170 LYS cc_start: 0.8486 (tttm) cc_final: 0.8177 (ttmp) REVERT: D 213 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8076 (mt-10) REVERT: E 29 GLU cc_start: 0.8870 (tt0) cc_final: 0.7925 (tp30) REVERT: E 45 GLU cc_start: 0.8710 (tt0) cc_final: 0.8496 (tt0) REVERT: E 71 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8042 (mt-10) REVERT: E 100 ARG cc_start: 0.6507 (mmt180) cc_final: 0.6104 (mmm160) REVERT: E 166 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: E 175 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: E 183 ASN cc_start: 0.8556 (m-40) cc_final: 0.8294 (m110) REVERT: F 25 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7721 (tppp) REVERT: F 63 GLN cc_start: 0.8189 (tp40) cc_final: 0.7973 (mm-40) REVERT: F 79 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: F 128 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7856 (mm-30) REVERT: F 180 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8445 (mp0) REVERT: F 237 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: G 35 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8084 (mt-10) REVERT: G 51 ASP cc_start: 0.8344 (m-30) cc_final: 0.8029 (m-30) REVERT: G 120 ASN cc_start: 0.8435 (t0) cc_final: 0.7930 (t0) REVERT: G 166 ASP cc_start: 0.8751 (m-30) cc_final: 0.8474 (m-30) REVERT: H 29 GLU cc_start: 0.8709 (tt0) cc_final: 0.7812 (tp30) REVERT: H 41 SER cc_start: 0.8384 (t) cc_final: 0.8049 (p) REVERT: H 74 ASN cc_start: 0.8908 (m110) cc_final: 0.8505 (m-40) REVERT: H 170 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8061 (ttmp) REVERT: I 25 LYS cc_start: 0.8221 (tppp) cc_final: 0.7934 (mmmm) REVERT: I 70 LYS cc_start: 0.8648 (mtpm) cc_final: 0.8210 (ttmt) REVERT: I 143 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8100 (mtm110) REVERT: I 158 LYS cc_start: 0.9309 (mmtp) cc_final: 0.9022 (mmtm) REVERT: I 173 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7578 (ttt180) REVERT: I 180 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8220 (mp0) REVERT: J 67 GLN cc_start: 0.8437 (tp-100) cc_final: 0.7990 (tp-100) REVERT: J 70 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8359 (ttmt) REVERT: J 71 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8330 (mt-10) REVERT: J 120 ASN cc_start: 0.8528 (t0) cc_final: 0.8164 (t0) REVERT: J 143 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7818 (mtm110) REVERT: K 29 GLU cc_start: 0.8841 (tt0) cc_final: 0.7818 (tp30) REVERT: K 100 ARG cc_start: 0.6431 (mtp85) cc_final: 0.6014 (mtp85) REVERT: K 108 THR cc_start: 0.8719 (m) cc_final: 0.8352 (p) REVERT: K 158 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6797 (mttt) REVERT: K 159 GLU cc_start: 0.8797 (tt0) cc_final: 0.8363 (tt0) REVERT: K 183 ASN cc_start: 0.8335 (m110) cc_final: 0.8055 (m-40) REVERT: L 25 LYS cc_start: 0.8287 (tppp) cc_final: 0.7913 (mmmm) REVERT: L 112 GLN cc_start: 0.8689 (mt0) cc_final: 0.8440 (mm-40) REVERT: L 173 ARG cc_start: 0.8320 (mtt90) cc_final: 0.7616 (ttt180) REVERT: M 25 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8294 (tptp) REVERT: M 63 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8159 (mp10) REVERT: M 70 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8179 (ttmt) REVERT: M 79 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: M 100 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6588 (tpm-80) REVERT: M 108 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7910 (p) REVERT: M 120 ASN cc_start: 0.8492 (t0) cc_final: 0.8011 (t0) REVERT: M 145 TYR cc_start: 0.8600 (t80) cc_final: 0.8197 (t80) REVERT: N 44 SER cc_start: 0.8969 (p) cc_final: 0.8749 (p) REVERT: N 67 GLN cc_start: 0.8530 (tp40) cc_final: 0.8278 (tp-100) REVERT: N 71 GLU cc_start: 0.8395 (tp30) cc_final: 0.8136 (mm-30) REVERT: N 74 ASN cc_start: 0.8894 (m-40) cc_final: 0.8514 (m110) REVERT: N 128 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7727 (mm-30) REVERT: O 25 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7609 (tppp) REVERT: O 82 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7965 (ttp80) REVERT: O 104 ILE cc_start: 0.8764 (mt) cc_final: 0.8540 (mp) REVERT: P 112 GLN cc_start: 0.8596 (mm110) cc_final: 0.8270 (tt0) REVERT: P 120 ASN cc_start: 0.8301 (t0) cc_final: 0.7838 (t0) REVERT: P 143 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7996 (mtm110) REVERT: Q 25 LYS cc_start: 0.7687 (mttp) cc_final: 0.7205 (tttp) REVERT: Q 29 GLU cc_start: 0.8764 (tt0) cc_final: 0.7928 (tp30) REVERT: Q 45 GLU cc_start: 0.8458 (tt0) cc_final: 0.7897 (tt0) REVERT: Q 63 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7481 (tm-30) REVERT: Q 74 ASN cc_start: 0.8955 (m110) cc_final: 0.8515 (m-40) REVERT: Q 100 ARG cc_start: 0.6416 (mmt180) cc_final: 0.5496 (mmm160) REVERT: Q 104 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8403 (mp) REVERT: Q 128 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7519 (mm-30) REVERT: Q 144 MET cc_start: 0.8534 (ppp) cc_final: 0.8077 (pp-130) REVERT: Q 170 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8101 (ttmm) REVERT: Q 199 LYS cc_start: 0.8029 (tttt) cc_final: 0.7761 (tttt) REVERT: R 25 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7794 (tppp) REVERT: R 29 GLU cc_start: 0.8586 (tt0) cc_final: 0.7923 (tp30) REVERT: R 70 LYS cc_start: 0.8554 (tttm) cc_final: 0.8160 (ttpt) REVERT: R 97 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.5956 (ptt-90) REVERT: R 104 ILE cc_start: 0.8732 (mt) cc_final: 0.8491 (mp) REVERT: R 113 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7633 (pt0) REVERT: R 237 GLN cc_start: 0.8308 (tt0) cc_final: 0.8045 (tm-30) outliers start: 93 outliers final: 57 residues processed: 1148 average time/residue: 0.8181 time to fit residues: 1071.1607 Evaluate side-chains 1150 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1078 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 237 GLN Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 149 SER Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain P residue 175 GLU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 104 ILE Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 147 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 chunk 391 optimal weight: 8.9990 chunk 366 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 183 ASN C 74 ASN E 57 ASN F 67 GLN G 74 ASN J 21 ASN K 74 ASN L 63 GLN L 67 GLN L 183 ASN M 67 GLN P 74 ASN P 237 GLN Q 67 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094640 restraints weight = 201867.110| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 5.63 r_work: 0.2834 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31896 Z= 0.155 Angle : 0.575 12.239 43360 Z= 0.281 Chirality : 0.039 0.269 4842 Planarity : 0.005 0.057 5666 Dihedral : 6.543 104.886 4454 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.01 % Allowed : 27.58 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.13), residues: 4002 helix: 2.55 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : -0.14 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 143 TYR 0.024 0.002 TYR O 145 PHE 0.013 0.001 PHE J 32 TRP 0.006 0.001 TRP K 23 HIS 0.003 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00384 (31896) covalent geometry : angle 0.57501 (43360) hydrogen bonds : bond 0.03604 ( 2182) hydrogen bonds : angle 3.72607 ( 6462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1091 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8625 (mtpm) cc_final: 0.8351 (ttmt) REVERT: A 108 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 112 GLN cc_start: 0.8501 (tp40) cc_final: 0.8205 (tt0) REVERT: A 120 ASN cc_start: 0.8542 (t0) cc_final: 0.8130 (t0) REVERT: A 128 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 143 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7757 (mtm110) REVERT: B 18 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7962 (mtp85) REVERT: B 25 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7890 (tppp) REVERT: B 29 GLU cc_start: 0.8389 (tt0) cc_final: 0.7910 (tp30) REVERT: B 67 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8170 (tp-100) REVERT: B 70 LYS cc_start: 0.8566 (tttm) cc_final: 0.8209 (ttpt) REVERT: B 158 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8902 (mmtm) REVERT: B 173 ARG cc_start: 0.8393 (mtt90) cc_final: 0.7755 (ttt180) REVERT: C 21 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7669 (t0) REVERT: C 25 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7887 (tmtt) REVERT: C 63 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: C 79 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 159 GLU cc_start: 0.8938 (tt0) cc_final: 0.8567 (tt0) REVERT: C 170 LYS cc_start: 0.8520 (tttm) cc_final: 0.8258 (ttmp) REVERT: C 175 GLU cc_start: 0.8218 (tp30) cc_final: 0.7812 (tp30) REVERT: C 183 ASN cc_start: 0.8416 (m110) cc_final: 0.8004 (m-40) REVERT: D 25 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8007 (mmmm) REVERT: D 67 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8113 (tp-100) REVERT: D 70 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8256 (ttmt) REVERT: D 119 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8945 (p) REVERT: D 120 ASN cc_start: 0.8490 (t0) cc_final: 0.8062 (t0) REVERT: D 170 LYS cc_start: 0.8513 (tttm) cc_final: 0.8202 (ttmp) REVERT: D 175 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: D 213 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8129 (mt-10) REVERT: E 29 GLU cc_start: 0.8885 (tt0) cc_final: 0.7947 (tp30) REVERT: E 71 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8176 (mm-30) REVERT: E 100 ARG cc_start: 0.6602 (mmt180) cc_final: 0.6196 (mmm160) REVERT: E 118 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.4468 (mpt) REVERT: E 166 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: E 175 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: E 183 ASN cc_start: 0.8587 (m-40) cc_final: 0.8317 (m110) REVERT: F 25 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7734 (tppp) REVERT: F 63 GLN cc_start: 0.8256 (tp40) cc_final: 0.8025 (mm-40) REVERT: F 128 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7843 (mm-30) REVERT: F 180 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8478 (mp0) REVERT: G 35 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8028 (mt-10) REVERT: G 51 ASP cc_start: 0.8412 (m-30) cc_final: 0.8148 (m-30) REVERT: G 120 ASN cc_start: 0.8427 (t0) cc_final: 0.7920 (t0) REVERT: G 166 ASP cc_start: 0.8763 (m-30) cc_final: 0.8531 (m-30) REVERT: H 29 GLU cc_start: 0.8731 (tt0) cc_final: 0.7844 (tp30) REVERT: H 74 ASN cc_start: 0.8940 (m110) cc_final: 0.8457 (m110) REVERT: H 128 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 170 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8113 (ttmp) REVERT: I 25 LYS cc_start: 0.8233 (tppp) cc_final: 0.7941 (mmmm) REVERT: I 70 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8345 (tppt) REVERT: I 143 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8154 (mtm110) REVERT: I 173 ARG cc_start: 0.8391 (mtt90) cc_final: 0.7635 (ttt180) REVERT: J 70 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (ttmp) REVERT: J 71 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8422 (mt-10) REVERT: J 120 ASN cc_start: 0.8553 (t0) cc_final: 0.8196 (t0) REVERT: J 143 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7897 (mtm110) REVERT: K 29 GLU cc_start: 0.8844 (tt0) cc_final: 0.7816 (tp30) REVERT: K 100 ARG cc_start: 0.6611 (mtp85) cc_final: 0.6205 (mtp85) REVERT: K 108 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8312 (p) REVERT: K 158 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6819 (mttt) REVERT: K 183 ASN cc_start: 0.8337 (m110) cc_final: 0.8070 (m-40) REVERT: L 25 LYS cc_start: 0.8319 (tppp) cc_final: 0.7957 (mmmm) REVERT: L 97 ARG cc_start: 0.5850 (ptm-80) cc_final: 0.5411 (ptm-80) REVERT: L 112 GLN cc_start: 0.8785 (mt0) cc_final: 0.8530 (mm-40) REVERT: L 173 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7663 (ttt180) REVERT: M 21 ASN cc_start: 0.8437 (m110) cc_final: 0.7997 (m110) REVERT: M 25 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8108 (ttmt) REVERT: M 63 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8216 (mp10) REVERT: M 70 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8211 (ttmt) REVERT: M 79 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: M 100 ARG cc_start: 0.7135 (ttm-80) cc_final: 0.6672 (tpm-80) REVERT: M 108 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7826 (p) REVERT: M 120 ASN cc_start: 0.8478 (t0) cc_final: 0.8016 (t0) REVERT: N 20 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7610 (tt) REVERT: N 44 SER cc_start: 0.9050 (p) cc_final: 0.8823 (p) REVERT: N 74 ASN cc_start: 0.8928 (m-40) cc_final: 0.8525 (m110) REVERT: N 79 GLU cc_start: 0.8668 (tt0) cc_final: 0.8306 (tp30) REVERT: O 25 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7624 (tppp) REVERT: O 104 ILE cc_start: 0.8792 (mt) cc_final: 0.8567 (mp) REVERT: O 173 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.5006 (ttt180) REVERT: P 97 ARG cc_start: 0.6198 (ttp80) cc_final: 0.5859 (ttp80) REVERT: P 100 ARG cc_start: 0.6945 (mmp80) cc_final: 0.6586 (mtp85) REVERT: P 112 GLN cc_start: 0.8619 (mm110) cc_final: 0.8302 (tt0) REVERT: P 120 ASN cc_start: 0.8271 (t0) cc_final: 0.7870 (t0) REVERT: P 143 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7931 (mtm110) REVERT: P 231 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8370 (tt) REVERT: Q 25 LYS cc_start: 0.7737 (mttp) cc_final: 0.7263 (tttp) REVERT: Q 29 GLU cc_start: 0.8768 (tt0) cc_final: 0.7926 (OUTLIER) REVERT: Q 45 GLU cc_start: 0.8635 (tt0) cc_final: 0.8001 (tt0) REVERT: Q 63 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7555 (tm-30) REVERT: Q 74 ASN cc_start: 0.8975 (m110) cc_final: 0.8489 (m110) REVERT: Q 100 ARG cc_start: 0.6499 (mmt180) cc_final: 0.5618 (mmm160) REVERT: Q 104 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8436 (mp) REVERT: Q 144 MET cc_start: 0.8539 (ppp) cc_final: 0.8223 (pp-130) REVERT: Q 170 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8109 (ttmm) REVERT: R 25 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7780 (tppp) REVERT: R 29 GLU cc_start: 0.8586 (tt0) cc_final: 0.7931 (tp30) REVERT: R 70 LYS cc_start: 0.8597 (tttm) cc_final: 0.8196 (ttpt) REVERT: R 97 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5867 (ptt-90) REVERT: R 104 ILE cc_start: 0.8757 (mt) cc_final: 0.8514 (mp) REVERT: R 113 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7731 (pt0) REVERT: R 237 GLN cc_start: 0.8320 (tt0) cc_final: 0.8058 (tm-30) outliers start: 115 outliers final: 64 residues processed: 1149 average time/residue: 0.7847 time to fit residues: 1028.8396 Evaluate side-chains 1144 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1059 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 173 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 149 SER Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 104 ILE Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 97 ARG Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 184 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 134 optimal weight: 0.0020 chunk 160 optimal weight: 0.9980 chunk 335 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 63 GLN B 183 ASN B 192 GLN C 74 ASN F 67 GLN F 219 GLN G 74 ASN H 67 GLN K 219 GLN L 183 ASN M 67 GLN N 67 GLN O 183 ASN P 74 ASN R 63 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097130 restraints weight = 216362.376| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 5.69 r_work: 0.2876 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31896 Z= 0.114 Angle : 0.554 12.067 43360 Z= 0.271 Chirality : 0.038 0.271 4842 Planarity : 0.005 0.058 5666 Dihedral : 6.061 91.498 4448 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.41 % Allowed : 28.15 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.13), residues: 4002 helix: 2.63 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : -0.05 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 97 TYR 0.024 0.001 TYR I 145 PHE 0.013 0.001 PHE J 32 TRP 0.010 0.001 TRP K 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00273 (31896) covalent geometry : angle 0.55358 (43360) hydrogen bonds : bond 0.03314 ( 2182) hydrogen bonds : angle 3.66175 ( 6462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1047 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8639 (mmmm) cc_final: 0.7886 (tppp) REVERT: A 70 LYS cc_start: 0.8697 (mtpm) cc_final: 0.8407 (ttmt) REVERT: A 108 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 112 GLN cc_start: 0.8509 (tp40) cc_final: 0.8227 (tt0) REVERT: A 120 ASN cc_start: 0.8587 (t0) cc_final: 0.8166 (t0) REVERT: B 18 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7976 (mtp85) REVERT: B 25 LYS cc_start: 0.8296 (mmmm) cc_final: 0.7942 (tppp) REVERT: B 29 GLU cc_start: 0.8429 (tt0) cc_final: 0.7940 (tp30) REVERT: B 70 LYS cc_start: 0.8608 (tttm) cc_final: 0.8248 (ttpt) REVERT: B 158 LYS cc_start: 0.9253 (mmtp) cc_final: 0.8906 (mmtm) REVERT: B 173 ARG cc_start: 0.8409 (mtt90) cc_final: 0.7815 (ttt180) REVERT: C 21 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7751 (t0) REVERT: C 63 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7629 (tp40) REVERT: C 79 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 159 GLU cc_start: 0.8971 (tt0) cc_final: 0.8643 (tt0) REVERT: C 170 LYS cc_start: 0.8621 (tttm) cc_final: 0.8376 (ttmp) REVERT: C 175 GLU cc_start: 0.8284 (tp30) cc_final: 0.7950 (tp30) REVERT: D 25 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8083 (mmmm) REVERT: D 67 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8246 (tp-100) REVERT: D 70 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8344 (ttmt) REVERT: D 119 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8937 (p) REVERT: D 120 ASN cc_start: 0.8578 (t0) cc_final: 0.8149 (t0) REVERT: D 170 LYS cc_start: 0.8625 (tttm) cc_final: 0.8321 (ttmp) REVERT: D 175 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: D 213 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8219 (mt-10) REVERT: E 29 GLU cc_start: 0.8921 (tt0) cc_final: 0.7980 (tp30) REVERT: E 45 GLU cc_start: 0.8697 (tt0) cc_final: 0.8377 (tt0) REVERT: E 74 ASN cc_start: 0.9066 (m110) cc_final: 0.8475 (m110) REVERT: E 100 ARG cc_start: 0.6708 (mmt180) cc_final: 0.6280 (mmm160) REVERT: E 118 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.4409 (mpt) REVERT: E 166 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: E 175 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: E 183 ASN cc_start: 0.8689 (m-40) cc_final: 0.8432 (m110) REVERT: F 25 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7789 (tppp) REVERT: F 128 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7901 (mm-30) REVERT: F 180 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8495 (mp0) REVERT: F 237 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8103 (tm-30) REVERT: G 35 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8107 (mt-10) REVERT: G 51 ASP cc_start: 0.8491 (m-30) cc_final: 0.8238 (m-30) REVERT: G 120 ASN cc_start: 0.8509 (t0) cc_final: 0.7996 (t0) REVERT: G 166 ASP cc_start: 0.8820 (m-30) cc_final: 0.8569 (m-30) REVERT: H 29 GLU cc_start: 0.8726 (tt0) cc_final: 0.7867 (tp30) REVERT: H 74 ASN cc_start: 0.8999 (m110) cc_final: 0.8569 (m-40) REVERT: H 128 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7717 (mm-30) REVERT: H 170 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8220 (ttmp) REVERT: I 25 LYS cc_start: 0.8315 (tppp) cc_final: 0.7993 (mmmm) REVERT: I 70 LYS cc_start: 0.8730 (mtpm) cc_final: 0.8323 (ttmt) REVERT: I 158 LYS cc_start: 0.9318 (mmtp) cc_final: 0.9094 (mmtm) REVERT: I 173 ARG cc_start: 0.8414 (mtt90) cc_final: 0.7663 (ttt180) REVERT: I 180 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8264 (mp0) REVERT: J 67 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8097 (tp-100) REVERT: J 70 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8457 (ttmt) REVERT: J 71 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8411 (mt-10) REVERT: J 120 ASN cc_start: 0.8616 (t0) cc_final: 0.8285 (t0) REVERT: J 143 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7981 (mtm110) REVERT: K 29 GLU cc_start: 0.8883 (tt0) cc_final: 0.7839 (tp30) REVERT: K 100 ARG cc_start: 0.6586 (mtp85) cc_final: 0.6176 (mtp85) REVERT: K 108 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8365 (p) REVERT: K 158 LYS cc_start: 0.7242 (mmtt) cc_final: 0.6894 (mttt) REVERT: K 159 GLU cc_start: 0.8867 (tt0) cc_final: 0.8348 (tt0) REVERT: K 183 ASN cc_start: 0.8483 (m110) cc_final: 0.8178 (m-40) REVERT: K 233 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7803 (mt-10) REVERT: L 25 LYS cc_start: 0.8377 (tppp) cc_final: 0.8007 (mmmm) REVERT: L 112 GLN cc_start: 0.8737 (mt0) cc_final: 0.8509 (mm-40) REVERT: L 170 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: L 173 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7719 (ttt180) REVERT: M 21 ASN cc_start: 0.8494 (m110) cc_final: 0.8157 (m110) REVERT: M 25 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8168 (ttmt) REVERT: M 63 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8259 (mp10) REVERT: M 70 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8288 (ttmt) REVERT: M 100 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6754 (tpm-80) REVERT: M 108 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8009 (p) REVERT: M 120 ASN cc_start: 0.8545 (t0) cc_final: 0.8074 (t0) REVERT: N 20 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7718 (tt) REVERT: N 44 SER cc_start: 0.8940 (p) cc_final: 0.8730 (p) REVERT: N 67 GLN cc_start: 0.8542 (tp40) cc_final: 0.8283 (tp40) REVERT: N 74 ASN cc_start: 0.8970 (m-40) cc_final: 0.8569 (m110) REVERT: N 79 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: O 25 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7686 (tppp) REVERT: O 82 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8052 (ttp80) REVERT: O 104 ILE cc_start: 0.8896 (mt) cc_final: 0.8659 (mp) REVERT: O 143 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8434 (ttp80) REVERT: P 112 GLN cc_start: 0.8599 (mm110) cc_final: 0.8302 (tt0) REVERT: P 120 ASN cc_start: 0.8347 (t0) cc_final: 0.7898 (t0) REVERT: P 143 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8181 (mtm110) REVERT: Q 25 LYS cc_start: 0.7814 (mttp) cc_final: 0.7316 (tttp) REVERT: Q 29 GLU cc_start: 0.8775 (tt0) cc_final: 0.7939 (OUTLIER) REVERT: Q 45 GLU cc_start: 0.8546 (tt0) cc_final: 0.7869 (tt0) REVERT: Q 63 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7574 (tm-30) REVERT: Q 74 ASN cc_start: 0.9015 (m110) cc_final: 0.8578 (m-40) REVERT: Q 100 ARG cc_start: 0.6587 (mmt180) cc_final: 0.6233 (mmm160) REVERT: Q 144 MET cc_start: 0.8614 (ppp) cc_final: 0.8155 (pp-130) REVERT: Q 170 LYS cc_start: 0.8493 (ttpp) cc_final: 0.8231 (ttmm) REVERT: Q 199 LYS cc_start: 0.8197 (tttt) cc_final: 0.7923 (tttt) REVERT: R 25 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7851 (tppp) REVERT: R 29 GLU cc_start: 0.8621 (tt0) cc_final: 0.7949 (tp30) REVERT: R 70 LYS cc_start: 0.8667 (tttm) cc_final: 0.8261 (ttpt) REVERT: R 104 ILE cc_start: 0.8837 (mt) cc_final: 0.8600 (mp) REVERT: R 113 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7776 (pt0) REVERT: R 237 GLN cc_start: 0.8356 (tt0) cc_final: 0.8094 (tm-30) outliers start: 95 outliers final: 58 residues processed: 1094 average time/residue: 0.8061 time to fit residues: 1007.8846 Evaluate side-chains 1097 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1023 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 70 LYS Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 195 ASN Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 292 optimal weight: 0.9990 chunk 302 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 183 ASN C 74 ASN E 57 ASN E 219 GLN F 219 GLN G 74 ASN K 74 ASN L 63 GLN L 67 GLN M 67 GLN P 74 ASN Q 67 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098178 restraints weight = 204451.717| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.38 r_work: 0.2887 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31896 Z= 0.115 Angle : 0.576 13.663 43360 Z= 0.278 Chirality : 0.038 0.325 4842 Planarity : 0.005 0.058 5666 Dihedral : 5.764 85.016 4447 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.33 % Allowed : 28.56 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.13), residues: 4002 helix: 2.65 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : -0.01 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 97 TYR 0.025 0.002 TYR O 145 PHE 0.013 0.001 PHE J 32 TRP 0.011 0.001 TRP I 133 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00280 (31896) covalent geometry : angle 0.57560 (43360) hydrogen bonds : bond 0.03290 ( 2182) hydrogen bonds : angle 3.66655 ( 6462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1045 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8520 (mmmm) cc_final: 0.7779 (tppp) REVERT: A 70 LYS cc_start: 0.8620 (mtpm) cc_final: 0.8338 (ttmt) REVERT: A 108 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8279 (p) REVERT: A 112 GLN cc_start: 0.8470 (tp40) cc_final: 0.8192 (tt0) REVERT: A 120 ASN cc_start: 0.8546 (t0) cc_final: 0.8141 (t0) REVERT: B 18 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7910 (mtp85) REVERT: B 25 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7884 (tppp) REVERT: B 29 GLU cc_start: 0.8405 (tt0) cc_final: 0.7896 (tp30) REVERT: B 67 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8162 (tp-100) REVERT: B 70 LYS cc_start: 0.8555 (tttm) cc_final: 0.8183 (ttpt) REVERT: B 158 LYS cc_start: 0.9220 (mmtp) cc_final: 0.8875 (mmtm) REVERT: B 173 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7746 (ttt180) REVERT: C 21 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7649 (t0) REVERT: C 63 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7470 (tp-100) REVERT: C 79 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 159 GLU cc_start: 0.8967 (tt0) cc_final: 0.8584 (tt0) REVERT: C 170 LYS cc_start: 0.8491 (tttm) cc_final: 0.8249 (ttmp) REVERT: C 175 GLU cc_start: 0.8212 (tp30) cc_final: 0.7871 (tp30) REVERT: D 25 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7996 (mmmm) REVERT: D 67 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8204 (tp40) REVERT: D 70 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8263 (ttmt) REVERT: D 119 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8900 (p) REVERT: D 120 ASN cc_start: 0.8538 (t0) cc_final: 0.8089 (t0) REVERT: D 170 LYS cc_start: 0.8519 (tttm) cc_final: 0.8210 (ttmp) REVERT: D 175 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: D 203 LYS cc_start: 0.8652 (mptm) cc_final: 0.8386 (mmtp) REVERT: D 213 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8077 (mt-10) REVERT: E 29 GLU cc_start: 0.8894 (tt0) cc_final: 0.7944 (tp30) REVERT: E 45 GLU cc_start: 0.8680 (tt0) cc_final: 0.8305 (tt0) REVERT: E 71 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8085 (mt-10) REVERT: E 74 ASN cc_start: 0.9035 (m110) cc_final: 0.8446 (m110) REVERT: E 100 ARG cc_start: 0.6557 (mmt180) cc_final: 0.6218 (mmm160) REVERT: E 118 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.4437 (mpt) REVERT: E 128 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7776 (mp0) REVERT: E 166 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: E 175 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: E 183 ASN cc_start: 0.8561 (m-40) cc_final: 0.8290 (m110) REVERT: F 128 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7845 (mm-30) REVERT: F 180 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8436 (mp0) REVERT: F 237 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8009 (tm-30) REVERT: G 21 ASN cc_start: 0.8444 (m-40) cc_final: 0.8187 (m110) REVERT: G 35 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8055 (mt-10) REVERT: G 51 ASP cc_start: 0.8394 (m-30) cc_final: 0.8118 (m-30) REVERT: G 120 ASN cc_start: 0.8451 (t0) cc_final: 0.7957 (t0) REVERT: G 166 ASP cc_start: 0.8736 (m-30) cc_final: 0.8467 (m-30) REVERT: H 29 GLU cc_start: 0.8705 (tt0) cc_final: 0.7826 (tp30) REVERT: H 74 ASN cc_start: 0.8945 (m110) cc_final: 0.8514 (m-40) REVERT: H 159 GLU cc_start: 0.8762 (tt0) cc_final: 0.8471 (tt0) REVERT: H 170 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8117 (ttmp) REVERT: I 25 LYS cc_start: 0.8235 (tppp) cc_final: 0.7942 (mmmm) REVERT: I 70 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8324 (tppt) REVERT: I 158 LYS cc_start: 0.9286 (mmtp) cc_final: 0.9051 (mmtm) REVERT: I 173 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7573 (ttp-170) REVERT: J 70 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8388 (ttmt) REVERT: J 71 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8390 (mt-10) REVERT: J 118 MET cc_start: 0.7513 (mmm) cc_final: 0.7291 (mpt) REVERT: J 120 ASN cc_start: 0.8574 (t0) cc_final: 0.8233 (t0) REVERT: J 143 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7870 (mtm110) REVERT: K 29 GLU cc_start: 0.8840 (tt0) cc_final: 0.7814 (tp30) REVERT: K 100 ARG cc_start: 0.6496 (mtp85) cc_final: 0.6085 (mtp85) REVERT: K 108 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8294 (p) REVERT: K 158 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6807 (mttt) REVERT: K 159 GLU cc_start: 0.8818 (tt0) cc_final: 0.8341 (tt0) REVERT: K 183 ASN cc_start: 0.8381 (m110) cc_final: 0.8066 (m-40) REVERT: K 233 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7756 (mt-10) REVERT: L 25 LYS cc_start: 0.8308 (tppp) cc_final: 0.7935 (mmmm) REVERT: L 112 GLN cc_start: 0.8741 (mt0) cc_final: 0.8497 (mm-40) REVERT: L 170 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7966 (ttpp) REVERT: L 173 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7615 (ttt180) REVERT: M 21 ASN cc_start: 0.8431 (m110) cc_final: 0.7975 (m110) REVERT: M 25 LYS cc_start: 0.8620 (mmmm) cc_final: 0.7901 (ttmt) REVERT: M 63 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8212 (mp10) REVERT: M 70 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8212 (ttmt) REVERT: M 100 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6667 (tpm-80) REVERT: M 108 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.7940 (p) REVERT: M 120 ASN cc_start: 0.8505 (t0) cc_final: 0.8057 (t0) REVERT: M 143 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8161 (ttp80) REVERT: N 20 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7573 (tt) REVERT: N 44 SER cc_start: 0.8917 (p) cc_final: 0.8700 (p) REVERT: N 67 GLN cc_start: 0.8561 (tp40) cc_final: 0.8303 (tp40) REVERT: N 74 ASN cc_start: 0.8918 (m-40) cc_final: 0.8520 (m110) REVERT: N 79 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: O 25 LYS cc_start: 0.8005 (mmmm) cc_final: 0.7647 (tppp) REVERT: O 82 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7978 (ttp80) REVERT: O 104 ILE cc_start: 0.8831 (mt) cc_final: 0.8593 (mp) REVERT: O 143 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8360 (ttp80) REVERT: P 112 GLN cc_start: 0.8597 (mm110) cc_final: 0.8285 (tt0) REVERT: P 120 ASN cc_start: 0.8308 (t0) cc_final: 0.7856 (t0) REVERT: P 143 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8092 (mtm110) REVERT: P 231 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8379 (tt) REVERT: Q 25 LYS cc_start: 0.7720 (mttp) cc_final: 0.7243 (tttp) REVERT: Q 29 GLU cc_start: 0.8755 (tt0) cc_final: 0.7903 (OUTLIER) REVERT: Q 45 GLU cc_start: 0.8591 (tt0) cc_final: 0.7948 (tt0) REVERT: Q 63 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7509 (tm-30) REVERT: Q 74 ASN cc_start: 0.8971 (m110) cc_final: 0.8552 (m-40) REVERT: Q 100 ARG cc_start: 0.6495 (mmt180) cc_final: 0.6172 (mmm160) REVERT: Q 144 MET cc_start: 0.8542 (ppp) cc_final: 0.8079 (pp-130) REVERT: Q 170 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8131 (ttmm) REVERT: Q 199 LYS cc_start: 0.8055 (tttt) cc_final: 0.7777 (tttt) REVERT: R 25 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7743 (tppp) REVERT: R 29 GLU cc_start: 0.8584 (tt0) cc_final: 0.7914 (tp30) REVERT: R 70 LYS cc_start: 0.8579 (tttm) cc_final: 0.8183 (ttpt) REVERT: R 104 ILE cc_start: 0.8769 (mt) cc_final: 0.8541 (mp) REVERT: R 113 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7784 (pt0) REVERT: R 237 GLN cc_start: 0.8315 (tt0) cc_final: 0.8053 (tm-30) outliers start: 92 outliers final: 60 residues processed: 1097 average time/residue: 0.8034 time to fit residues: 1007.4347 Evaluate side-chains 1095 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1017 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 155 GLN Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 67 GLN Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.0270 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 96 optimal weight: 0.0030 chunk 273 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 63 GLN B 183 ASN E 57 ASN F 67 GLN G 74 ASN H 67 GLN H 179 GLN L 67 GLN L 183 ASN M 67 GLN O 183 ASN P 74 ASN Q 67 GLN R 63 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098548 restraints weight = 211674.302| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 5.63 r_work: 0.2896 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31896 Z= 0.112 Angle : 0.576 13.754 43360 Z= 0.279 Chirality : 0.038 0.334 4842 Planarity : 0.005 0.058 5666 Dihedral : 5.614 86.370 4444 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.88 % Allowed : 29.48 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.13), residues: 4002 helix: 2.66 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : 0.04 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 97 TYR 0.024 0.001 TYR O 145 PHE 0.013 0.001 PHE J 32 TRP 0.010 0.001 TRP M 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00265 (31896) covalent geometry : angle 0.57639 (43360) hydrogen bonds : bond 0.03228 ( 2182) hydrogen bonds : angle 3.65969 ( 6462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1044 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8510 (mmmm) cc_final: 0.7767 (tppp) REVERT: A 70 LYS cc_start: 0.8582 (mtpm) cc_final: 0.8307 (ttmt) REVERT: A 108 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 112 GLN cc_start: 0.8429 (tp40) cc_final: 0.8154 (tt0) REVERT: A 120 ASN cc_start: 0.8540 (t0) cc_final: 0.8132 (t0) REVERT: B 18 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7893 (mtp85) REVERT: B 25 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7889 (tppp) REVERT: B 29 GLU cc_start: 0.8404 (tt0) cc_final: 0.7865 (tp30) REVERT: B 67 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8139 (tp-100) REVERT: B 70 LYS cc_start: 0.8589 (tttm) cc_final: 0.8226 (ttpt) REVERT: B 158 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8941 (mmtp) REVERT: B 173 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7725 (ttt180) REVERT: C 21 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7610 (t0) REVERT: C 63 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7462 (tp-100) REVERT: C 79 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 159 GLU cc_start: 0.8962 (tt0) cc_final: 0.8647 (tt0) REVERT: C 170 LYS cc_start: 0.8483 (tttm) cc_final: 0.8231 (ttmp) REVERT: C 175 GLU cc_start: 0.8157 (tp30) cc_final: 0.7814 (tp30) REVERT: C 199 LYS cc_start: 0.8012 (tttt) cc_final: 0.7803 (tttt) REVERT: D 25 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7963 (mmmm) REVERT: D 67 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8208 (tp40) REVERT: D 70 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8207 (ttmp) REVERT: D 119 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8781 (p) REVERT: D 120 ASN cc_start: 0.8525 (t0) cc_final: 0.8069 (t0) REVERT: D 131 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7717 (ttmm) REVERT: D 170 LYS cc_start: 0.8480 (tttm) cc_final: 0.8171 (ttmp) REVERT: D 175 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: D 213 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8040 (mt-10) REVERT: E 29 GLU cc_start: 0.8898 (tt0) cc_final: 0.7943 (tp30) REVERT: E 45 GLU cc_start: 0.8690 (tt0) cc_final: 0.8288 (tt0) REVERT: E 71 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8078 (mt-10) REVERT: E 74 ASN cc_start: 0.9017 (m110) cc_final: 0.8430 (m110) REVERT: E 100 ARG cc_start: 0.6504 (mmt180) cc_final: 0.6099 (mmm160) REVERT: E 118 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.4422 (mpt) REVERT: E 128 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7771 (mp0) REVERT: E 166 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: E 175 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: E 183 ASN cc_start: 0.8526 (m-40) cc_final: 0.8263 (m110) REVERT: F 128 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7827 (mm-30) REVERT: F 180 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8410 (mp0) REVERT: F 237 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7985 (tm-30) REVERT: G 21 ASN cc_start: 0.8425 (m-40) cc_final: 0.8174 (m110) REVERT: G 35 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8075 (mt-10) REVERT: G 51 ASP cc_start: 0.8374 (m-30) cc_final: 0.8097 (m-30) REVERT: G 120 ASN cc_start: 0.8455 (t0) cc_final: 0.7973 (t0) REVERT: G 166 ASP cc_start: 0.8710 (m-30) cc_final: 0.8443 (m-30) REVERT: H 29 GLU cc_start: 0.8698 (tt0) cc_final: 0.7813 (tp30) REVERT: H 74 ASN cc_start: 0.8934 (m110) cc_final: 0.8519 (m-40) REVERT: H 144 MET cc_start: 0.8346 (ppp) cc_final: 0.7902 (pp-130) REVERT: H 170 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8079 (ttmp) REVERT: I 25 LYS cc_start: 0.8189 (tppp) cc_final: 0.7891 (mmmm) REVERT: I 70 LYS cc_start: 0.8629 (mtpm) cc_final: 0.8300 (tppt) REVERT: I 143 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8219 (mtm110) REVERT: I 158 LYS cc_start: 0.9264 (mmtp) cc_final: 0.9035 (mmtm) REVERT: I 173 ARG cc_start: 0.8367 (mtt90) cc_final: 0.7555 (ttp-170) REVERT: I 180 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8226 (mp0) REVERT: J 67 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8060 (tp-100) REVERT: J 70 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: J 71 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8333 (mt-10) REVERT: J 120 ASN cc_start: 0.8566 (t0) cc_final: 0.8238 (t0) REVERT: J 143 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7826 (mtm110) REVERT: K 29 GLU cc_start: 0.8844 (tt0) cc_final: 0.7823 (tp30) REVERT: K 100 ARG cc_start: 0.6410 (mtp85) cc_final: 0.6113 (mtp85) REVERT: K 108 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 158 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6696 (mttt) REVERT: K 159 GLU cc_start: 0.8794 (tt0) cc_final: 0.8263 (tt0) REVERT: K 183 ASN cc_start: 0.8347 (m110) cc_final: 0.8037 (m-40) REVERT: K 233 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7760 (mt-10) REVERT: L 25 LYS cc_start: 0.8287 (tppp) cc_final: 0.7914 (mmmm) REVERT: L 110 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8199 (p) REVERT: L 112 GLN cc_start: 0.8735 (mt0) cc_final: 0.8500 (mm-40) REVERT: L 170 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7971 (ttpp) REVERT: L 173 ARG cc_start: 0.8267 (mtt90) cc_final: 0.7606 (ttt180) REVERT: M 21 ASN cc_start: 0.8402 (m110) cc_final: 0.7934 (m110) REVERT: M 63 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8186 (mp10) REVERT: M 70 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8192 (ttmt) REVERT: M 100 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6583 (tpm-80) REVERT: M 108 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7973 (p) REVERT: M 120 ASN cc_start: 0.8489 (t0) cc_final: 0.8037 (t0) REVERT: M 143 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8142 (ttp80) REVERT: N 20 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (tt) REVERT: N 44 SER cc_start: 0.8879 (p) cc_final: 0.8664 (p) REVERT: N 67 GLN cc_start: 0.8546 (tp40) cc_final: 0.8279 (tp40) REVERT: N 74 ASN cc_start: 0.8899 (m-40) cc_final: 0.8500 (m110) REVERT: N 79 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: N 190 LEU cc_start: 0.9100 (tp) cc_final: 0.8885 (tm) REVERT: O 25 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7613 (tppp) REVERT: O 104 ILE cc_start: 0.8801 (mt) cc_final: 0.8563 (mp) REVERT: O 143 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8365 (ttp80) REVERT: P 112 GLN cc_start: 0.8591 (mm110) cc_final: 0.8279 (tt0) REVERT: P 120 ASN cc_start: 0.8304 (t0) cc_final: 0.7863 (t0) REVERT: P 143 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7943 (mtm110) REVERT: P 231 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8353 (tt) REVERT: Q 25 LYS cc_start: 0.7684 (mttp) cc_final: 0.7204 (tttp) REVERT: Q 29 GLU cc_start: 0.8772 (tt0) cc_final: 0.7931 (tp30) REVERT: Q 45 GLU cc_start: 0.8586 (tt0) cc_final: 0.7938 (tt0) REVERT: Q 63 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7532 (tm-30) REVERT: Q 71 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8217 (mm-30) REVERT: Q 74 ASN cc_start: 0.8940 (m110) cc_final: 0.8459 (m-40) REVERT: Q 100 ARG cc_start: 0.6440 (mmt180) cc_final: 0.6125 (mmm160) REVERT: Q 128 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7447 (mm-30) REVERT: Q 144 MET cc_start: 0.8519 (ppp) cc_final: 0.8080 (pp-130) REVERT: Q 170 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8097 (ttmm) REVERT: Q 199 LYS cc_start: 0.8014 (tttt) cc_final: 0.7766 (tttt) REVERT: R 25 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7738 (tppp) REVERT: R 29 GLU cc_start: 0.8597 (tt0) cc_final: 0.7923 (tp30) REVERT: R 70 LYS cc_start: 0.8559 (tttm) cc_final: 0.8157 (ttpt) REVERT: R 104 ILE cc_start: 0.8714 (mt) cc_final: 0.8481 (mp) REVERT: R 113 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7736 (pt0) REVERT: R 237 GLN cc_start: 0.8326 (tt0) cc_final: 0.8068 (tm-30) outliers start: 77 outliers final: 55 residues processed: 1089 average time/residue: 0.8088 time to fit residues: 1006.1192 Evaluate side-chains 1085 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1011 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 155 GLN Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain R residue 25 LYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 78 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 388 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 208 optimal weight: 0.1980 chunk 153 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 74 ASN E 57 ASN G 74 ASN L 63 GLN L 67 GLN M 67 GLN P 74 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099184 restraints weight = 203244.012| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 5.55 r_work: 0.2905 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31896 Z= 0.112 Angle : 0.587 13.617 43360 Z= 0.282 Chirality : 0.038 0.354 4842 Planarity : 0.005 0.058 5666 Dihedral : 5.531 87.787 4444 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.91 % Allowed : 29.51 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.13), residues: 4002 helix: 2.68 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : 0.07 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 97 TYR 0.024 0.001 TYR O 145 PHE 0.013 0.001 PHE J 32 TRP 0.010 0.001 TRP M 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00268 (31896) covalent geometry : angle 0.58724 (43360) hydrogen bonds : bond 0.03182 ( 2182) hydrogen bonds : angle 3.65336 ( 6462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8004 Ramachandran restraints generated. 4002 Oldfield, 0 Emsley, 4002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1031 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8487 (m110) cc_final: 0.7729 (t0) REVERT: A 25 LYS cc_start: 0.8498 (mmmm) cc_final: 0.7694 (tppp) REVERT: A 70 LYS cc_start: 0.8557 (mtpm) cc_final: 0.8290 (ttmt) REVERT: A 108 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 112 GLN cc_start: 0.8399 (tp40) cc_final: 0.8139 (tt0) REVERT: A 120 ASN cc_start: 0.8537 (t0) cc_final: 0.8127 (t0) REVERT: B 18 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7886 (mtp85) REVERT: B 25 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7879 (tppp) REVERT: B 29 GLU cc_start: 0.8411 (tt0) cc_final: 0.7868 (tp30) REVERT: B 70 LYS cc_start: 0.8519 (tttm) cc_final: 0.8138 (ttpt) REVERT: B 104 ILE cc_start: 0.8793 (mt) cc_final: 0.8509 (mp) REVERT: B 158 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8837 (mmtm) REVERT: B 173 ARG cc_start: 0.8343 (mtt90) cc_final: 0.7726 (ttt180) REVERT: B 199 LYS cc_start: 0.7012 (tptm) cc_final: 0.6710 (tptm) REVERT: C 21 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7486 (t0) REVERT: C 63 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7463 (tp-100) REVERT: C 79 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: C 159 GLU cc_start: 0.8961 (tt0) cc_final: 0.8632 (tt0) REVERT: C 170 LYS cc_start: 0.8461 (tttm) cc_final: 0.8223 (ttmp) REVERT: C 175 GLU cc_start: 0.8126 (tp30) cc_final: 0.7782 (tp30) REVERT: D 25 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7944 (mmmm) REVERT: D 67 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8233 (tp40) REVERT: D 70 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8198 (ttmp) REVERT: D 119 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8771 (p) REVERT: D 120 ASN cc_start: 0.8530 (t0) cc_final: 0.8076 (t0) REVERT: D 131 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7686 (ttmm) REVERT: D 170 LYS cc_start: 0.8451 (tttm) cc_final: 0.8140 (ttmp) REVERT: D 175 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 213 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 29 GLU cc_start: 0.8886 (tt0) cc_final: 0.7924 (tp30) REVERT: E 45 GLU cc_start: 0.8658 (tt0) cc_final: 0.8238 (tt0) REVERT: E 71 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8083 (mt-10) REVERT: E 74 ASN cc_start: 0.9004 (m110) cc_final: 0.8417 (m110) REVERT: E 100 ARG cc_start: 0.6508 (mmt180) cc_final: 0.6099 (mmm160) REVERT: E 118 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.4433 (mpt) REVERT: E 128 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7761 (mp0) REVERT: E 166 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: E 175 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 183 ASN cc_start: 0.8518 (m-40) cc_final: 0.8255 (m110) REVERT: F 128 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7873 (mm-30) REVERT: F 180 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8396 (mp0) REVERT: F 237 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7956 (tm-30) REVERT: G 21 ASN cc_start: 0.8413 (m-40) cc_final: 0.8168 (m110) REVERT: G 35 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8057 (mt-10) REVERT: G 51 ASP cc_start: 0.8354 (m-30) cc_final: 0.8063 (m-30) REVERT: G 120 ASN cc_start: 0.8461 (t0) cc_final: 0.7960 (t0) REVERT: G 166 ASP cc_start: 0.8731 (m-30) cc_final: 0.8462 (m-30) REVERT: H 29 GLU cc_start: 0.8643 (tt0) cc_final: 0.7773 (tp30) REVERT: H 74 ASN cc_start: 0.8922 (m110) cc_final: 0.8501 (m-40) REVERT: H 144 MET cc_start: 0.8414 (ppp) cc_final: 0.7952 (pp-130) REVERT: H 170 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8067 (ttmp) REVERT: I 25 LYS cc_start: 0.8185 (tppp) cc_final: 0.7884 (mmmm) REVERT: I 70 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8286 (tppt) REVERT: I 143 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8240 (mtm110) REVERT: I 158 LYS cc_start: 0.9248 (mmtp) cc_final: 0.9015 (mmtm) REVERT: I 173 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7571 (ttp-170) REVERT: I 180 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8223 (mp0) REVERT: J 67 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8053 (tp-100) REVERT: J 70 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: J 71 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8314 (mt-10) REVERT: J 120 ASN cc_start: 0.8575 (t0) cc_final: 0.8251 (t0) REVERT: J 143 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7818 (mtm110) REVERT: K 29 GLU cc_start: 0.8842 (tt0) cc_final: 0.7829 (tp30) REVERT: K 100 ARG cc_start: 0.6354 (mtp85) cc_final: 0.6049 (mtp85) REVERT: K 108 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8367 (p) REVERT: K 158 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6795 (mttt) REVERT: K 159 GLU cc_start: 0.8789 (tt0) cc_final: 0.8327 (tt0) REVERT: K 183 ASN cc_start: 0.8330 (m110) cc_final: 0.8022 (m-40) REVERT: K 233 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7761 (mt-10) REVERT: L 25 LYS cc_start: 0.8261 (tppp) cc_final: 0.7627 (mmmm) REVERT: L 110 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8189 (p) REVERT: L 112 GLN cc_start: 0.8723 (mt0) cc_final: 0.8484 (mm-40) REVERT: L 170 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7965 (ttpp) REVERT: L 173 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7591 (ttt180) REVERT: M 21 ASN cc_start: 0.8392 (m110) cc_final: 0.7916 (m110) REVERT: M 63 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8176 (mp10) REVERT: M 70 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8186 (ttmt) REVERT: M 100 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6565 (tpm-80) REVERT: M 108 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7994 (p) REVERT: M 120 ASN cc_start: 0.8487 (t0) cc_final: 0.8032 (t0) REVERT: M 143 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8141 (ttp80) REVERT: N 20 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7524 (tt) REVERT: N 67 GLN cc_start: 0.8554 (tp40) cc_final: 0.8277 (tp40) REVERT: N 74 ASN cc_start: 0.8872 (m-40) cc_final: 0.8478 (m110) REVERT: N 79 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: N 190 LEU cc_start: 0.9077 (tp) cc_final: 0.8825 (tm) REVERT: O 25 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7629 (tppp) REVERT: O 82 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7760 (ttp80) REVERT: O 104 ILE cc_start: 0.8789 (mt) cc_final: 0.8555 (mp) REVERT: P 112 GLN cc_start: 0.8581 (mm110) cc_final: 0.8265 (tt0) REVERT: P 120 ASN cc_start: 0.8314 (t0) cc_final: 0.7853 (t0) REVERT: P 143 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7950 (mtm110) REVERT: P 231 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8361 (tt) REVERT: Q 25 LYS cc_start: 0.7665 (mttp) cc_final: 0.7168 (tttp) REVERT: Q 29 GLU cc_start: 0.8757 (tt0) cc_final: 0.7890 (OUTLIER) REVERT: Q 45 GLU cc_start: 0.8573 (tt0) cc_final: 0.7917 (tt0) REVERT: Q 63 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7446 (tm-30) REVERT: Q 74 ASN cc_start: 0.8929 (m110) cc_final: 0.8512 (m-40) REVERT: Q 100 ARG cc_start: 0.6419 (mmt180) cc_final: 0.6106 (mmm160) REVERT: Q 144 MET cc_start: 0.8554 (ppp) cc_final: 0.8108 (pp-130) REVERT: Q 170 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8090 (ttmm) REVERT: Q 199 LYS cc_start: 0.7999 (tttt) cc_final: 0.7743 (tttt) REVERT: R 29 GLU cc_start: 0.8583 (tt0) cc_final: 0.7912 (tp30) REVERT: R 70 LYS cc_start: 0.8560 (tttm) cc_final: 0.8155 (ttpt) REVERT: R 104 ILE cc_start: 0.8677 (mt) cc_final: 0.8448 (mp) REVERT: R 113 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7702 (pt0) REVERT: R 199 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6833 (tptm) REVERT: R 237 GLN cc_start: 0.8314 (tt0) cc_final: 0.8057 (tm-30) outliers start: 78 outliers final: 53 residues processed: 1076 average time/residue: 0.8273 time to fit residues: 1015.3840 Evaluate side-chains 1087 residues out of total 3292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1015 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 195 ASN Chi-restraints excluded: chain I residue 199 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain J residue 155 GLN Chi-restraints excluded: chain J residue 238 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 170 LYS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 100 ARG Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 238 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 141 optimal weight: 0.0670 chunk 103 optimal weight: 0.6980 chunk 359 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 377 optimal weight: 0.1980 chunk 223 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 183 ASN E 57 ASN F 67 GLN G 74 ASN L 67 GLN L 183 ASN M 67 GLN P 74 ASN Q 67 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099288 restraints weight = 218537.427| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 5.60 r_work: 0.2912 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31896 Z= 0.111 Angle : 0.581 13.850 43360 Z= 0.279 Chirality : 0.038 0.359 4842 Planarity : 0.005 0.058 5666 Dihedral : 5.443 89.760 4444 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.94 % Allowed : 29.72 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.13), residues: 4002 helix: 2.70 (0.09), residues: 3046 sheet: None (None), residues: 0 loop : 0.12 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 97 TYR 0.024 0.001 TYR O 145 PHE 0.014 0.001 PHE J 32 TRP 0.010 0.001 TRP M 23 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00268 (31896) covalent geometry : angle 0.58121 (43360) hydrogen bonds : bond 0.03151 ( 2182) hydrogen bonds : angle 3.64760 ( 6462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19462.71 seconds wall clock time: 330 minutes 28.48 seconds (19828.48 seconds total)