Starting phenix.real_space_refine on Mon Feb 19 16:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvt_21925/02_2024/6wvt_21925_updated.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 216 5.16 5 C 15882 2.51 5 N 4296 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 4": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F ASP 286": "OD1" <-> "OD2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H ARG 206": "NH1" <-> "NH2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 256": "NH1" <-> "NH2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "H ASP 286": "OD1" <-> "OD2" Residue "H TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "H GLU 334": "OE1" <-> "OE2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 51": "OD1" <-> "OD2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "I ARG 206": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "I GLU 214": "OE1" <-> "OE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "I PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 256": "NH1" <-> "NH2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "I ASP 286": "OD1" <-> "OD2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 334": "OE1" <-> "OE2" Residue "I GLU 361": "OE1" <-> "OE2" Residue "K ASP 699": "OD1" <-> "OD2" Residue "K GLU 701": "OE1" <-> "OE2" Residue "K GLU 725": "OE1" <-> "OE2" Residue "K ASP 757": "OD1" <-> "OD2" Residue "K ASP 765": "OD1" <-> "OD2" Residue "K ASP 769": "OD1" <-> "OD2" Residue "K GLU 799": "OE1" <-> "OE2" Residue "K ASP 813": "OD1" <-> "OD2" Residue "L ASP 699": "OD1" <-> "OD2" Residue "L GLU 701": "OE1" <-> "OE2" Residue "L GLU 725": "OE1" <-> "OE2" Residue "L ASP 757": "OD1" <-> "OD2" Residue "L ASP 765": "OD1" <-> "OD2" Residue "L ASP 769": "OD1" <-> "OD2" Residue "L GLU 799": "OE1" <-> "OE2" Residue "L ASP 813": "OD1" <-> "OD2" Residue "N ASP 699": "OD1" <-> "OD2" Residue "N GLU 701": "OE1" <-> "OE2" Residue "N GLU 725": "OE1" <-> "OE2" Residue "N ASP 757": "OD1" <-> "OD2" Residue "N ASP 765": "OD1" <-> "OD2" Residue "N ASP 769": "OD1" <-> "OD2" Residue "N GLU 799": "OE1" <-> "OE2" Residue "N ASP 813": "OD1" <-> "OD2" Residue "O ASP 699": "OD1" <-> "OD2" Residue "O GLU 701": "OE1" <-> "OE2" Residue "O GLU 725": "OE1" <-> "OE2" Residue "O ASP 757": "OD1" <-> "OD2" Residue "O ASP 765": "OD1" <-> "OD2" Residue "O ASP 769": "OD1" <-> "OD2" Residue "O GLU 799": "OE1" <-> "OE2" Residue "O ASP 813": "OD1" <-> "OD2" Residue "Q ASP 699": "OD1" <-> "OD2" Residue "Q GLU 701": "OE1" <-> "OE2" Residue "Q GLU 725": "OE1" <-> "OE2" Residue "Q ASP 757": "OD1" <-> "OD2" Residue "Q ASP 765": "OD1" <-> "OD2" Residue "Q ASP 769": "OD1" <-> "OD2" Residue "Q GLU 799": "OE1" <-> "OE2" Residue "Q ASP 813": "OD1" <-> "OD2" Residue "X ASP 699": "OD1" <-> "OD2" Residue "X GLU 701": "OE1" <-> "OE2" Residue "X GLU 725": "OE1" <-> "OE2" Residue "X ASP 757": "OD1" <-> "OD2" Residue "X ASP 765": "OD1" <-> "OD2" Residue "X ASP 769": "OD1" <-> "OD2" Residue "X GLU 799": "OE1" <-> "OE2" Residue "X ASP 813": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "L" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "N" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "O" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "Q" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "X" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1271 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.21, per 1000 atoms: 0.52 Number of scatterers: 25248 At special positions: 0 Unit cell: (122.13, 104.535, 219.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 12 15.00 Mg 6 11.99 O 4836 8.00 N 4296 7.00 C 15882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.24 Conformation dependent library (CDL) restraints added in 4.6 seconds 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 24 sheets defined 47.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.623A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 362 No H-bonds generated for 'chain 'B' and resid 359 through 362' Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 372 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS B 374 " --> pdb=" O HIS B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 374' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 139 through 144 removed outlier: 3.754A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 318 Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 362 No H-bonds generated for 'chain 'D' and resid 359 through 362' Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 372 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS D 374 " --> pdb=" O HIS D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 374' Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.910A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.925A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 276 through 282 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 318 Processing helix chain 'E' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 359 through 362 No H-bonds generated for 'chain 'E' and resid 359 through 362' Processing helix chain 'E' and resid 366 through 374 removed outlier: 3.635A pdb=" N ILE E 369 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 372 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS E 374 " --> pdb=" O HIS E 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 366 through 374' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.825A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA F 231 " --> pdb=" O MET F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 318 Processing helix chain 'F' and resid 335 through 348 removed outlier: 4.892A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU F 346 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 362 No H-bonds generated for 'chain 'F' and resid 359 through 362' Processing helix chain 'F' and resid 366 through 374 removed outlier: 3.636A pdb=" N ILE F 369 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 372 " --> pdb=" O ILE F 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS F 374 " --> pdb=" O HIS F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 366 through 374' Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 90 removed outlier: 3.824A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 139 through 144 removed outlier: 3.754A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.624A pdb=" N ALA H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.924A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 276 through 282 Processing helix chain 'H' and resid 290 through 294 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 318 Processing helix chain 'H' and resid 335 through 348 removed outlier: 4.892A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY H 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU H 346 " --> pdb=" O GLY H 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 359 through 362 No H-bonds generated for 'chain 'H' and resid 359 through 362' Processing helix chain 'H' and resid 366 through 374 removed outlier: 3.635A pdb=" N ILE H 369 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 372 " --> pdb=" O ILE H 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS H 374 " --> pdb=" O HIS H 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 366 through 374' Processing helix chain 'I' and resid 55 through 59 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.824A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.755A pdb=" N TYR I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 194 removed outlier: 3.911A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 216 Processing helix chain 'I' and resid 223 through 231 removed outlier: 3.623A pdb=" N ALA I 231 " --> pdb=" O MET I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 256 removed outlier: 3.923A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 261 Processing helix chain 'I' and resid 276 through 282 Processing helix chain 'I' and resid 290 through 294 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 309 through 318 Processing helix chain 'I' and resid 335 through 348 removed outlier: 4.891A pdb=" N VAL I 339 " --> pdb=" O LYS I 336 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY I 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU I 346 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA I 347 " --> pdb=" O SER I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 359 through 362 No H-bonds generated for 'chain 'I' and resid 359 through 362' Processing helix chain 'I' and resid 366 through 374 removed outlier: 3.634A pdb=" N ILE I 369 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 370 " --> pdb=" O PRO I 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS I 371 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG I 372 " --> pdb=" O ILE I 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS I 374 " --> pdb=" O HIS I 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 366 through 374' Processing helix chain 'K' and resid 713 through 726 Processing helix chain 'K' and resid 728 through 731 No H-bonds generated for 'chain 'K' and resid 728 through 731' Processing helix chain 'K' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP K 765 " --> pdb=" O ARG K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE K 792 " --> pdb=" O HIS K 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 795 " --> pdb=" O ASN K 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL K 796 " --> pdb=" O ILE K 792 " (cutoff:3.500A) Processing helix chain 'K' and resid 813 through 842 removed outlier: 4.097A pdb=" N LEU K 818 " --> pdb=" O SER K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 849 through 852 No H-bonds generated for 'chain 'K' and resid 849 through 852' Processing helix chain 'L' and resid 713 through 726 Processing helix chain 'L' and resid 728 through 731 No H-bonds generated for 'chain 'L' and resid 728 through 731' Processing helix chain 'L' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP L 765 " --> pdb=" O ARG L 761 " (cutoff:3.500A) Processing helix chain 'L' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP L 775 " --> pdb=" O ALA L 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 792 " --> pdb=" O HIS L 788 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS L 795 " --> pdb=" O ASN L 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL L 796 " --> pdb=" O ILE L 792 " (cutoff:3.500A) Processing helix chain 'L' and resid 813 through 842 removed outlier: 4.098A pdb=" N LEU L 818 " --> pdb=" O SER L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 849 through 852 No H-bonds generated for 'chain 'L' and resid 849 through 852' Processing helix chain 'N' and resid 713 through 726 Processing helix chain 'N' and resid 728 through 731 No H-bonds generated for 'chain 'N' and resid 728 through 731' Processing helix chain 'N' and resid 740 through 765 removed outlier: 3.624A pdb=" N ASP N 765 " --> pdb=" O ARG N 761 " (cutoff:3.500A) Processing helix chain 'N' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP N 775 " --> pdb=" O ALA N 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE N 792 " --> pdb=" O HIS N 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS N 795 " --> pdb=" O ASN N 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL N 796 " --> pdb=" O ILE N 792 " (cutoff:3.500A) Processing helix chain 'N' and resid 813 through 842 removed outlier: 4.098A pdb=" N LEU N 818 " --> pdb=" O SER N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 849 through 852 No H-bonds generated for 'chain 'N' and resid 849 through 852' Processing helix chain 'O' and resid 713 through 726 Processing helix chain 'O' and resid 728 through 731 No H-bonds generated for 'chain 'O' and resid 728 through 731' Processing helix chain 'O' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP O 765 " --> pdb=" O ARG O 761 " (cutoff:3.500A) Processing helix chain 'O' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP O 775 " --> pdb=" O ALA O 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE O 792 " --> pdb=" O HIS O 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS O 795 " --> pdb=" O ASN O 791 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL O 796 " --> pdb=" O ILE O 792 " (cutoff:3.500A) Processing helix chain 'O' and resid 813 through 842 removed outlier: 4.099A pdb=" N LEU O 818 " --> pdb=" O SER O 814 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 852 No H-bonds generated for 'chain 'O' and resid 849 through 852' Processing helix chain 'Q' and resid 713 through 726 Processing helix chain 'Q' and resid 728 through 731 No H-bonds generated for 'chain 'Q' and resid 728 through 731' Processing helix chain 'Q' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP Q 765 " --> pdb=" O ARG Q 761 " (cutoff:3.500A) Processing helix chain 'Q' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP Q 775 " --> pdb=" O ALA Q 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE Q 792 " --> pdb=" O HIS Q 788 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS Q 795 " --> pdb=" O ASN Q 791 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL Q 796 " --> pdb=" O ILE Q 792 " (cutoff:3.500A) Processing helix chain 'Q' and resid 813 through 842 removed outlier: 4.098A pdb=" N LEU Q 818 " --> pdb=" O SER Q 814 " (cutoff:3.500A) Processing helix chain 'Q' and resid 849 through 852 No H-bonds generated for 'chain 'Q' and resid 849 through 852' Processing helix chain 'X' and resid 713 through 726 Processing helix chain 'X' and resid 728 through 731 No H-bonds generated for 'chain 'X' and resid 728 through 731' Processing helix chain 'X' and resid 740 through 765 removed outlier: 3.623A pdb=" N ASP X 765 " --> pdb=" O ARG X 761 " (cutoff:3.500A) Processing helix chain 'X' and resid 770 through 803 removed outlier: 5.362A pdb=" N ASP X 775 " --> pdb=" O ALA X 771 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE X 792 " --> pdb=" O HIS X 788 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS X 795 " --> pdb=" O ASN X 791 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL X 796 " --> pdb=" O ILE X 792 " (cutoff:3.500A) Processing helix chain 'X' and resid 813 through 842 removed outlier: 4.099A pdb=" N LEU X 818 " --> pdb=" O SER X 814 " (cutoff:3.500A) Processing helix chain 'X' and resid 849 through 852 No H-bonds generated for 'chain 'X' and resid 849 through 852' Processing sheet with id= A, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'B' and resid 150 through 155 Processing sheet with id= D, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'D' and resid 29 through 31 removed outlier: 7.644A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= G, first strand: chain 'D' and resid 150 through 155 Processing sheet with id= H, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'E' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS E 10 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN E 12 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR E 106 " --> pdb=" O ASN E 12 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'E' and resid 150 through 155 Processing sheet with id= L, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'F' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS F 10 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU F 104 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN F 12 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR F 106 " --> pdb=" O ASN F 12 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= O, first strand: chain 'F' and resid 150 through 155 Processing sheet with id= P, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'H' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS H 10 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU H 104 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN H 12 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR H 106 " --> pdb=" O ASN H 12 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 65 through 69 Processing sheet with id= S, first strand: chain 'H' and resid 150 through 155 Processing sheet with id= T, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'I' and resid 29 through 31 removed outlier: 7.643A pdb=" N CYS I 10 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU I 104 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN I 12 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR I 106 " --> pdb=" O ASN I 12 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 65 through 69 Processing sheet with id= W, first strand: chain 'I' and resid 150 through 155 Processing sheet with id= X, first strand: chain 'I' and resid 238 through 241 1032 hydrogen bonds defined for protein. 2790 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: 8.05 Time building geometry restraints manager: 10.96 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: 8197 1.34 - 1.46: 5023 1.46 - 1.58: 12106 1.58 - 1.70: 18 1.70 - 1.82: 372 Bond restraints: 25716 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC I 73 " pdb=" NE2 HIC I 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.66e+00 ... (remaining 25711 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.38: 633 105.38 - 112.97: 13814 112.97 - 120.56: 11644 120.56 - 128.15: 8504 128.15 - 135.74: 193 Bond angle restraints: 34788 Sorted by residual: angle pdb=" N SER N 770 " pdb=" CA SER N 770 " pdb=" C SER N 770 " ideal model delta sigma weight residual 111.28 116.61 -5.33 1.09e+00 8.42e-01 2.39e+01 angle pdb=" N SER K 770 " pdb=" CA SER K 770 " pdb=" C SER K 770 " ideal model delta sigma weight residual 111.28 116.58 -5.30 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER X 770 " pdb=" CA SER X 770 " pdb=" C SER X 770 " ideal model delta sigma weight residual 111.28 116.57 -5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER O 770 " pdb=" CA SER O 770 " pdb=" C SER O 770 " ideal model delta sigma weight residual 111.28 116.57 -5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N SER L 770 " pdb=" CA SER L 770 " pdb=" C SER L 770 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 34783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 14786 29.80 - 59.61: 809 59.61 - 89.41: 96 89.41 - 119.22: 8 119.22 - 149.02: 3 Dihedral angle restraints: 15702 sinusoidal: 6312 harmonic: 9390 Sorted by residual: dihedral pdb=" O1B ADP I 802 " pdb=" O3A ADP I 802 " pdb=" PB ADP I 802 " pdb=" PA ADP I 802 " ideal model delta sinusoidal sigma weight residual 300.00 150.97 149.02 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 802 " pdb=" O5' ADP H 802 " pdb=" PA ADP H 802 " pdb=" O2A ADP H 802 " ideal model delta sinusoidal sigma weight residual -60.00 85.97 -145.97 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP I 802 " pdb=" O5' ADP I 802 " pdb=" PA ADP I 802 " pdb=" O2A ADP I 802 " ideal model delta sinusoidal sigma weight residual -60.00 85.94 -145.94 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 15699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3073 0.063 - 0.126: 774 0.126 - 0.189: 65 0.189 - 0.252: 6 0.252 - 0.315: 6 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CB ILE F 330 " pdb=" CA ILE F 330 " pdb=" CG1 ILE F 330 " pdb=" CG2 ILE F 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE H 330 " pdb=" CA ILE H 330 " pdb=" CG1 ILE H 330 " pdb=" CG2 ILE H 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE D 330 " pdb=" CA ILE D 330 " pdb=" CG1 ILE D 330 " pdb=" CG2 ILE D 330 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3921 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 66 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C THR D 66 " 0.049 2.00e-02 2.50e+03 pdb=" O THR D 66 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 67 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 66 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR I 66 " -0.049 2.00e-02 2.50e+03 pdb=" O THR I 66 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU I 67 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 66 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C THR E 66 " 0.049 2.00e-02 2.50e+03 pdb=" O THR E 66 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU E 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 464 2.66 - 3.22: 22800 3.22 - 3.78: 39871 3.78 - 4.34: 52987 4.34 - 4.90: 87342 Nonbonded interactions: 203464 Sorted by model distance: nonbonded pdb="MG MG H 801 " pdb=" O1B ADP H 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG F 801 " pdb=" O1B ADP F 802 " model vdw 2.106 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.107 2.170 nonbonded pdb="MG MG E 801 " pdb=" O1B ADP E 802 " model vdw 2.107 2.170 ... (remaining 203459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.310 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: 2.580 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 66.800 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.007 0.056 25716 Z= 0.455 Angle : 0.967 9.326 34788 Z= 0.532 Chirality : 0.054 0.315 3924 Planarity : 0.007 0.062 4422 Dihedral : 17.684 149.025 9654 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.29 % Allowed : 13.44 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.12), residues: 3186 helix: -2.70 (0.09), residues: 1590 sheet: -1.17 (0.25), residues: 378 loop : -1.89 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 356 HIS 0.016 0.002 HIS I 161 PHE 0.015 0.002 PHE E 255 TYR 0.034 0.002 TYR B 166 ARG 0.016 0.001 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 918 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.7978 (t70) cc_final: 0.7752 (t0) REVERT: B 68 LYS cc_start: 0.8451 (mttt) cc_final: 0.8179 (mmtm) REVERT: B 119 MET cc_start: 0.8322 (ttm) cc_final: 0.8075 (ttp) REVERT: B 121 GLN cc_start: 0.8618 (tt0) cc_final: 0.8411 (tt0) REVERT: B 125 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 211 ASP cc_start: 0.8130 (t0) cc_final: 0.7741 (t0) REVERT: B 215 LYS cc_start: 0.8689 (mttm) cc_final: 0.8405 (mmtp) REVERT: B 237 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: B 244 ASP cc_start: 0.9020 (p0) cc_final: 0.8814 (p0) REVERT: B 252 ASN cc_start: 0.8665 (p0) cc_final: 0.8285 (p0) REVERT: B 305 MET cc_start: 0.8502 (mtp) cc_final: 0.8158 (mtp) REVERT: B 336 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8632 (tttt) REVERT: B 338 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (t) REVERT: D 49 GLN cc_start: 0.7877 (mm110) cc_final: 0.7458 (mm-40) REVERT: D 192 ILE cc_start: 0.9433 (tp) cc_final: 0.9218 (tt) REVERT: D 211 ASP cc_start: 0.8196 (t0) cc_final: 0.7893 (t0) REVERT: D 244 ASP cc_start: 0.9049 (p0) cc_final: 0.8686 (p0) REVERT: D 246 GLN cc_start: 0.8328 (mt0) cc_final: 0.8090 (mt0) REVERT: D 326 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (mmtm) REVERT: D 336 LYS cc_start: 0.9198 (ttpt) cc_final: 0.8991 (tttt) REVERT: D 360 GLN cc_start: 0.8877 (pt0) cc_final: 0.8539 (pt0) REVERT: D 361 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8147 (tt0) REVERT: E 51 ASP cc_start: 0.8244 (t70) cc_final: 0.7999 (t0) REVERT: E 101 HIS cc_start: 0.8949 (m-70) cc_final: 0.8670 (m90) REVERT: E 116 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7938 (ttm110) REVERT: E 192 ILE cc_start: 0.9503 (tp) cc_final: 0.9103 (tt) REVERT: E 211 ASP cc_start: 0.8196 (t0) cc_final: 0.7544 (t0) REVERT: E 224 GLU cc_start: 0.7954 (mp0) cc_final: 0.7650 (mp0) REVERT: E 226 GLU cc_start: 0.8535 (tp30) cc_final: 0.8191 (tp30) REVERT: E 252 ASN cc_start: 0.8805 (p0) cc_final: 0.8406 (p0) REVERT: E 271 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8813 (m) REVERT: E 280 ASN cc_start: 0.8930 (t0) cc_final: 0.8571 (t0) REVERT: E 336 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8769 (tttt) REVERT: F 78 ASN cc_start: 0.8538 (t0) cc_final: 0.8080 (t0) REVERT: F 151 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8986 (pt) REVERT: F 190 MET cc_start: 0.6265 (mtp) cc_final: 0.5963 (mtp) REVERT: F 192 ILE cc_start: 0.7643 (tp) cc_final: 0.7341 (tt) REVERT: F 226 GLU cc_start: 0.8194 (tp30) cc_final: 0.7750 (tp30) REVERT: F 271 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8844 (m) REVERT: F 280 ASN cc_start: 0.8825 (t0) cc_final: 0.8440 (t0) REVERT: F 296 ASN cc_start: 0.8790 (m-40) cc_final: 0.8547 (m-40) REVERT: F 336 LYS cc_start: 0.9241 (ttpt) cc_final: 0.8862 (tttt) REVERT: F 338 SER cc_start: 0.9514 (OUTLIER) cc_final: 0.9289 (t) REVERT: F 360 GLN cc_start: 0.8790 (pt0) cc_final: 0.8202 (pt0) REVERT: F 361 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 372 ARG cc_start: 0.8053 (ptt180) cc_final: 0.7851 (ptt-90) REVERT: H 78 ASN cc_start: 0.8469 (t0) cc_final: 0.8210 (t0) REVERT: H 192 ILE cc_start: 0.9482 (tp) cc_final: 0.8821 (tt) REVERT: H 205 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: H 211 ASP cc_start: 0.8356 (t0) cc_final: 0.8104 (t0) REVERT: H 237 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: H 325 MET cc_start: 0.8065 (ppp) cc_final: 0.7288 (ppp) REVERT: H 336 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8682 (tttt) REVERT: I 78 ASN cc_start: 0.8521 (t0) cc_final: 0.8211 (t0) REVERT: I 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.7963 (m-30) REVERT: I 82 MET cc_start: 0.9141 (tpt) cc_final: 0.8557 (tpt) REVERT: I 83 GLU cc_start: 0.7858 (pt0) cc_final: 0.7600 (pt0) REVERT: I 192 ILE cc_start: 0.9485 (tp) cc_final: 0.9057 (tt) REVERT: I 202 THR cc_start: 0.9056 (p) cc_final: 0.8437 (t) REVERT: I 280 ASN cc_start: 0.8644 (t0) cc_final: 0.8143 (t0) REVERT: I 314 GLN cc_start: 0.8717 (tt0) cc_final: 0.8437 (tt0) REVERT: I 325 MET cc_start: 0.7992 (ppp) cc_final: 0.7303 (ppp) REVERT: I 326 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7833 (pttp) REVERT: I 329 ILE cc_start: 0.9603 (mm) cc_final: 0.9395 (mm) REVERT: I 336 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8368 (tttt) REVERT: I 361 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7856 (tt0) REVERT: K 701 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: K 723 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7737 (tmm) REVERT: K 781 GLN cc_start: 0.8276 (mt0) cc_final: 0.7999 (mt0) REVERT: K 791 ASN cc_start: 0.8734 (t0) cc_final: 0.8254 (t0) REVERT: K 801 GLN cc_start: 0.8769 (tp40) cc_final: 0.8505 (tp-100) REVERT: K 827 ASN cc_start: 0.8394 (m-40) cc_final: 0.7894 (t0) REVERT: K 845 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8558 (tptp) REVERT: L 718 GLN cc_start: 0.9266 (mt0) cc_final: 0.9002 (mt0) REVERT: L 723 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6879 (tmm) REVERT: L 751 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7377 (tm-30) REVERT: L 791 ASN cc_start: 0.8740 (t0) cc_final: 0.8393 (m-40) REVERT: N 701 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: N 723 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7166 (tpt) REVERT: N 740 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8132 (p) REVERT: N 791 ASN cc_start: 0.8639 (t0) cc_final: 0.8098 (t0) REVERT: N 845 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8420 (tptp) REVERT: N 853 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8366 (m-40) REVERT: O 701 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: O 740 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8532 (p) REVERT: O 791 ASN cc_start: 0.8834 (t0) cc_final: 0.8262 (t0) REVERT: O 797 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8457 (mmtm) REVERT: O 831 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8501 (mm110) REVERT: O 845 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8384 (tptp) REVERT: Q 701 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: Q 713 ILE cc_start: 0.8960 (mm) cc_final: 0.8751 (mm) REVERT: Q 718 GLN cc_start: 0.8971 (mt0) cc_final: 0.8763 (mt0) REVERT: Q 724 MET cc_start: 0.8389 (tpp) cc_final: 0.7904 (tpt) REVERT: X 701 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: X 718 GLN cc_start: 0.9247 (mt0) cc_final: 0.9033 (mt0) REVERT: X 723 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6591 (tmm) REVERT: X 792 ILE cc_start: 0.9195 (pt) cc_final: 0.8833 (pt) REVERT: X 801 GLN cc_start: 0.8810 (tp40) cc_final: 0.8505 (tp40) REVERT: X 803 LEU cc_start: 0.8956 (tp) cc_final: 0.8662 (tp) REVERT: X 865 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7729 (mm-30) outliers start: 144 outliers final: 47 residues processed: 1010 average time/residue: 0.3554 time to fit residues: 559.2032 Evaluate side-chains 762 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 689 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 316 GLU Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain K residue 701 GLU Chi-restraints excluded: chain K residue 723 MET Chi-restraints excluded: chain K residue 725 GLU Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 800 VAL Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 701 GLU Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain L residue 865 GLU Chi-restraints excluded: chain N residue 701 GLU Chi-restraints excluded: chain N residue 723 MET Chi-restraints excluded: chain N residue 725 GLU Chi-restraints excluded: chain N residue 740 SER Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain N residue 853 ASN Chi-restraints excluded: chain N residue 865 GLU Chi-restraints excluded: chain O residue 701 GLU Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 740 SER Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain O residue 865 GLU Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 725 GLU Chi-restraints excluded: chain Q residue 740 SER Chi-restraints excluded: chain Q residue 796 VAL Chi-restraints excluded: chain Q residue 800 VAL Chi-restraints excluded: chain X residue 701 GLU Chi-restraints excluded: chain X residue 723 MET Chi-restraints excluded: chain X residue 725 GLU Chi-restraints excluded: chain X residue 865 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 263 GLN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN E 41 GLN E 92 ASN H 314 GLN I 41 GLN I 263 GLN K 824 ASN K 844 GLN L 824 ASN N 718 GLN N 824 ASN O 781 GLN O 824 ASN Q 824 ASN X 824 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25716 Z= 0.214 Angle : 0.621 12.606 34788 Z= 0.305 Chirality : 0.042 0.140 3924 Planarity : 0.004 0.037 4422 Dihedral : 11.459 156.810 3717 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 20.19 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3186 helix: -1.29 (0.12), residues: 1602 sheet: -0.73 (0.26), residues: 366 loop : -1.26 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 356 HIS 0.004 0.001 HIS D 161 PHE 0.022 0.001 PHE O 729 TYR 0.016 0.001 TYR B 166 ARG 0.003 0.000 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 725 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8261 (ttm) cc_final: 0.8031 (ttp) REVERT: B 128 ASN cc_start: 0.8722 (m110) cc_final: 0.8451 (m-40) REVERT: B 198 TYR cc_start: 0.9070 (m-80) cc_final: 0.8831 (m-80) REVERT: B 211 ASP cc_start: 0.8152 (t0) cc_final: 0.7762 (t0) REVERT: B 215 LYS cc_start: 0.8648 (mttm) cc_final: 0.8358 (mmtp) REVERT: B 305 MET cc_start: 0.8534 (mtp) cc_final: 0.8334 (mtp) REVERT: B 336 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8769 (tttt) REVERT: D 44 MET cc_start: 0.7820 (mmm) cc_final: 0.7611 (mmm) REVERT: D 83 GLU cc_start: 0.8015 (pt0) cc_final: 0.7725 (pt0) REVERT: D 226 GLU cc_start: 0.8132 (tp30) cc_final: 0.7821 (tp30) REVERT: D 246 GLN cc_start: 0.8294 (mt0) cc_final: 0.8090 (mt0) REVERT: D 263 GLN cc_start: 0.8326 (mt0) cc_final: 0.8106 (mt0) REVERT: D 355 MET cc_start: 0.8102 (ttm) cc_final: 0.7852 (ttm) REVERT: E 51 ASP cc_start: 0.8119 (t70) cc_final: 0.7833 (t0) REVERT: E 78 ASN cc_start: 0.8315 (t0) cc_final: 0.7794 (t0) REVERT: E 192 ILE cc_start: 0.9440 (tp) cc_final: 0.8924 (tt) REVERT: E 211 ASP cc_start: 0.8254 (t0) cc_final: 0.7571 (t0) REVERT: E 280 ASN cc_start: 0.8773 (t0) cc_final: 0.8331 (t0) REVERT: E 325 MET cc_start: 0.8328 (ppp) cc_final: 0.7636 (ppp) REVERT: E 336 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8838 (tttt) REVERT: F 78 ASN cc_start: 0.8352 (t0) cc_final: 0.7895 (t0) REVERT: F 151 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8986 (pt) REVERT: F 190 MET cc_start: 0.6502 (mtp) cc_final: 0.6210 (mtp) REVERT: F 192 ILE cc_start: 0.7675 (tp) cc_final: 0.7380 (tp) REVERT: F 252 ASN cc_start: 0.8637 (p0) cc_final: 0.8038 (p0) REVERT: F 280 ASN cc_start: 0.8755 (t0) cc_final: 0.8320 (t0) REVERT: F 336 LYS cc_start: 0.9298 (ttpt) cc_final: 0.8950 (tttt) REVERT: H 192 ILE cc_start: 0.9295 (tp) cc_final: 0.8959 (tt) REVERT: H 205 GLU cc_start: 0.8072 (mp0) cc_final: 0.7474 (mp0) REVERT: H 246 GLN cc_start: 0.8466 (mt0) cc_final: 0.8220 (mt0) REVERT: H 325 MET cc_start: 0.8170 (ppp) cc_final: 0.7591 (ppp) REVERT: H 336 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8805 (tttt) REVERT: I 81 ASP cc_start: 0.8414 (m-30) cc_final: 0.8003 (m-30) REVERT: I 83 GLU cc_start: 0.7883 (pt0) cc_final: 0.7586 (pt0) REVERT: I 192 ILE cc_start: 0.9408 (tp) cc_final: 0.9004 (tp) REVERT: I 205 GLU cc_start: 0.7848 (mp0) cc_final: 0.7609 (mp0) REVERT: I 269 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7803 (ttt) REVERT: I 280 ASN cc_start: 0.8701 (t0) cc_final: 0.8120 (t0) REVERT: I 314 GLN cc_start: 0.8738 (tt0) cc_final: 0.8432 (tt0) REVERT: I 325 MET cc_start: 0.7988 (ppp) cc_final: 0.7588 (ppp) REVERT: I 336 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8608 (tttt) REVERT: K 758 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8347 (mmtm) REVERT: K 791 ASN cc_start: 0.8691 (t0) cc_final: 0.8276 (t0) REVERT: K 827 ASN cc_start: 0.8260 (m-40) cc_final: 0.7902 (t0) REVERT: K 837 TYR cc_start: 0.8664 (t80) cc_final: 0.8382 (t80) REVERT: K 845 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8562 (tptp) REVERT: L 718 GLN cc_start: 0.9289 (mt0) cc_final: 0.9024 (mt0) REVERT: L 791 ASN cc_start: 0.8726 (t0) cc_final: 0.8224 (t0) REVERT: L 797 LYS cc_start: 0.9223 (tppt) cc_final: 0.9011 (tppt) REVERT: N 837 TYR cc_start: 0.8692 (t80) cc_final: 0.8401 (t80) REVERT: N 845 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8478 (tptp) REVERT: O 740 SER cc_start: 0.8821 (m) cc_final: 0.8491 (t) REVERT: O 791 ASN cc_start: 0.8784 (t0) cc_final: 0.8433 (m-40) REVERT: O 797 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8556 (mmtm) REVERT: O 826 MET cc_start: 0.7186 (ttp) cc_final: 0.6966 (ttp) REVERT: O 845 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8459 (tptp) REVERT: Q 718 GLN cc_start: 0.9002 (mt0) cc_final: 0.8709 (mt0) REVERT: Q 724 MET cc_start: 0.8515 (tpp) cc_final: 0.7991 (tpt) REVERT: X 801 GLN cc_start: 0.8773 (tp40) cc_final: 0.8438 (tp40) REVERT: X 803 LEU cc_start: 0.8736 (tp) cc_final: 0.8393 (tp) outliers start: 82 outliers final: 47 residues processed: 759 average time/residue: 0.3244 time to fit residues: 398.3098 Evaluate side-chains 697 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 645 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain K residue 845 LYS Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 794 SER Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 826 MET Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 0.0670 chunk 286 optimal weight: 40.0000 chunk 98 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 162 ASN B 275 HIS D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 101 HIS E 128 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN K 844 GLN N 789 GLN O 844 GLN Q 788 HIS X 718 GLN X 844 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25716 Z= 0.286 Angle : 0.622 9.911 34788 Z= 0.307 Chirality : 0.044 0.142 3924 Planarity : 0.003 0.030 4422 Dihedral : 9.294 169.361 3575 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.96 % Allowed : 21.48 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3186 helix: -0.59 (0.13), residues: 1548 sheet: -1.03 (0.26), residues: 396 loop : -0.85 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 356 HIS 0.007 0.001 HIS Q 788 PHE 0.027 0.001 PHE K 729 TYR 0.016 0.001 TYR K 779 ARG 0.003 0.000 ARG I 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 688 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8691 (tt0) cc_final: 0.8470 (tt0) REVERT: B 132 MET cc_start: 0.5081 (ppp) cc_final: 0.4191 (ppp) REVERT: B 202 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8897 (t) REVERT: B 269 MET cc_start: 0.8448 (ttp) cc_final: 0.8226 (ttt) REVERT: B 303 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9019 (p) REVERT: B 305 MET cc_start: 0.8644 (mtp) cc_final: 0.8428 (mtp) REVERT: B 336 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8840 (tttt) REVERT: D 44 MET cc_start: 0.7914 (mmm) cc_final: 0.7554 (mmm) REVERT: D 226 GLU cc_start: 0.8300 (tp30) cc_final: 0.8074 (tp30) REVERT: D 246 GLN cc_start: 0.8453 (mt0) cc_final: 0.8176 (mt0) REVERT: D 263 GLN cc_start: 0.8415 (mt0) cc_final: 0.8193 (mt0) REVERT: E 51 ASP cc_start: 0.8112 (t70) cc_final: 0.7809 (t0) REVERT: E 72 GLU cc_start: 0.7108 (pp20) cc_final: 0.6751 (pp20) REVERT: E 157 ASP cc_start: 0.8623 (t70) cc_final: 0.8324 (t0) REVERT: E 192 ILE cc_start: 0.9412 (tp) cc_final: 0.9138 (tp) REVERT: E 280 ASN cc_start: 0.8797 (t0) cc_final: 0.8390 (t0) REVERT: E 296 ASN cc_start: 0.8816 (m-40) cc_final: 0.8561 (m-40) REVERT: E 325 MET cc_start: 0.8575 (ppp) cc_final: 0.7084 (ppp) REVERT: E 336 LYS cc_start: 0.9125 (ttpt) cc_final: 0.8848 (tttt) REVERT: F 78 ASN cc_start: 0.8333 (t0) cc_final: 0.8051 (t0) REVERT: F 151 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9123 (pt) REVERT: F 190 MET cc_start: 0.6657 (mtp) cc_final: 0.6432 (mtp) REVERT: F 192 ILE cc_start: 0.7840 (tp) cc_final: 0.7551 (tp) REVERT: F 325 MET cc_start: 0.8384 (ppp) cc_final: 0.8175 (ppp) REVERT: F 336 LYS cc_start: 0.9335 (ttpt) cc_final: 0.9065 (tttt) REVERT: H 83 GLU cc_start: 0.7950 (pt0) cc_final: 0.7650 (pt0) REVERT: H 192 ILE cc_start: 0.9293 (tp) cc_final: 0.9034 (tp) REVERT: H 205 GLU cc_start: 0.8069 (mp0) cc_final: 0.7603 (mp0) REVERT: H 246 GLN cc_start: 0.8434 (mt0) cc_final: 0.8085 (mt0) REVERT: H 325 MET cc_start: 0.8338 (ppp) cc_final: 0.7786 (ppp) REVERT: H 336 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8897 (tttt) REVERT: H 372 ARG cc_start: 0.8153 (ptt-90) cc_final: 0.7823 (mtm110) REVERT: I 25 ASP cc_start: 0.8309 (p0) cc_final: 0.8059 (p0) REVERT: I 81 ASP cc_start: 0.8373 (m-30) cc_final: 0.8138 (m-30) REVERT: I 83 GLU cc_start: 0.7864 (pt0) cc_final: 0.7602 (pt0) REVERT: I 192 ILE cc_start: 0.9405 (tp) cc_final: 0.8843 (tp) REVERT: I 205 GLU cc_start: 0.7993 (mp0) cc_final: 0.7625 (mp0) REVERT: I 269 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7784 (ttt) REVERT: I 280 ASN cc_start: 0.8789 (t0) cc_final: 0.8276 (t0) REVERT: I 314 GLN cc_start: 0.8758 (tt0) cc_final: 0.8459 (tt0) REVERT: I 325 MET cc_start: 0.8196 (ppp) cc_final: 0.7928 (ppp) REVERT: I 336 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8748 (tttt) REVERT: I 372 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7862 (mtm110) REVERT: K 758 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8311 (mmtm) REVERT: K 791 ASN cc_start: 0.8687 (t0) cc_final: 0.8237 (t0) REVERT: K 845 LYS cc_start: 0.8986 (tttp) cc_final: 0.8516 (tptp) REVERT: L 718 GLN cc_start: 0.9205 (mt0) cc_final: 0.8961 (mt0) REVERT: L 791 ASN cc_start: 0.8760 (t0) cc_final: 0.8234 (t0) REVERT: N 837 TYR cc_start: 0.8669 (t80) cc_final: 0.8344 (t80) REVERT: N 845 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8524 (tptp) REVERT: O 723 MET cc_start: 0.8152 (tmm) cc_final: 0.7402 (tmm) REVERT: O 724 MET cc_start: 0.8610 (tpp) cc_final: 0.8193 (tpt) REVERT: O 740 SER cc_start: 0.8804 (m) cc_final: 0.8524 (t) REVERT: O 791 ASN cc_start: 0.8759 (t0) cc_final: 0.8164 (t0) REVERT: O 845 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8540 (tptp) REVERT: Q 718 GLN cc_start: 0.9022 (mt0) cc_final: 0.8707 (mt0) REVERT: Q 724 MET cc_start: 0.8591 (tpp) cc_final: 0.8104 (tpt) REVERT: Q 779 TYR cc_start: 0.9001 (m-80) cc_final: 0.8748 (m-80) REVERT: X 803 LEU cc_start: 0.8749 (tp) cc_final: 0.8500 (tp) REVERT: X 826 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7221 (ptt) outliers start: 108 outliers final: 68 residues processed: 738 average time/residue: 0.3268 time to fit residues: 391.6544 Evaluate side-chains 733 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 658 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain L residue 845 LYS Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 845 LYS Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 845 LYS Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 789 GLN Chi-restraints excluded: chain X residue 796 VAL Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 290 optimal weight: 20.0000 chunk 307 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 275 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 128 ASN H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25716 Z= 0.306 Angle : 0.619 7.799 34788 Z= 0.305 Chirality : 0.044 0.144 3924 Planarity : 0.003 0.030 4422 Dihedral : 9.045 178.595 3571 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.33 % Allowed : 24.01 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3186 helix: -0.28 (0.13), residues: 1542 sheet: -0.95 (0.27), residues: 396 loop : -0.76 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 356 HIS 0.004 0.001 HIS I 371 PHE 0.019 0.001 PHE L 729 TYR 0.026 0.001 TYR F 166 ARG 0.003 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 684 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.5203 (ppp) cc_final: 0.4660 (ppp) REVERT: B 269 MET cc_start: 0.8464 (ttp) cc_final: 0.8160 (ttt) REVERT: B 299 MET cc_start: 0.3609 (mtm) cc_final: 0.2718 (mtm) REVERT: B 303 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9066 (p) REVERT: B 305 MET cc_start: 0.8688 (mtp) cc_final: 0.8469 (mtp) REVERT: B 336 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8923 (tttt) REVERT: D 44 MET cc_start: 0.7944 (mmm) cc_final: 0.7485 (mmm) REVERT: D 205 GLU cc_start: 0.7977 (mp0) cc_final: 0.7733 (mp0) REVERT: D 246 GLN cc_start: 0.8506 (mt0) cc_final: 0.8235 (mt0) REVERT: D 263 GLN cc_start: 0.8461 (mt0) cc_final: 0.8236 (mt0) REVERT: E 51 ASP cc_start: 0.8145 (t70) cc_final: 0.7854 (t0) REVERT: E 72 GLU cc_start: 0.7091 (pp20) cc_final: 0.6724 (pp20) REVERT: E 157 ASP cc_start: 0.8616 (t70) cc_final: 0.8356 (t0) REVERT: E 192 ILE cc_start: 0.9366 (tp) cc_final: 0.9043 (tp) REVERT: E 280 ASN cc_start: 0.8794 (t0) cc_final: 0.8401 (t0) REVERT: E 296 ASN cc_start: 0.8854 (m-40) cc_final: 0.8559 (m-40) REVERT: E 325 MET cc_start: 0.8704 (ppp) cc_final: 0.7521 (ppp) REVERT: E 336 LYS cc_start: 0.9120 (ttpt) cc_final: 0.8843 (tttt) REVERT: F 78 ASN cc_start: 0.8359 (t0) cc_final: 0.8100 (t0) REVERT: F 192 ILE cc_start: 0.7810 (tp) cc_final: 0.7549 (tp) REVERT: F 325 MET cc_start: 0.8578 (ppp) cc_final: 0.8085 (ppp) REVERT: F 336 LYS cc_start: 0.9323 (ttpt) cc_final: 0.9056 (tttt) REVERT: H 72 GLU cc_start: 0.7516 (pp20) cc_final: 0.7217 (pp20) REVERT: H 83 GLU cc_start: 0.7900 (pt0) cc_final: 0.7613 (pt0) REVERT: H 192 ILE cc_start: 0.9269 (tp) cc_final: 0.9008 (tp) REVERT: H 205 GLU cc_start: 0.8041 (mp0) cc_final: 0.7577 (mp0) REVERT: H 325 MET cc_start: 0.8425 (ppp) cc_final: 0.7853 (ppp) REVERT: H 336 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8952 (tttt) REVERT: I 25 ASP cc_start: 0.8244 (p0) cc_final: 0.7945 (p0) REVERT: I 83 GLU cc_start: 0.7849 (pt0) cc_final: 0.7583 (pt0) REVERT: I 192 ILE cc_start: 0.9280 (tp) cc_final: 0.8944 (tp) REVERT: I 269 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7780 (ttt) REVERT: I 280 ASN cc_start: 0.8809 (t0) cc_final: 0.8332 (t0) REVERT: I 314 GLN cc_start: 0.8763 (tt0) cc_final: 0.8491 (tt0) REVERT: I 325 MET cc_start: 0.8281 (ppp) cc_final: 0.8009 (ppp) REVERT: I 336 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8809 (tttt) REVERT: I 372 ARG cc_start: 0.8199 (ptt-90) cc_final: 0.7990 (mtm110) REVERT: K 758 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8293 (mmtm) REVERT: K 791 ASN cc_start: 0.8731 (t0) cc_final: 0.8329 (t0) REVERT: K 837 TYR cc_start: 0.8585 (t80) cc_final: 0.7917 (t80) REVERT: K 845 LYS cc_start: 0.8979 (tttp) cc_final: 0.8511 (tptp) REVERT: L 718 GLN cc_start: 0.9236 (mt0) cc_final: 0.9012 (mt0) REVERT: L 791 ASN cc_start: 0.8785 (t0) cc_final: 0.8255 (t0) REVERT: N 845 LYS cc_start: 0.8976 (tttp) cc_final: 0.8551 (tptp) REVERT: O 723 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7430 (tmm) REVERT: O 740 SER cc_start: 0.8831 (m) cc_final: 0.8565 (t) REVERT: O 791 ASN cc_start: 0.8707 (t0) cc_final: 0.8200 (t0) REVERT: O 797 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8512 (mmtm) REVERT: O 845 LYS cc_start: 0.9063 (tttp) cc_final: 0.8567 (tptp) REVERT: Q 718 GLN cc_start: 0.9053 (mt0) cc_final: 0.8700 (mt0) REVERT: Q 724 MET cc_start: 0.8671 (tpp) cc_final: 0.8119 (tpt) REVERT: Q 779 TYR cc_start: 0.8945 (m-80) cc_final: 0.8690 (m-80) REVERT: X 756 MET cc_start: 0.8821 (tpp) cc_final: 0.8610 (tpp) REVERT: X 801 GLN cc_start: 0.8952 (tp40) cc_final: 0.8613 (tm-30) REVERT: X 826 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7166 (ptt) outliers start: 118 outliers final: 85 residues processed: 733 average time/residue: 0.3240 time to fit residues: 386.8268 Evaluate side-chains 742 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 653 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 829 VAL Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 819 ILE Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 796 VAL Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Chi-restraints excluded: chain X residue 849 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 111 ASN B 246 GLN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 92 ASN E 128 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN N 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 789 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 25716 Z= 0.469 Angle : 0.697 8.549 34788 Z= 0.343 Chirality : 0.046 0.157 3924 Planarity : 0.004 0.030 4422 Dihedral : 8.856 171.087 3556 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.40 % Allowed : 24.74 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3186 helix: -0.20 (0.13), residues: 1548 sheet: -0.30 (0.29), residues: 330 loop : -0.83 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 79 HIS 0.006 0.001 HIS H 371 PHE 0.021 0.001 PHE O 729 TYR 0.023 0.002 TYR E 166 ARG 0.004 0.000 ARG H 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 673 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9467 (tt) cc_final: 0.9252 (tt) REVERT: B 269 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: B 303 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9069 (p) REVERT: B 305 MET cc_start: 0.8698 (mtp) cc_final: 0.8465 (mtp) REVERT: B 336 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8902 (tttt) REVERT: D 92 ASN cc_start: 0.9050 (m-40) cc_final: 0.8837 (m110) REVERT: D 246 GLN cc_start: 0.8580 (mt0) cc_final: 0.8183 (mt0) REVERT: D 263 GLN cc_start: 0.8546 (mt0) cc_final: 0.8339 (mt0) REVERT: E 51 ASP cc_start: 0.8207 (t70) cc_final: 0.7953 (t0) REVERT: E 72 GLU cc_start: 0.7217 (pp20) cc_final: 0.6892 (pp20) REVERT: E 192 ILE cc_start: 0.9344 (tp) cc_final: 0.9016 (tp) REVERT: E 269 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8040 (ttt) REVERT: E 325 MET cc_start: 0.8813 (ppp) cc_final: 0.7862 (ppp) REVERT: E 336 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8914 (tttt) REVERT: F 72 GLU cc_start: 0.7411 (pp20) cc_final: 0.7197 (pp20) REVERT: F 78 ASN cc_start: 0.8382 (t0) cc_final: 0.8039 (t0) REVERT: F 192 ILE cc_start: 0.8067 (tp) cc_final: 0.7840 (tp) REVERT: F 253 GLU cc_start: 0.8433 (mp0) cc_final: 0.8222 (mp0) REVERT: F 325 MET cc_start: 0.8741 (ppp) cc_final: 0.7527 (ppp) REVERT: F 336 LYS cc_start: 0.9352 (ttpt) cc_final: 0.9089 (tttt) REVERT: H 25 ASP cc_start: 0.8280 (p0) cc_final: 0.8059 (p0) REVERT: H 83 GLU cc_start: 0.7875 (pt0) cc_final: 0.7589 (pt0) REVERT: H 192 ILE cc_start: 0.9246 (tp) cc_final: 0.8974 (tp) REVERT: H 205 GLU cc_start: 0.8045 (mp0) cc_final: 0.7673 (mp0) REVERT: H 214 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7918 (mm-30) REVERT: H 246 GLN cc_start: 0.8552 (mt0) cc_final: 0.8345 (mt0) REVERT: H 325 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7932 (ppp) REVERT: H 336 LYS cc_start: 0.9307 (ttpt) cc_final: 0.9043 (tttt) REVERT: I 25 ASP cc_start: 0.8294 (p0) cc_final: 0.7994 (p0) REVERT: I 83 GLU cc_start: 0.7904 (pt0) cc_final: 0.7644 (pt0) REVERT: I 178 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8368 (tt) REVERT: I 192 ILE cc_start: 0.9363 (tp) cc_final: 0.9043 (tp) REVERT: I 205 GLU cc_start: 0.8027 (mp0) cc_final: 0.7565 (mp0) REVERT: I 269 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7687 (ttt) REVERT: I 314 GLN cc_start: 0.8833 (tt0) cc_final: 0.8591 (tt0) REVERT: I 325 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7908 (ppp) REVERT: I 336 LYS cc_start: 0.9287 (ttpt) cc_final: 0.8905 (tttt) REVERT: K 791 ASN cc_start: 0.8853 (t0) cc_final: 0.8341 (t0) REVERT: K 845 LYS cc_start: 0.9010 (tttp) cc_final: 0.8533 (tptp) REVERT: L 718 GLN cc_start: 0.9251 (mt0) cc_final: 0.8969 (mt0) REVERT: L 791 ASN cc_start: 0.8833 (t0) cc_final: 0.8270 (t0) REVERT: L 803 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8263 (tt) REVERT: N 781 GLN cc_start: 0.8086 (mt0) cc_final: 0.7853 (mm-40) REVERT: N 845 LYS cc_start: 0.9031 (tttp) cc_final: 0.8576 (tptp) REVERT: O 723 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: O 740 SER cc_start: 0.8886 (m) cc_final: 0.8644 (t) REVERT: O 791 ASN cc_start: 0.8750 (t0) cc_final: 0.8467 (m-40) REVERT: O 845 LYS cc_start: 0.9093 (tttp) cc_final: 0.8565 (tptp) REVERT: Q 701 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: Q 718 GLN cc_start: 0.9105 (mt0) cc_final: 0.8716 (mt0) REVERT: Q 724 MET cc_start: 0.8697 (tpp) cc_final: 0.8199 (tpt) REVERT: Q 779 TYR cc_start: 0.8969 (m-80) cc_final: 0.8694 (m-80) REVERT: X 756 MET cc_start: 0.8840 (tpp) cc_final: 0.8514 (tpp) REVERT: X 826 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7324 (ptt) outliers start: 147 outliers final: 106 residues processed: 725 average time/residue: 0.3245 time to fit residues: 381.3105 Evaluate side-chains 778 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 661 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 217 CYS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 751 GLU Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 794 SER Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 783 ILE Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 792 ILE Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 819 ILE Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 796 VAL Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Chi-restraints excluded: chain X residue 849 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 115 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN E 41 GLN F 92 ASN H 59 GLN H 314 GLN I 41 GLN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN L 781 GLN N 718 GLN N 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25716 Z= 0.225 Angle : 0.604 8.979 34788 Z= 0.296 Chirality : 0.043 0.148 3924 Planarity : 0.003 0.029 4422 Dihedral : 8.645 177.948 3556 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.89 % Allowed : 26.98 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3186 helix: 0.16 (0.13), residues: 1494 sheet: -0.15 (0.29), residues: 330 loop : -0.78 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 356 HIS 0.003 0.001 HIS H 371 PHE 0.021 0.001 PHE O 729 TYR 0.020 0.001 TYR D 166 ARG 0.006 0.000 ARG I 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 688 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9442 (tt) cc_final: 0.9212 (tt) REVERT: B 205 GLU cc_start: 0.8180 (mp0) cc_final: 0.7937 (mp0) REVERT: B 303 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9004 (p) REVERT: B 336 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8822 (tttt) REVERT: D 44 MET cc_start: 0.7827 (mmm) cc_final: 0.7480 (mmm) REVERT: D 92 ASN cc_start: 0.9023 (m-40) cc_final: 0.8797 (m110) REVERT: D 119 MET cc_start: 0.8546 (ttp) cc_final: 0.8313 (ttp) REVERT: D 205 GLU cc_start: 0.7996 (mp0) cc_final: 0.7790 (mp0) REVERT: D 246 GLN cc_start: 0.8531 (mt0) cc_final: 0.8174 (mt0) REVERT: D 263 GLN cc_start: 0.8452 (mt0) cc_final: 0.8239 (mt0) REVERT: E 51 ASP cc_start: 0.8156 (t70) cc_final: 0.7905 (t0) REVERT: E 72 GLU cc_start: 0.7112 (pp20) cc_final: 0.6715 (pp20) REVERT: E 192 ILE cc_start: 0.9349 (tp) cc_final: 0.9024 (tp) REVERT: E 269 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8095 (ttt) REVERT: E 325 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7922 (ppp) REVERT: E 336 LYS cc_start: 0.9137 (ttpt) cc_final: 0.8860 (tttt) REVERT: F 72 GLU cc_start: 0.7303 (pp20) cc_final: 0.7051 (pp20) REVERT: F 78 ASN cc_start: 0.8297 (t0) cc_final: 0.8048 (t0) REVERT: F 192 ILE cc_start: 0.7992 (tp) cc_final: 0.7765 (tp) REVERT: F 325 MET cc_start: 0.8692 (ppp) cc_final: 0.7466 (ppp) REVERT: F 336 LYS cc_start: 0.9303 (ttpt) cc_final: 0.9020 (tttt) REVERT: H 83 GLU cc_start: 0.7877 (pt0) cc_final: 0.7597 (pt0) REVERT: H 192 ILE cc_start: 0.9251 (tp) cc_final: 0.8978 (tp) REVERT: H 205 GLU cc_start: 0.8014 (mp0) cc_final: 0.7662 (mp0) REVERT: H 214 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7883 (mm-30) REVERT: H 325 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7971 (ppp) REVERT: H 326 LYS cc_start: 0.8574 (pttp) cc_final: 0.8359 (ptmt) REVERT: H 336 LYS cc_start: 0.9273 (ttpt) cc_final: 0.9015 (tttt) REVERT: I 25 ASP cc_start: 0.8242 (p0) cc_final: 0.7876 (p0) REVERT: I 83 GLU cc_start: 0.7846 (pt0) cc_final: 0.7586 (pt0) REVERT: I 192 ILE cc_start: 0.9316 (tp) cc_final: 0.8995 (tp) REVERT: I 205 GLU cc_start: 0.7933 (mp0) cc_final: 0.7618 (mp0) REVERT: I 269 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7770 (ttt) REVERT: I 314 GLN cc_start: 0.8780 (tt0) cc_final: 0.8532 (tt0) REVERT: I 325 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8038 (ppp) REVERT: I 336 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8849 (tttt) REVERT: K 781 GLN cc_start: 0.8259 (mt0) cc_final: 0.8044 (mt0) REVERT: K 791 ASN cc_start: 0.8768 (t0) cc_final: 0.8360 (t0) REVERT: K 845 LYS cc_start: 0.8998 (tttp) cc_final: 0.8527 (tptp) REVERT: L 791 ASN cc_start: 0.8786 (t0) cc_final: 0.8268 (t0) REVERT: L 801 GLN cc_start: 0.8776 (tp40) cc_final: 0.8556 (tm-30) REVERT: L 803 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8329 (tt) REVERT: N 781 GLN cc_start: 0.8039 (mt0) cc_final: 0.7813 (mm-40) REVERT: N 845 LYS cc_start: 0.9017 (tttp) cc_final: 0.8580 (tptp) REVERT: O 723 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7511 (tmm) REVERT: O 740 SER cc_start: 0.8840 (m) cc_final: 0.8594 (t) REVERT: O 791 ASN cc_start: 0.8668 (t0) cc_final: 0.8204 (t0) REVERT: O 845 LYS cc_start: 0.9086 (tttp) cc_final: 0.8557 (tptp) REVERT: Q 718 GLN cc_start: 0.9095 (mt0) cc_final: 0.8736 (mt0) REVERT: Q 724 MET cc_start: 0.8665 (tpp) cc_final: 0.8126 (tpt) REVERT: Q 779 TYR cc_start: 0.8903 (m-80) cc_final: 0.8645 (m-80) REVERT: X 801 GLN cc_start: 0.8916 (tp40) cc_final: 0.8594 (tm-30) REVERT: X 826 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7332 (ptt) outliers start: 106 outliers final: 69 residues processed: 728 average time/residue: 0.3308 time to fit residues: 394.5309 Evaluate side-chains 745 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 667 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain Q residue 849 MET Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 246 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN K 831 GLN N 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 789 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 25716 Z= 0.425 Angle : 0.678 8.237 34788 Z= 0.332 Chirality : 0.045 0.156 3924 Planarity : 0.003 0.031 4422 Dihedral : 8.555 172.905 3556 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.81 % Allowed : 26.91 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3186 helix: 0.28 (0.14), residues: 1458 sheet: -0.16 (0.30), residues: 330 loop : -0.86 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 79 HIS 0.005 0.001 HIS I 371 PHE 0.023 0.001 PHE N 729 TYR 0.015 0.001 TYR O 779 ARG 0.007 0.000 ARG I 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 674 time to evaluate : 2.870 Fit side-chains revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9467 (tt) cc_final: 0.9246 (tt) REVERT: B 205 GLU cc_start: 0.8219 (mp0) cc_final: 0.7950 (mp0) REVERT: B 303 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9032 (p) REVERT: B 336 LYS cc_start: 0.9189 (ttpt) cc_final: 0.8908 (tttt) REVERT: B 355 MET cc_start: -0.5830 (OUTLIER) cc_final: -0.6588 (ttm) REVERT: D 44 MET cc_start: 0.7980 (mmm) cc_final: 0.7600 (mmm) REVERT: D 92 ASN cc_start: 0.9061 (m-40) cc_final: 0.8836 (m110) REVERT: D 167 GLU cc_start: 0.8399 (pm20) cc_final: 0.8060 (mp0) REVERT: D 246 GLN cc_start: 0.8573 (mt0) cc_final: 0.8135 (mt0) REVERT: D 263 GLN cc_start: 0.8542 (mt0) cc_final: 0.8326 (mt0) REVERT: D 326 LYS cc_start: 0.8493 (pttp) cc_final: 0.8220 (pttm) REVERT: E 51 ASP cc_start: 0.8230 (t70) cc_final: 0.7976 (t0) REVERT: E 72 GLU cc_start: 0.7231 (pp20) cc_final: 0.6841 (pp20) REVERT: E 192 ILE cc_start: 0.9327 (tp) cc_final: 0.9018 (tp) REVERT: E 325 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7996 (ppp) REVERT: E 336 LYS cc_start: 0.9182 (ttpt) cc_final: 0.8894 (tttt) REVERT: F 72 GLU cc_start: 0.7403 (pp20) cc_final: 0.7200 (pp20) REVERT: F 78 ASN cc_start: 0.8349 (t0) cc_final: 0.8084 (t0) REVERT: F 192 ILE cc_start: 0.8022 (tp) cc_final: 0.7798 (tp) REVERT: F 253 GLU cc_start: 0.8468 (mp0) cc_final: 0.8257 (mp0) REVERT: F 325 MET cc_start: 0.8686 (ppp) cc_final: 0.7649 (ppp) REVERT: F 336 LYS cc_start: 0.9344 (ttpt) cc_final: 0.9059 (tttt) REVERT: H 83 GLU cc_start: 0.7869 (pt0) cc_final: 0.7588 (pt0) REVERT: H 192 ILE cc_start: 0.9239 (tp) cc_final: 0.8967 (tp) REVERT: H 205 GLU cc_start: 0.8069 (mp0) cc_final: 0.7707 (mp0) REVERT: H 214 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8033 (mm-30) REVERT: H 325 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7987 (ppp) REVERT: H 336 LYS cc_start: 0.9344 (ttpt) cc_final: 0.9095 (tttt) REVERT: I 25 ASP cc_start: 0.8238 (p0) cc_final: 0.7959 (p0) REVERT: I 83 GLU cc_start: 0.7886 (pt0) cc_final: 0.7605 (pt0) REVERT: I 178 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (tt) REVERT: I 192 ILE cc_start: 0.9361 (tp) cc_final: 0.9061 (tp) REVERT: I 205 GLU cc_start: 0.8000 (mp0) cc_final: 0.7642 (mp0) REVERT: I 269 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7710 (ttt) REVERT: I 313 MET cc_start: 0.9367 (tpp) cc_final: 0.9104 (mmm) REVERT: I 314 GLN cc_start: 0.8819 (tt0) cc_final: 0.8618 (tt0) REVERT: I 325 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7889 (ppp) REVERT: K 781 GLN cc_start: 0.8316 (mt0) cc_final: 0.8089 (mt0) REVERT: K 791 ASN cc_start: 0.8834 (t0) cc_final: 0.8346 (t0) REVERT: K 845 LYS cc_start: 0.9061 (tttp) cc_final: 0.8540 (tptp) REVERT: L 791 ASN cc_start: 0.8807 (t0) cc_final: 0.8324 (t0) REVERT: L 797 LYS cc_start: 0.9184 (tppt) cc_final: 0.8908 (mmmt) REVERT: L 801 GLN cc_start: 0.8852 (tp40) cc_final: 0.8491 (tm-30) REVERT: L 803 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8257 (tt) REVERT: N 781 GLN cc_start: 0.8124 (mt0) cc_final: 0.7868 (mm-40) REVERT: N 845 LYS cc_start: 0.9031 (tttp) cc_final: 0.8566 (tptp) REVERT: O 723 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: O 740 SER cc_start: 0.8895 (m) cc_final: 0.8661 (t) REVERT: O 791 ASN cc_start: 0.8720 (t0) cc_final: 0.8450 (m-40) REVERT: O 845 LYS cc_start: 0.9100 (tttp) cc_final: 0.8576 (tptp) REVERT: Q 718 GLN cc_start: 0.9122 (mt0) cc_final: 0.8766 (mt0) REVERT: Q 724 MET cc_start: 0.8740 (tpp) cc_final: 0.8261 (tpt) REVERT: Q 779 TYR cc_start: 0.8955 (m-80) cc_final: 0.8648 (m-80) REVERT: X 801 GLN cc_start: 0.8961 (tp40) cc_final: 0.8599 (tm-30) REVERT: X 826 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7379 (ptt) outliers start: 131 outliers final: 98 residues processed: 722 average time/residue: 0.3268 time to fit residues: 385.3428 Evaluate side-chains 769 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 661 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 792 ILE Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 794 SER Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 792 ILE Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain N residue 826 MET Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain Q residue 849 MET Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 92 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 831 GLN L 718 GLN O 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 789 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 25716 Z= 0.369 Angle : 0.657 8.766 34788 Z= 0.322 Chirality : 0.045 0.149 3924 Planarity : 0.003 0.031 4422 Dihedral : 8.409 160.816 3556 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.19 % Allowed : 28.12 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3186 helix: 0.35 (0.14), residues: 1458 sheet: -0.13 (0.30), residues: 330 loop : -0.81 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 356 HIS 0.004 0.001 HIS I 371 PHE 0.024 0.001 PHE N 729 TYR 0.017 0.001 TYR Q 837 ARG 0.008 0.000 ARG H 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 675 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9464 (tt) cc_final: 0.9242 (tt) REVERT: B 205 GLU cc_start: 0.8214 (mp0) cc_final: 0.7978 (mp0) REVERT: B 303 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9057 (p) REVERT: B 336 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8887 (tttt) REVERT: B 355 MET cc_start: -0.5836 (OUTLIER) cc_final: -0.6870 (ttm) REVERT: D 8 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8938 (mp) REVERT: D 44 MET cc_start: 0.7933 (mmm) cc_final: 0.7587 (mmm) REVERT: D 92 ASN cc_start: 0.9054 (m-40) cc_final: 0.8828 (m110) REVERT: D 167 GLU cc_start: 0.8311 (pm20) cc_final: 0.8058 (mp0) REVERT: D 205 GLU cc_start: 0.8045 (mp0) cc_final: 0.7811 (mp0) REVERT: D 246 GLN cc_start: 0.8544 (mt0) cc_final: 0.8132 (mt0) REVERT: D 263 GLN cc_start: 0.8537 (mt0) cc_final: 0.8334 (mt0) REVERT: D 326 LYS cc_start: 0.8523 (pttp) cc_final: 0.8233 (pttm) REVERT: E 51 ASP cc_start: 0.8209 (t70) cc_final: 0.7955 (t0) REVERT: E 72 GLU cc_start: 0.7245 (pp20) cc_final: 0.6855 (pp20) REVERT: E 192 ILE cc_start: 0.9347 (tp) cc_final: 0.9033 (tp) REVERT: E 269 MET cc_start: 0.8419 (ttp) cc_final: 0.8105 (ttt) REVERT: E 325 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8033 (ppp) REVERT: E 336 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8887 (tttt) REVERT: F 72 GLU cc_start: 0.7392 (pp20) cc_final: 0.7182 (pp20) REVERT: F 78 ASN cc_start: 0.8338 (t0) cc_final: 0.8086 (t0) REVERT: F 192 ILE cc_start: 0.8065 (tp) cc_final: 0.7848 (tp) REVERT: F 253 GLU cc_start: 0.8441 (mp0) cc_final: 0.8235 (mp0) REVERT: F 325 MET cc_start: 0.8644 (ppp) cc_final: 0.7757 (ppp) REVERT: F 326 LYS cc_start: 0.8810 (pttp) cc_final: 0.8360 (mmtm) REVERT: F 336 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9040 (tttt) REVERT: H 83 GLU cc_start: 0.7867 (pt0) cc_final: 0.7584 (pt0) REVERT: H 192 ILE cc_start: 0.9236 (tp) cc_final: 0.8962 (tp) REVERT: H 205 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: H 214 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8057 (mm-30) REVERT: H 325 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8006 (ppp) REVERT: H 336 LYS cc_start: 0.9353 (ttpt) cc_final: 0.9110 (tttt) REVERT: I 25 ASP cc_start: 0.8216 (p0) cc_final: 0.7913 (p0) REVERT: I 83 GLU cc_start: 0.7877 (pt0) cc_final: 0.7594 (pt0) REVERT: I 178 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8334 (tt) REVERT: I 192 ILE cc_start: 0.9329 (tp) cc_final: 0.9026 (tp) REVERT: I 269 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7711 (ttt) REVERT: I 325 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7876 (ppp) REVERT: K 781 GLN cc_start: 0.8292 (mt0) cc_final: 0.8061 (mt0) REVERT: K 791 ASN cc_start: 0.8843 (t0) cc_final: 0.8380 (t0) REVERT: K 845 LYS cc_start: 0.9058 (tttp) cc_final: 0.8542 (tptp) REVERT: L 724 MET cc_start: 0.8592 (tpp) cc_final: 0.8083 (tpt) REVERT: L 791 ASN cc_start: 0.8829 (t0) cc_final: 0.8331 (t0) REVERT: L 797 LYS cc_start: 0.9184 (tppt) cc_final: 0.8914 (mmmt) REVERT: L 801 GLN cc_start: 0.8853 (tp40) cc_final: 0.8468 (tm-30) REVERT: N 723 MET cc_start: 0.8440 (tmm) cc_final: 0.8204 (tmm) REVERT: N 781 GLN cc_start: 0.8136 (mt0) cc_final: 0.7873 (mm-40) REVERT: N 845 LYS cc_start: 0.9029 (tttp) cc_final: 0.8559 (tptp) REVERT: O 723 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7610 (tmm) REVERT: O 740 SER cc_start: 0.8873 (m) cc_final: 0.8637 (t) REVERT: O 845 LYS cc_start: 0.9102 (tttp) cc_final: 0.8576 (tptp) REVERT: Q 701 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: Q 718 GLN cc_start: 0.9123 (mt0) cc_final: 0.8821 (mt0) REVERT: Q 724 MET cc_start: 0.8739 (tpp) cc_final: 0.8281 (tpt) REVERT: Q 779 TYR cc_start: 0.8914 (m-80) cc_final: 0.8639 (m-80) REVERT: X 801 GLN cc_start: 0.8944 (tp40) cc_final: 0.8586 (tm-30) REVERT: X 826 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7514 (ptt) outliers start: 114 outliers final: 95 residues processed: 717 average time/residue: 0.3269 time to fit residues: 381.3938 Evaluate side-chains 772 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 665 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 718 GLN Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 794 SER Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain N residue 833 VAL Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain Q residue 849 MET Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 285 optimal weight: 0.0570 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 overall best weight: 2.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 41 GLN E 41 GLN F 92 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 314 GLN I 41 GLN K 789 GLN K 831 GLN L 718 GLN O 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25716 Z= 0.216 Angle : 0.612 9.599 34788 Z= 0.300 Chirality : 0.043 0.159 3924 Planarity : 0.003 0.030 4422 Dihedral : 8.151 146.563 3556 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.11 % Allowed : 28.19 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3186 helix: 0.34 (0.13), residues: 1506 sheet: -0.06 (0.30), residues: 330 loop : -0.65 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 356 HIS 0.004 0.001 HIS N 788 PHE 0.022 0.001 PHE N 729 TYR 0.017 0.001 TYR X 837 ARG 0.009 0.000 ARG H 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 686 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9447 (tt) cc_final: 0.9216 (tt) REVERT: B 198 TYR cc_start: 0.9224 (m-80) cc_final: 0.8807 (m-80) REVERT: B 303 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9045 (p) REVERT: B 336 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8849 (tttt) REVERT: D 44 MET cc_start: 0.7857 (mmm) cc_final: 0.7521 (mmm) REVERT: D 92 ASN cc_start: 0.9025 (m-40) cc_final: 0.8790 (m110) REVERT: D 205 GLU cc_start: 0.8002 (mp0) cc_final: 0.7799 (mp0) REVERT: D 246 GLN cc_start: 0.8520 (mt0) cc_final: 0.8134 (mt0) REVERT: D 326 LYS cc_start: 0.8462 (pttp) cc_final: 0.8175 (pttm) REVERT: E 51 ASP cc_start: 0.8174 (t70) cc_final: 0.7912 (t0) REVERT: E 192 ILE cc_start: 0.9345 (tp) cc_final: 0.9032 (tp) REVERT: E 269 MET cc_start: 0.8344 (ttp) cc_final: 0.7826 (ttt) REVERT: E 325 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8000 (ppp) REVERT: E 336 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8833 (tttt) REVERT: F 72 GLU cc_start: 0.7338 (pp20) cc_final: 0.7089 (pp20) REVERT: F 78 ASN cc_start: 0.8295 (t0) cc_final: 0.8053 (t0) REVERT: F 100 GLU cc_start: 0.7946 (mp0) cc_final: 0.7739 (mm-30) REVERT: F 192 ILE cc_start: 0.8006 (tp) cc_final: 0.7788 (tp) REVERT: F 325 MET cc_start: 0.8501 (ppp) cc_final: 0.7640 (ppp) REVERT: F 326 LYS cc_start: 0.8739 (pttp) cc_final: 0.8363 (mmtt) REVERT: F 336 LYS cc_start: 0.9307 (ttpt) cc_final: 0.9024 (tttt) REVERT: H 83 GLU cc_start: 0.7889 (pt0) cc_final: 0.7609 (pt0) REVERT: H 192 ILE cc_start: 0.9230 (tp) cc_final: 0.8971 (tp) REVERT: H 205 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: H 325 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8066 (ppp) REVERT: H 336 LYS cc_start: 0.9325 (ttpt) cc_final: 0.9075 (tttt) REVERT: I 25 ASP cc_start: 0.8199 (p0) cc_final: 0.7861 (p0) REVERT: I 83 GLU cc_start: 0.7844 (pt0) cc_final: 0.7575 (pt0) REVERT: I 192 ILE cc_start: 0.9330 (tp) cc_final: 0.9009 (tp) REVERT: I 269 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7725 (ttt) REVERT: I 325 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: I 336 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8867 (tttt) REVERT: K 781 GLN cc_start: 0.8296 (mt0) cc_final: 0.8082 (mt0) REVERT: K 791 ASN cc_start: 0.8783 (t0) cc_final: 0.8358 (t0) REVERT: K 845 LYS cc_start: 0.9004 (tttp) cc_final: 0.8532 (tptp) REVERT: L 724 MET cc_start: 0.8660 (tpp) cc_final: 0.8109 (tpt) REVERT: L 791 ASN cc_start: 0.8775 (t0) cc_final: 0.8338 (t0) REVERT: L 797 LYS cc_start: 0.9179 (tppt) cc_final: 0.8958 (mmmt) REVERT: L 801 GLN cc_start: 0.8745 (tp40) cc_final: 0.8388 (tm-30) REVERT: L 803 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8352 (tt) REVERT: N 781 GLN cc_start: 0.8089 (mt0) cc_final: 0.7827 (mm-40) REVERT: N 845 LYS cc_start: 0.9008 (tttp) cc_final: 0.8553 (tptp) REVERT: O 723 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7578 (tmm) REVERT: O 740 SER cc_start: 0.8848 (m) cc_final: 0.8604 (t) REVERT: O 791 ASN cc_start: 0.8616 (t0) cc_final: 0.8100 (t0) REVERT: O 845 LYS cc_start: 0.9089 (tttp) cc_final: 0.8554 (tptp) REVERT: Q 718 GLN cc_start: 0.9134 (mt0) cc_final: 0.8898 (mt0) REVERT: Q 724 MET cc_start: 0.8686 (tpp) cc_final: 0.8256 (tpt) REVERT: Q 779 TYR cc_start: 0.8890 (m-80) cc_final: 0.8620 (m-80) REVERT: X 801 GLN cc_start: 0.8903 (tp40) cc_final: 0.8634 (tm-30) REVERT: X 826 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7492 (ptt) outliers start: 112 outliers final: 95 residues processed: 728 average time/residue: 0.3503 time to fit residues: 417.5575 Evaluate side-chains 775 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 671 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 217 CYS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 718 GLN Chi-restraints excluded: chain L residue 725 GLU Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 736 LEU Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 787 CYS Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 40.0000 chunk 184 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN L 718 GLN N 718 GLN N 789 GLN O 789 GLN O 844 GLN ** X 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25716 Z= 0.227 Angle : 0.620 9.756 34788 Z= 0.302 Chirality : 0.043 0.174 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.993 138.903 3556 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.11 % Allowed : 28.41 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3186 helix: 0.41 (0.13), residues: 1506 sheet: -0.03 (0.30), residues: 330 loop : -0.60 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 705 HIS 0.004 0.001 HIS N 788 PHE 0.028 0.001 PHE N 729 TYR 0.021 0.001 TYR D 166 ARG 0.009 0.000 ARG H 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 683 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ILE cc_start: 0.9441 (tt) cc_final: 0.9216 (tt) REVERT: B 198 TYR cc_start: 0.9233 (m-80) cc_final: 0.8820 (m-80) REVERT: B 303 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9086 (p) REVERT: B 336 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8867 (tttt) REVERT: B 355 MET cc_start: -0.5776 (OUTLIER) cc_final: -0.6745 (ttm) REVERT: D 8 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 44 MET cc_start: 0.7692 (mmm) cc_final: 0.7308 (mmm) REVERT: D 92 ASN cc_start: 0.9025 (m-40) cc_final: 0.8807 (m110) REVERT: D 205 GLU cc_start: 0.8004 (mp0) cc_final: 0.7787 (mp0) REVERT: D 246 GLN cc_start: 0.8524 (mt0) cc_final: 0.8131 (mt0) REVERT: D 326 LYS cc_start: 0.8483 (pttp) cc_final: 0.8201 (pttm) REVERT: E 51 ASP cc_start: 0.8167 (t70) cc_final: 0.7902 (t0) REVERT: E 192 ILE cc_start: 0.9345 (tp) cc_final: 0.9037 (tp) REVERT: E 269 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8055 (ttt) REVERT: E 325 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8020 (ppp) REVERT: E 336 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8868 (tttt) REVERT: F 72 GLU cc_start: 0.7264 (pp20) cc_final: 0.7018 (pp20) REVERT: F 78 ASN cc_start: 0.8303 (t0) cc_final: 0.8052 (t0) REVERT: F 192 ILE cc_start: 0.7996 (tp) cc_final: 0.7780 (tp) REVERT: F 325 MET cc_start: 0.8487 (ppp) cc_final: 0.7603 (ppp) REVERT: F 326 LYS cc_start: 0.8693 (pttp) cc_final: 0.8345 (mmtt) REVERT: F 336 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9004 (tttt) REVERT: H 83 GLU cc_start: 0.7891 (pt0) cc_final: 0.7624 (pt0) REVERT: H 192 ILE cc_start: 0.9217 (tp) cc_final: 0.8954 (tp) REVERT: H 205 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: H 325 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8194 (ppp) REVERT: H 336 LYS cc_start: 0.9329 (ttpt) cc_final: 0.9086 (tttt) REVERT: I 25 ASP cc_start: 0.8207 (p0) cc_final: 0.7921 (p0) REVERT: I 83 GLU cc_start: 0.7851 (pt0) cc_final: 0.7582 (pt0) REVERT: I 192 ILE cc_start: 0.9328 (tp) cc_final: 0.9003 (tp) REVERT: I 269 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7757 (ttt) REVERT: I 325 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8023 (ppp) REVERT: I 336 LYS cc_start: 0.9234 (ttpt) cc_final: 0.8870 (tttt) REVERT: K 781 GLN cc_start: 0.8303 (mt0) cc_final: 0.8098 (mt0) REVERT: K 791 ASN cc_start: 0.8759 (t0) cc_final: 0.8348 (t0) REVERT: K 845 LYS cc_start: 0.8998 (tttp) cc_final: 0.8530 (tptp) REVERT: L 724 MET cc_start: 0.8643 (tpp) cc_final: 0.8101 (tpt) REVERT: L 791 ASN cc_start: 0.8731 (t0) cc_final: 0.8313 (t0) REVERT: L 797 LYS cc_start: 0.9169 (tppt) cc_final: 0.8958 (mmmt) REVERT: L 801 GLN cc_start: 0.8707 (tp40) cc_final: 0.8360 (tm-30) REVERT: L 803 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8274 (tt) REVERT: N 781 GLN cc_start: 0.8092 (mt0) cc_final: 0.7818 (mm-40) REVERT: N 845 LYS cc_start: 0.9003 (tttp) cc_final: 0.8554 (tptp) REVERT: O 723 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7577 (tmm) REVERT: O 740 SER cc_start: 0.8852 (m) cc_final: 0.8608 (t) REVERT: O 791 ASN cc_start: 0.8585 (t0) cc_final: 0.8150 (t0) REVERT: O 845 LYS cc_start: 0.9079 (tttp) cc_final: 0.8570 (tptp) REVERT: Q 701 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: Q 724 MET cc_start: 0.8676 (tpp) cc_final: 0.8243 (tpt) REVERT: Q 779 TYR cc_start: 0.8871 (m-80) cc_final: 0.8591 (m-80) REVERT: X 801 GLN cc_start: 0.8905 (tp40) cc_final: 0.8641 (tm-30) REVERT: X 826 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7441 (ptt) outliers start: 112 outliers final: 92 residues processed: 722 average time/residue: 0.3465 time to fit residues: 409.2764 Evaluate side-chains 774 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 669 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 217 CYS Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 311 ASP Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 360 GLN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain K residue 702 VAL Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 740 SER Chi-restraints excluded: chain K residue 787 CYS Chi-restraints excluded: chain K residue 789 GLN Chi-restraints excluded: chain K residue 796 VAL Chi-restraints excluded: chain K residue 816 MET Chi-restraints excluded: chain L residue 714 VAL Chi-restraints excluded: chain L residue 718 GLN Chi-restraints excluded: chain L residue 796 VAL Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 826 MET Chi-restraints excluded: chain N residue 714 VAL Chi-restraints excluded: chain N residue 718 GLN Chi-restraints excluded: chain N residue 787 CYS Chi-restraints excluded: chain N residue 789 GLN Chi-restraints excluded: chain N residue 796 VAL Chi-restraints excluded: chain N residue 803 LEU Chi-restraints excluded: chain O residue 714 VAL Chi-restraints excluded: chain O residue 723 MET Chi-restraints excluded: chain O residue 725 GLU Chi-restraints excluded: chain O residue 789 GLN Chi-restraints excluded: chain O residue 792 ILE Chi-restraints excluded: chain Q residue 701 GLU Chi-restraints excluded: chain Q residue 702 VAL Chi-restraints excluded: chain Q residue 714 VAL Chi-restraints excluded: chain Q residue 787 CYS Chi-restraints excluded: chain Q residue 829 VAL Chi-restraints excluded: chain X residue 714 VAL Chi-restraints excluded: chain X residue 787 CYS Chi-restraints excluded: chain X residue 792 ILE Chi-restraints excluded: chain X residue 826 MET Chi-restraints excluded: chain X residue 829 VAL Chi-restraints excluded: chain X residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 41 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 41 GLN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 789 GLN N 718 GLN O 789 GLN O 844 GLN Q 718 GLN ** X 718 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 = 0.3843 r_free = 0.3843 target = 0.157708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110452 restraints weight = 34529.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115517 restraints weight = 18368.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118769 restraints weight = 12458.699| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25716 Z= 0.308 Angle : 0.645 11.992 34788 Z= 0.314 Chirality : 0.044 0.206 3924 Planarity : 0.003 0.029 4422 Dihedral : 7.955 135.143 3556 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.30 % Allowed : 28.45 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3186 helix: 0.51 (0.14), residues: 1470 sheet: -0.05 (0.30), residues: 330 loop : -0.65 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 705 HIS 0.004 0.001 HIS N 788 PHE 0.026 0.001 PHE N 729 TYR 0.030 0.001 TYR I 166 ARG 0.009 0.000 ARG H 372 =============================================================================== Job complete usr+sys time: 6654.09 seconds wall clock time: 121 minutes 6.28 seconds (7266.28 seconds total)