Starting phenix.real_space_refine on Sun Mar 17 16:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ufi_26476/03_2024/7ufi_26476_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 77 5.16 5 C 11446 2.51 5 N 3177 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 6": "OE1" <-> "OE2" Residue "1 GLU 121": "OE1" <-> "OE2" Residue "1 GLU 135": "OE1" <-> "OE2" Residue "1 GLU 142": "OE1" <-> "OE2" Residue "1 ARG 143": "NH1" <-> "NH2" Residue "1 ARG 146": "NH1" <-> "NH2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 220": "OE1" <-> "OE2" Residue "1 GLU 266": "OE1" <-> "OE2" Residue "1 GLU 267": "OE1" <-> "OE2" Residue "1 GLU 289": "OE1" <-> "OE2" Residue "1 GLU 309": "OE1" <-> "OE2" Residue "2 GLU 6": "OE1" <-> "OE2" Residue "2 GLU 121": "OE1" <-> "OE2" Residue "2 GLU 135": "OE1" <-> "OE2" Residue "2 GLU 142": "OE1" <-> "OE2" Residue "2 ARG 143": "NH1" <-> "NH2" Residue "2 ARG 146": "NH1" <-> "NH2" Residue "2 GLU 193": "OE1" <-> "OE2" Residue "2 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 220": "OE1" <-> "OE2" Residue "2 GLU 266": "OE1" <-> "OE2" Residue "2 GLU 267": "OE1" <-> "OE2" Residue "2 GLU 289": "OE1" <-> "OE2" Residue "2 GLU 309": "OE1" <-> "OE2" Residue "3 GLU 6": "OE1" <-> "OE2" Residue "3 GLU 121": "OE1" <-> "OE2" Residue "3 GLU 135": "OE1" <-> "OE2" Residue "3 GLU 142": "OE1" <-> "OE2" Residue "3 ARG 143": "NH1" <-> "NH2" Residue "3 ARG 146": "NH1" <-> "NH2" Residue "3 GLU 193": "OE1" <-> "OE2" Residue "3 GLU 220": "OE1" <-> "OE2" Residue "3 GLU 266": "OE1" <-> "OE2" Residue "3 GLU 267": "OE1" <-> "OE2" Residue "3 GLU 289": "OE1" <-> "OE2" Residue "3 GLU 309": "OE1" <-> "OE2" Residue "4 GLU 6": "OE1" <-> "OE2" Residue "4 GLU 121": "OE1" <-> "OE2" Residue "4 GLU 135": "OE1" <-> "OE2" Residue "4 GLU 142": "OE1" <-> "OE2" Residue "4 ARG 143": "NH1" <-> "NH2" Residue "4 ARG 146": "NH1" <-> "NH2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 220": "OE1" <-> "OE2" Residue "4 GLU 266": "OE1" <-> "OE2" Residue "4 GLU 267": "OE1" <-> "OE2" Residue "4 GLU 289": "OE1" <-> "OE2" Residue "4 GLU 309": "OE1" <-> "OE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 GLU 121": "OE1" <-> "OE2" Residue "5 GLU 135": "OE1" <-> "OE2" Residue "5 GLU 142": "OE1" <-> "OE2" Residue "5 ARG 143": "NH1" <-> "NH2" Residue "5 ARG 146": "NH1" <-> "NH2" Residue "5 GLU 193": "OE1" <-> "OE2" Residue "5 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 220": "OE1" <-> "OE2" Residue "5 GLU 266": "OE1" <-> "OE2" Residue "5 GLU 267": "OE1" <-> "OE2" Residue "5 GLU 289": "OE1" <-> "OE2" Residue "5 GLU 309": "OE1" <-> "OE2" Residue "6 GLU 121": "OE1" <-> "OE2" Residue "6 GLU 135": "OE1" <-> "OE2" Residue "6 GLU 142": "OE1" <-> "OE2" Residue "6 ARG 143": "NH1" <-> "NH2" Residue "6 ARG 146": "NH1" <-> "NH2" Residue "6 GLU 193": "OE1" <-> "OE2" Residue "6 GLU 220": "OE1" <-> "OE2" Residue "6 GLU 266": "OE1" <-> "OE2" Residue "6 GLU 267": "OE1" <-> "OE2" Residue "6 GLU 289": "OE1" <-> "OE2" Residue "6 GLU 309": "OE1" <-> "OE2" Residue "7 ASP 34": "OD1" <-> "OD2" Residue "7 GLU 121": "OE1" <-> "OE2" Residue "7 GLU 135": "OE1" <-> "OE2" Residue "7 GLU 142": "OE1" <-> "OE2" Residue "7 ARG 143": "NH1" <-> "NH2" Residue "7 ARG 146": "NH1" <-> "NH2" Residue "7 GLU 193": "OE1" <-> "OE2" Residue "7 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 GLU 266": "OE1" <-> "OE2" Residue "7 GLU 267": "OE1" <-> "OE2" Residue "7 GLU 289": "OE1" <-> "OE2" Residue "7 GLU 309": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18319 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "1" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "2" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "3" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "4" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "5" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "6" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "7" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 16, 'TRANS': 294} Chain: "1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.10, per 1000 atoms: 0.55 Number of scatterers: 18319 At special positions: 0 Unit cell: (99.594, 144.864, 150.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 63 15.00 O 3556 8.00 N 3177 7.00 C 11446 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 3.1 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 14 sheets defined 47.3% alpha, 4.4% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 7.25 Creating SS restraints... Processing helix chain '1' and resid 6 through 13 Processing helix chain '1' and resid 20 through 35 Processing helix chain '1' and resid 55 through 73 removed outlier: 6.885A pdb=" N ALA 1 69 " --> pdb=" O GLN 1 65 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 90 through 100 Processing helix chain '1' and resid 114 through 126 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 137 through 139 No H-bonds generated for 'chain '1' and resid 137 through 139' Processing helix chain '1' and resid 150 through 161 Processing helix chain '1' and resid 172 through 180 removed outlier: 4.150A pdb=" N VAL 1 176 " --> pdb=" O TYR 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 187 Processing helix chain '1' and resid 205 through 216 Processing helix chain '1' and resid 228 through 237 removed outlier: 3.720A pdb=" N LYS 1 232 " --> pdb=" O GLU 1 228 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 258 Processing helix chain '1' and resid 269 through 275 Processing helix chain '1' and resid 309 through 312 No H-bonds generated for 'chain '1' and resid 309 through 312' Processing helix chain '2' and resid 6 through 13 Processing helix chain '2' and resid 20 through 35 Processing helix chain '2' and resid 55 through 73 removed outlier: 6.860A pdb=" N ALA 2 69 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 90 through 100 Processing helix chain '2' and resid 114 through 126 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 137 through 139 No H-bonds generated for 'chain '2' and resid 137 through 139' Processing helix chain '2' and resid 150 through 161 Processing helix chain '2' and resid 172 through 180 removed outlier: 3.977A pdb=" N VAL 2 176 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 205 through 216 Processing helix chain '2' and resid 228 through 237 removed outlier: 3.735A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 242 through 258 Processing helix chain '2' and resid 269 through 275 Processing helix chain '2' and resid 309 through 312 No H-bonds generated for 'chain '2' and resid 309 through 312' Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 20 through 35 Processing helix chain '3' and resid 55 through 73 removed outlier: 6.706A pdb=" N ALA 3 69 " --> pdb=" O GLN 3 65 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 90 through 100 Processing helix chain '3' and resid 114 through 126 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 137 through 139 No H-bonds generated for 'chain '3' and resid 137 through 139' Processing helix chain '3' and resid 150 through 161 Processing helix chain '3' and resid 172 through 180 removed outlier: 4.013A pdb=" N VAL 3 176 " --> pdb=" O TYR 3 173 " (cutoff:3.500A) Processing helix chain '3' and resid 182 through 187 Processing helix chain '3' and resid 205 through 216 Processing helix chain '3' and resid 228 through 237 removed outlier: 3.723A pdb=" N LYS 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 258 Processing helix chain '3' and resid 269 through 275 Processing helix chain '3' and resid 309 through 312 No H-bonds generated for 'chain '3' and resid 309 through 312' Processing helix chain '4' and resid 6 through 13 Processing helix chain '4' and resid 20 through 35 Processing helix chain '4' and resid 55 through 73 removed outlier: 6.768A pdb=" N ALA 4 69 " --> pdb=" O GLN 4 65 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA 4 70 " --> pdb=" O ALA 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 100 Processing helix chain '4' and resid 114 through 126 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 137 through 139 No H-bonds generated for 'chain '4' and resid 137 through 139' Processing helix chain '4' and resid 150 through 161 Processing helix chain '4' and resid 172 through 180 removed outlier: 4.086A pdb=" N VAL 4 176 " --> pdb=" O TYR 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 182 through 187 Processing helix chain '4' and resid 205 through 216 Processing helix chain '4' and resid 228 through 237 removed outlier: 3.741A pdb=" N LYS 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 258 Processing helix chain '4' and resid 269 through 275 Processing helix chain '4' and resid 309 through 312 No H-bonds generated for 'chain '4' and resid 309 through 312' Processing helix chain '5' and resid 6 through 13 Processing helix chain '5' and resid 20 through 35 Processing helix chain '5' and resid 55 through 73 removed outlier: 6.929A pdb=" N ALA 5 69 " --> pdb=" O GLN 5 65 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA 5 70 " --> pdb=" O ALA 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 90 through 100 Processing helix chain '5' and resid 114 through 126 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 137 through 139 No H-bonds generated for 'chain '5' and resid 137 through 139' Processing helix chain '5' and resid 150 through 161 Processing helix chain '5' and resid 172 through 180 removed outlier: 4.060A pdb=" N VAL 5 176 " --> pdb=" O TYR 5 173 " (cutoff:3.500A) Processing helix chain '5' and resid 182 through 187 Processing helix chain '5' and resid 205 through 216 Processing helix chain '5' and resid 228 through 237 removed outlier: 3.768A pdb=" N LYS 5 232 " --> pdb=" O GLU 5 228 " (cutoff:3.500A) Processing helix chain '5' and resid 242 through 258 Processing helix chain '5' and resid 269 through 275 Processing helix chain '5' and resid 309 through 312 No H-bonds generated for 'chain '5' and resid 309 through 312' Processing helix chain '6' and resid 6 through 13 Processing helix chain '6' and resid 20 through 35 Processing helix chain '6' and resid 55 through 73 removed outlier: 6.810A pdb=" N ALA 6 69 " --> pdb=" O GLN 6 65 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA 6 70 " --> pdb=" O ALA 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 90 through 100 Processing helix chain '6' and resid 114 through 126 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 137 through 139 No H-bonds generated for 'chain '6' and resid 137 through 139' Processing helix chain '6' and resid 150 through 161 Processing helix chain '6' and resid 172 through 180 removed outlier: 4.016A pdb=" N VAL 6 176 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) Processing helix chain '6' and resid 182 through 187 Processing helix chain '6' and resid 205 through 216 Processing helix chain '6' and resid 228 through 237 removed outlier: 3.695A pdb=" N LYS 6 232 " --> pdb=" O GLU 6 228 " (cutoff:3.500A) Processing helix chain '6' and resid 242 through 258 Processing helix chain '6' and resid 269 through 275 Processing helix chain '6' and resid 309 through 312 No H-bonds generated for 'chain '6' and resid 309 through 312' Processing helix chain '7' and resid 6 through 13 Processing helix chain '7' and resid 20 through 35 Processing helix chain '7' and resid 55 through 73 removed outlier: 6.785A pdb=" N ALA 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA 7 70 " --> pdb=" O ALA 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 90 through 100 Processing helix chain '7' and resid 114 through 126 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 137 through 139 No H-bonds generated for 'chain '7' and resid 137 through 139' Processing helix chain '7' and resid 150 through 161 Processing helix chain '7' and resid 172 through 180 removed outlier: 3.959A pdb=" N VAL 7 176 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 187 Processing helix chain '7' and resid 205 through 216 Processing helix chain '7' and resid 228 through 237 removed outlier: 3.695A pdb=" N LYS 7 232 " --> pdb=" O GLU 7 228 " (cutoff:3.500A) Processing helix chain '7' and resid 242 through 258 Processing helix chain '7' and resid 269 through 275 Processing helix chain '7' and resid 309 through 312 No H-bonds generated for 'chain '7' and resid 309 through 312' Processing sheet with id= A, first strand: chain '1' and resid 45 through 49 removed outlier: 6.529A pdb=" N ILE 1 190 " --> pdb=" O MET 1 46 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR 1 48 " --> pdb=" O ILE 1 190 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL 1 192 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '1' and resid 130 through 133 removed outlier: 7.800A pdb=" N ILE 1 133 " --> pdb=" O PRO 1 165 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL 1 167 " --> pdb=" O ILE 1 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '2' and resid 45 through 49 removed outlier: 6.442A pdb=" N ILE 2 190 " --> pdb=" O MET 2 46 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR 2 48 " --> pdb=" O ILE 2 190 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL 2 192 " --> pdb=" O TYR 2 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain '2' and resid 130 through 133 removed outlier: 7.789A pdb=" N ILE 2 133 " --> pdb=" O PRO 2 165 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL 2 167 " --> pdb=" O ILE 2 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '3' and resid 45 through 49 removed outlier: 6.476A pdb=" N ILE 3 190 " --> pdb=" O MET 3 46 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N TYR 3 48 " --> pdb=" O ILE 3 190 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL 3 192 " --> pdb=" O TYR 3 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '3' and resid 130 through 133 removed outlier: 7.770A pdb=" N ILE 3 133 " --> pdb=" O PRO 3 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL 3 167 " --> pdb=" O ILE 3 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '4' and resid 45 through 49 removed outlier: 6.403A pdb=" N ILE 4 190 " --> pdb=" O MET 4 46 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N TYR 4 48 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL 4 192 " --> pdb=" O TYR 4 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '4' and resid 130 through 133 removed outlier: 7.787A pdb=" N ILE 4 133 " --> pdb=" O PRO 4 165 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL 4 167 " --> pdb=" O ILE 4 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '5' and resid 46 through 49 Processing sheet with id= J, first strand: chain '5' and resid 130 through 133 removed outlier: 7.782A pdb=" N ILE 5 133 " --> pdb=" O PRO 5 165 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL 5 167 " --> pdb=" O ILE 5 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '6' and resid 45 through 49 removed outlier: 6.484A pdb=" N ILE 6 190 " --> pdb=" O MET 6 46 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N TYR 6 48 " --> pdb=" O ILE 6 190 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL 6 192 " --> pdb=" O TYR 6 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '6' and resid 130 through 133 removed outlier: 7.841A pdb=" N ILE 6 133 " --> pdb=" O PRO 6 165 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL 6 167 " --> pdb=" O ILE 6 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain '7' and resid 45 through 49 removed outlier: 6.437A pdb=" N ILE 7 190 " --> pdb=" O MET 7 46 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N TYR 7 48 " --> pdb=" O ILE 7 190 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL 7 192 " --> pdb=" O TYR 7 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain '7' and resid 130 through 133 removed outlier: 7.786A pdb=" N ILE 7 133 " --> pdb=" O PRO 7 165 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL 7 167 " --> pdb=" O ILE 7 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 605 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3581 1.33 - 1.46: 4386 1.46 - 1.58: 10556 1.58 - 1.70: 116 1.70 - 1.82: 133 Bond restraints: 18772 Sorted by residual: bond pdb=" N ILE 5 76 " pdb=" CA ILE 5 76 " ideal model delta sigma weight residual 1.458 1.497 -0.039 9.00e-03 1.23e+04 1.86e+01 bond pdb=" N ILE 4 76 " pdb=" CA ILE 4 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.81e+01 bond pdb=" N ILE 2 76 " pdb=" CA ILE 2 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" N ILE 6 76 " pdb=" CA ILE 6 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 bond pdb=" N ILE 3 76 " pdb=" CA ILE 3 76 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.76e+01 ... (remaining 18767 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.96: 772 105.96 - 113.06: 9139 113.06 - 120.16: 8880 120.16 - 127.26: 6625 127.26 - 134.37: 196 Bond angle restraints: 25612 Sorted by residual: angle pdb=" PB ATP 2 401 " pdb=" O3B ATP 2 401 " pdb=" PG ATP 2 401 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP 1 401 " pdb=" O3B ATP 1 401 " pdb=" PG ATP 1 401 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP 7 401 " pdb=" O3B ATP 7 401 " pdb=" PG ATP 7 401 " ideal model delta sigma weight residual 139.87 120.77 19.10 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP 3 401 " pdb=" O3B ATP 3 401 " pdb=" PG ATP 3 401 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP 6 401 " pdb=" O3B ATP 6 401 " pdb=" PG ATP 6 401 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.17e+02 ... (remaining 25607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 9413 17.38 - 34.76: 1222 34.76 - 52.14: 671 52.14 - 69.52: 146 69.52 - 86.90: 33 Dihedral angle restraints: 11485 sinusoidal: 5143 harmonic: 6342 Sorted by residual: dihedral pdb=" CA PHE 2 288 " pdb=" C PHE 2 288 " pdb=" N GLU 2 289 " pdb=" CA GLU 2 289 " ideal model delta harmonic sigma weight residual -180.00 -153.78 -26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE 4 288 " pdb=" C PHE 4 288 " pdb=" N GLU 4 289 " pdb=" CA GLU 4 289 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE 5 288 " pdb=" C PHE 5 288 " pdb=" N GLU 5 289 " pdb=" CA GLU 5 289 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1151 0.045 - 0.089: 933 0.089 - 0.134: 528 0.134 - 0.178: 209 0.178 - 0.223: 42 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CA VAL 1 17 " pdb=" N VAL 1 17 " pdb=" C VAL 1 17 " pdb=" CB VAL 1 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL 3 17 " pdb=" N VAL 3 17 " pdb=" C VAL 3 17 " pdb=" CB VAL 3 17 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL 7 17 " pdb=" N VAL 7 17 " pdb=" C VAL 7 17 " pdb=" CB VAL 7 17 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2860 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP 7 401 " -0.020 2.00e-02 2.50e+03 8.57e-03 2.02e+00 pdb=" C2 ATP 7 401 " -0.002 2.00e-02 2.50e+03 pdb=" C4 ATP 7 401 " 0.008 2.00e-02 2.50e+03 pdb=" C5 ATP 7 401 " 0.005 2.00e-02 2.50e+03 pdb=" C6 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ATP 7 401 " 0.002 2.00e-02 2.50e+03 pdb=" N1 ATP 7 401 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ATP 7 401 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ATP 7 401 " -0.011 2.00e-02 2.50e+03 pdb=" N7 ATP 7 401 " 0.001 2.00e-02 2.50e+03 pdb=" N9 ATP 7 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 7 168 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.64e+00 pdb=" C ILE 7 168 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE 7 168 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE 7 169 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 199 " -0.015 2.00e-02 2.50e+03 9.04e-03 1.63e+00 pdb=" CG TYR 2 199 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 199 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 199 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 2 199 " -0.005 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 14 2.30 - 2.95: 6872 2.95 - 3.60: 26757 3.60 - 4.25: 41259 4.25 - 4.90: 69263 Nonbonded interactions: 144165 Sorted by model distance: nonbonded pdb=" OE1 GLN 5 200 " pdb=" CG LEU 5 299 " model vdw 1.645 3.470 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CB LEU 5 299 " model vdw 1.709 3.440 nonbonded pdb=" NE2 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.874 3.540 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD1 LEU 5 299 " model vdw 1.929 3.460 nonbonded pdb=" OE1 GLN 5 200 " pdb=" CD2 LEU 5 299 " model vdw 1.953 3.460 ... (remaining 144160 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 3.340 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 52.290 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 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 : 0.013 0.046 18772 Z= 0.865 Angle : 1.831 19.404 25612 Z= 1.363 Chirality : 0.079 0.223 2863 Planarity : 0.003 0.015 3122 Dihedral : 20.086 86.898 7383 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.11 % Favored : 90.38 % Rotamer: Outliers : 11.94 % Allowed : 14.23 % Favored : 73.83 % 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: -3.89 (0.15), residues: 2163 helix: -1.98 (0.12), residues: 1127 sheet: -3.45 (0.31), residues: 224 loop : -2.99 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP 4 154 HIS 0.006 0.001 HIS 2 138 PHE 0.017 0.003 PHE 7 209 TYR 0.020 0.003 TYR 2 199 ARG 0.004 0.001 ARG 6 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 732 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.6934 (t) REVERT: 1 22 VAL cc_start: 0.6374 (t) cc_final: 0.6116 (p) REVERT: 1 23 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7830 (mtm110) REVERT: 1 26 LEU cc_start: 0.7049 (mt) cc_final: 0.6679 (mt) REVERT: 1 30 ASP cc_start: 0.7085 (m-30) cc_final: 0.6725 (m-30) REVERT: 1 37 ASP cc_start: 0.7944 (p0) cc_final: 0.6600 (p0) REVERT: 1 38 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6946 (mp) REVERT: 1 39 GLU cc_start: 0.6615 (mp0) cc_final: 0.5311 (mp0) REVERT: 1 46 MET cc_start: 0.8275 (tpt) cc_final: 0.7632 (tpp) REVERT: 1 60 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7608 (mmmm) REVERT: 1 64 ASN cc_start: 0.7741 (m-40) cc_final: 0.7505 (m110) REVERT: 1 83 GLU cc_start: 0.7792 (tt0) cc_final: 0.7116 (mt-10) REVERT: 1 86 ASP cc_start: 0.7946 (t70) cc_final: 0.7570 (t70) REVERT: 1 92 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7456 (t0) REVERT: 1 109 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5961 (tt0) REVERT: 1 110 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.6607 (p) REVERT: 1 114 ARG cc_start: 0.6952 (ptp90) cc_final: 0.6619 (mtm-85) REVERT: 1 118 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7704 (ttm-80) REVERT: 1 129 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7954 (mtpt) REVERT: 1 150 GLN cc_start: 0.8078 (mt0) cc_final: 0.7763 (mt0) REVERT: 1 168 ILE cc_start: 0.8086 (pt) cc_final: 0.7574 (pt) REVERT: 1 175 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7172 (tttm) REVERT: 1 179 GLN cc_start: 0.7236 (mt0) cc_final: 0.6837 (mt0) REVERT: 1 187 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7400 (mtt-85) REVERT: 1 192 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8031 (m) REVERT: 1 193 GLU cc_start: 0.8014 (tp30) cc_final: 0.7385 (tp30) REVERT: 1 197 PHE cc_start: 0.8456 (m-80) cc_final: 0.8211 (m-10) REVERT: 1 215 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7563 (mmtt) REVERT: 1 259 ASN cc_start: 0.7072 (p0) cc_final: 0.6839 (p0) REVERT: 1 261 HIS cc_start: 0.6245 (m170) cc_final: 0.5828 (m90) REVERT: 1 274 LYS cc_start: 0.8035 (mttt) cc_final: 0.7806 (mtmm) REVERT: 1 285 LYS cc_start: 0.7301 (tppt) cc_final: 0.6783 (tppt) REVERT: 1 300 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7342 (m-30) cc_final: 0.7013 (m-30) REVERT: 1 311 TYR cc_start: 0.7894 (t80) cc_final: 0.7546 (t80) REVERT: 2 8 ARG cc_start: 0.7355 (ttm170) cc_final: 0.7105 (ttp-170) REVERT: 2 14 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: 2 24 LYS cc_start: 0.7295 (tttt) cc_final: 0.7037 (ttmm) REVERT: 2 33 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7356 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6237 (mp0) cc_final: 0.5705 (mp0) REVERT: 2 40 SER cc_start: 0.7082 (m) cc_final: 0.6715 (t) REVERT: 2 89 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7119 (mmmt) REVERT: 2 96 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7346 (tm-30) REVERT: 2 100 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7807 (tm-30) REVERT: 2 122 LEU cc_start: 0.7672 (tp) cc_final: 0.7380 (tp) REVERT: 2 141 GLU cc_start: 0.7481 (tt0) cc_final: 0.6901 (tt0) REVERT: 2 150 GLN cc_start: 0.7622 (mt0) cc_final: 0.6909 (mm-40) REVERT: 2 162 THR cc_start: 0.8349 (t) cc_final: 0.7967 (p) REVERT: 2 163 LYS cc_start: 0.8062 (mppt) cc_final: 0.7541 (mmtp) REVERT: 2 164 CYS cc_start: 0.8115 (t) cc_final: 0.7459 (p) REVERT: 2 171 MET cc_start: 0.8519 (mtp) cc_final: 0.8264 (mtp) REVERT: 2 179 GLN cc_start: 0.7721 (mt0) cc_final: 0.7512 (mt0) REVERT: 2 193 GLU cc_start: 0.7542 (tp30) cc_final: 0.7098 (tp30) REVERT: 2 200 GLN cc_start: 0.3924 (OUTLIER) cc_final: 0.3654 (tm-30) REVERT: 2 214 ASP cc_start: 0.7525 (t70) cc_final: 0.7178 (t0) REVERT: 2 235 TYR cc_start: 0.7771 (t80) cc_final: 0.7135 (t80) REVERT: 2 242 MET cc_start: 0.7350 (tpp) cc_final: 0.7052 (tmm) REVERT: 2 255 GLU cc_start: 0.8038 (tp30) cc_final: 0.7205 (mm-30) REVERT: 2 259 ASN cc_start: 0.7530 (p0) cc_final: 0.7319 (p0) REVERT: 2 262 GLU cc_start: 0.6711 (mp0) cc_final: 0.6281 (mp0) REVERT: 2 268 ASP cc_start: 0.6802 (p0) cc_final: 0.6464 (p0) REVERT: 2 286 ASN cc_start: 0.8600 (t0) cc_final: 0.8166 (t0) REVERT: 2 310 ASP cc_start: 0.7014 (m-30) cc_final: 0.6550 (m-30) REVERT: 3 30 ASP cc_start: 0.7717 (m-30) cc_final: 0.6917 (m-30) REVERT: 3 33 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7628 (ttp-110) REVERT: 3 34 ASP cc_start: 0.7513 (m-30) cc_final: 0.6469 (m-30) REVERT: 3 39 GLU cc_start: 0.7284 (mp0) cc_final: 0.6853 (mp0) REVERT: 3 46 MET cc_start: 0.8169 (tpt) cc_final: 0.7540 (tpp) REVERT: 3 48 TYR cc_start: 0.7704 (m-80) cc_final: 0.7472 (m-80) REVERT: 3 61 LYS cc_start: 0.8198 (tptp) cc_final: 0.7846 (tptp) REVERT: 3 81 HIS cc_start: 0.8467 (t70) cc_final: 0.8044 (t-90) REVERT: 3 89 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7789 (mmmt) REVERT: 3 118 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7349 (ttt90) REVERT: 3 126 VAL cc_start: 0.8197 (m) cc_final: 0.7930 (p) REVERT: 3 143 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7367 (ppt170) REVERT: 3 157 MET cc_start: 0.7671 (ttm) cc_final: 0.7080 (tpp) REVERT: 3 173 TYR cc_start: 0.8455 (p90) cc_final: 0.7759 (p90) REVERT: 3 175 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7351 (ttmm) REVERT: 3 179 GLN cc_start: 0.7736 (mt0) cc_final: 0.7475 (mt0) REVERT: 3 207 LYS cc_start: 0.8144 (tttt) cc_final: 0.7562 (ttmt) REVERT: 3 214 ASP cc_start: 0.7636 (t70) cc_final: 0.7302 (t0) REVERT: 3 220 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: 3 225 LEU cc_start: 0.7561 (mp) cc_final: 0.7358 (mt) REVERT: 3 233 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6827 (mtmm) REVERT: 3 247 ASN cc_start: 0.8171 (m-40) cc_final: 0.7876 (m-40) REVERT: 3 250 TYR cc_start: 0.7707 (t80) cc_final: 0.7174 (t80) REVERT: 3 268 ASP cc_start: 0.7042 (p0) cc_final: 0.6677 (p0) REVERT: 3 282 ASN cc_start: 0.8012 (t0) cc_final: 0.7732 (t0) REVERT: 3 289 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5706 (pt0) REVERT: 3 300 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7630 (mtt90) REVERT: 4 16 PHE cc_start: 0.7528 (t80) cc_final: 0.7232 (t80) REVERT: 4 18 SER cc_start: 0.7927 (p) cc_final: 0.7410 (p) REVERT: 4 19 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7075 (p) REVERT: 4 23 ARG cc_start: 0.6925 (mtm180) cc_final: 0.6383 (mtm-85) REVERT: 4 46 MET cc_start: 0.7926 (tpt) cc_final: 0.7615 (tpt) REVERT: 4 53 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7512 (m) REVERT: 4 55 LYS cc_start: 0.7047 (mtmt) cc_final: 0.6803 (mtmm) REVERT: 4 62 TYR cc_start: 0.7875 (t80) cc_final: 0.7609 (t80) REVERT: 4 64 ASN cc_start: 0.7528 (m-40) cc_final: 0.7247 (m-40) REVERT: 4 83 GLU cc_start: 0.7323 (tt0) cc_final: 0.6252 (tt0) REVERT: 4 98 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7862 (mm) REVERT: 4 109 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: 4 133 ILE cc_start: 0.6833 (mt) cc_final: 0.6630 (mm) REVERT: 4 149 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4878 (t) REVERT: 4 154 TRP cc_start: 0.7475 (t60) cc_final: 0.7075 (t60) REVERT: 4 155 LEU cc_start: 0.8123 (mt) cc_final: 0.7865 (mm) REVERT: 4 192 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7423 (p) REVERT: 4 220 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: 4 227 ASN cc_start: 0.6222 (m-40) cc_final: 0.6015 (p0) REVERT: 4 238 SER cc_start: 0.7646 (p) cc_final: 0.7398 (p) REVERT: 4 239 GLN cc_start: 0.6386 (mp10) cc_final: 0.6182 (mp10) REVERT: 4 242 MET cc_start: 0.7918 (tpp) cc_final: 0.7676 (tpt) REVERT: 4 247 ASN cc_start: 0.7610 (m-40) cc_final: 0.7310 (t0) REVERT: 4 253 SER cc_start: 0.7753 (p) cc_final: 0.7420 (p) REVERT: 4 271 PHE cc_start: 0.7634 (t80) cc_final: 0.7377 (t80) REVERT: 4 274 LYS cc_start: 0.7871 (mttt) cc_final: 0.7387 (mttt) REVERT: 4 279 ASP cc_start: 0.7729 (p0) cc_final: 0.7462 (t70) REVERT: 4 295 THR cc_start: 0.7989 (p) cc_final: 0.7538 (p) REVERT: 4 298 MET cc_start: 0.6436 (mtt) cc_final: 0.5909 (mtt) REVERT: 5 60 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6684 (mmtt) REVERT: 5 105 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6508 (mm) REVERT: 5 109 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3279 (tt0) REVERT: 5 142 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4552 (mm-30) REVERT: 5 171 MET cc_start: 0.7619 (mtp) cc_final: 0.6815 (mtp) REVERT: 5 215 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6911 (tmtt) REVERT: 6 19 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7228 (p) REVERT: 6 30 ASP cc_start: 0.6853 (m-30) cc_final: 0.6504 (m-30) REVERT: 6 33 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7638 (ttp-110) REVERT: 6 53 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7181 (m) REVERT: 6 62 TYR cc_start: 0.7766 (t80) cc_final: 0.7352 (t80) REVERT: 6 64 ASN cc_start: 0.6537 (m-40) cc_final: 0.6290 (m110) REVERT: 6 76 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6194 (mm) REVERT: 6 83 GLU cc_start: 0.7076 (tt0) cc_final: 0.6842 (tt0) REVERT: 6 96 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6973 (mt-10) REVERT: 6 105 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7235 (pt) REVERT: 6 111 ASP cc_start: 0.7032 (t70) cc_final: 0.6707 (t0) REVERT: 6 134 ASP cc_start: 0.6673 (t0) cc_final: 0.6094 (t0) REVERT: 6 137 GLN cc_start: 0.7960 (pm20) cc_final: 0.6833 (pm20) REVERT: 6 141 GLU cc_start: 0.7220 (tt0) cc_final: 0.6465 (tt0) REVERT: 6 149 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7302 (p) REVERT: 6 150 GLN cc_start: 0.7514 (mt0) cc_final: 0.7227 (mt0) REVERT: 6 156 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7302 (ttpp) REVERT: 6 158 ILE cc_start: 0.7359 (tp) cc_final: 0.7098 (mm) REVERT: 6 164 CYS cc_start: 0.7742 (t) cc_final: 0.7164 (p) REVERT: 6 171 MET cc_start: 0.8255 (mtp) cc_final: 0.7951 (mmm) REVERT: 6 175 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7424 (ttmm) REVERT: 6 181 ASN cc_start: 0.7956 (t0) cc_final: 0.7737 (t0) REVERT: 6 187 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7258 (tpp80) REVERT: 6 189 SER cc_start: 0.8548 (p) cc_final: 0.8161 (m) REVERT: 6 191 GLN cc_start: 0.7939 (mt0) cc_final: 0.7715 (mt0) REVERT: 6 192 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8182 (t) REVERT: 6 198 SER cc_start: 0.7506 (p) cc_final: 0.6927 (t) REVERT: 6 231 GLN cc_start: 0.8344 (tt0) cc_final: 0.8017 (tt0) REVERT: 6 233 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7501 (mmtm) REVERT: 6 234 LEU cc_start: 0.8154 (mt) cc_final: 0.7933 (mt) REVERT: 6 242 MET cc_start: 0.8142 (tpp) cc_final: 0.7682 (tmm) REVERT: 6 255 GLU cc_start: 0.7122 (tp30) cc_final: 0.6651 (tt0) REVERT: 6 268 ASP cc_start: 0.8177 (p0) cc_final: 0.7148 (p0) REVERT: 6 274 LYS cc_start: 0.7962 (mttt) cc_final: 0.7717 (mmtt) REVERT: 6 283 SER cc_start: 0.8121 (p) cc_final: 0.7791 (t) REVERT: 7 24 LYS cc_start: 0.7684 (tttt) cc_final: 0.7272 (ttpp) REVERT: 7 28 TYR cc_start: 0.8021 (m-10) cc_final: 0.7769 (m-10) REVERT: 7 33 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6938 (ttm170) REVERT: 7 38 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6967 (mt) REVERT: 7 39 GLU cc_start: 0.7686 (mp0) cc_final: 0.6861 (mp0) REVERT: 7 41 GLU cc_start: 0.7547 (tt0) cc_final: 0.7244 (tt0) REVERT: 7 43 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7165 (m) REVERT: 7 44 CYS cc_start: 0.7985 (m) cc_final: 0.7598 (m) REVERT: 7 83 GLU cc_start: 0.7206 (tt0) cc_final: 0.6898 (mt-10) REVERT: 7 86 ASP cc_start: 0.8378 (t70) cc_final: 0.8053 (t0) REVERT: 7 98 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6391 (mm) REVERT: 7 111 ASP cc_start: 0.6858 (t70) cc_final: 0.6523 (t70) REVERT: 7 115 LEU cc_start: 0.6541 (pp) cc_final: 0.6334 (pp) REVERT: 7 119 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7477 (pt) REVERT: 7 146 ARG cc_start: 0.7566 (ptm160) cc_final: 0.7225 (ptm160) REVERT: 7 147 VAL cc_start: 0.7468 (m) cc_final: 0.7218 (p) REVERT: 7 156 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7089 (tttm) REVERT: 7 157 MET cc_start: 0.7693 (ttm) cc_final: 0.7164 (ttm) REVERT: 7 160 ASN cc_start: 0.7611 (m-40) cc_final: 0.7263 (p0) REVERT: 7 166 ILE cc_start: 0.8259 (mt) cc_final: 0.7921 (tp) REVERT: 7 175 LYS cc_start: 0.7369 (ttmt) cc_final: 0.7080 (ttmt) REVERT: 7 181 ASN cc_start: 0.7465 (t0) cc_final: 0.6991 (t0) REVERT: 7 192 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (t) REVERT: 7 214 ASP cc_start: 0.7416 (t70) cc_final: 0.7009 (t0) REVERT: 7 225 LEU cc_start: 0.7094 (mp) cc_final: 0.6577 (mt) REVERT: 7 232 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7099 (ttpp) REVERT: 7 241 ASN cc_start: 0.7234 (t0) cc_final: 0.6996 (t0) REVERT: 7 246 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7332 (mmm160) REVERT: 7 250 TYR cc_start: 0.7774 (t80) cc_final: 0.7238 (t80) REVERT: 7 279 ASP cc_start: 0.7862 (p0) cc_final: 0.7533 (p0) REVERT: 7 309 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6461 (mt-10) REVERT: 7 313 ARG cc_start: 0.6960 (ttp-170) cc_final: 0.6450 (ttp-170) outliers start: 224 outliers final: 72 residues processed: 883 average time/residue: 0.3810 time to fit residues: 465.2755 Evaluate side-chains 749 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 645 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 38 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 92 ASP Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 211 GLU Chi-restraints excluded: chain 1 residue 289 GLU Chi-restraints excluded: chain 1 residue 294 VAL Chi-restraints excluded: chain 2 residue 14 ARG Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 119 LEU Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 200 GLN Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 211 GLU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 32 CYS Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 119 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 211 GLU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 289 GLU Chi-restraints excluded: chain 4 residue 14 ARG Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 29 MET Chi-restraints excluded: chain 4 residue 53 VAL Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 109 GLU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 220 GLU Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 289 GLU Chi-restraints excluded: chain 4 residue 294 VAL Chi-restraints excluded: chain 5 residue 14 ARG Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 29 MET Chi-restraints excluded: chain 5 residue 32 CYS Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 77 ILE Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 109 GLU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 220 GLU Chi-restraints excluded: chain 5 residue 263 THR Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 5 residue 293 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 14 ARG Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 32 CYS Chi-restraints excluded: chain 6 residue 53 VAL Chi-restraints excluded: chain 6 residue 76 ILE Chi-restraints excluded: chain 6 residue 105 LEU Chi-restraints excluded: chain 6 residue 119 LEU Chi-restraints excluded: chain 6 residue 120 THR Chi-restraints excluded: chain 6 residue 123 ILE Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 211 GLU Chi-restraints excluded: chain 6 residue 263 THR Chi-restraints excluded: chain 6 residue 289 GLU Chi-restraints excluded: chain 6 residue 293 GLU Chi-restraints excluded: chain 6 residue 294 VAL Chi-restraints excluded: chain 7 residue 14 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 123 ILE Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 270 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 138 HIS ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 138 HIS 2 231 GLN 2 261 HIS ** 3 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 150 GLN 3 259 ASN 4 138 HIS 4 259 ASN 5 138 HIS 6 138 HIS 6 150 GLN ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18772 Z= 0.247 Angle : 0.679 12.204 25612 Z= 0.343 Chirality : 0.042 0.155 2863 Planarity : 0.004 0.045 3122 Dihedral : 18.347 87.888 3267 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.18 % Allowed : 23.72 % Favored : 70.10 % 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: -2.28 (0.17), residues: 2163 helix: -0.50 (0.14), residues: 1190 sheet: -3.01 (0.33), residues: 238 loop : -2.53 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 6 154 HIS 0.006 0.001 HIS 4 261 PHE 0.021 0.002 PHE 3 206 TYR 0.021 0.002 TYR 6 199 ARG 0.007 0.001 ARG 1 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 670 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.6657 (t) REVERT: 1 22 VAL cc_start: 0.6484 (t) cc_final: 0.6251 (p) REVERT: 1 26 LEU cc_start: 0.6939 (mt) cc_final: 0.6632 (mt) REVERT: 1 30 ASP cc_start: 0.6981 (m-30) cc_final: 0.6662 (m-30) REVERT: 1 37 ASP cc_start: 0.7943 (p0) cc_final: 0.7075 (p0) REVERT: 1 38 LEU cc_start: 0.7352 (mp) cc_final: 0.6836 (mt) REVERT: 1 39 GLU cc_start: 0.6488 (mp0) cc_final: 0.5242 (mp0) REVERT: 1 45 MET cc_start: 0.8525 (ttm) cc_final: 0.8278 (ttp) REVERT: 1 46 MET cc_start: 0.8039 (tpt) cc_final: 0.7684 (tpp) REVERT: 1 65 GLN cc_start: 0.7436 (pt0) cc_final: 0.7135 (pp30) REVERT: 1 83 GLU cc_start: 0.7839 (tt0) cc_final: 0.7350 (mt-10) REVERT: 1 92 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.7081 (t0) REVERT: 1 100 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7139 (tm-30) REVERT: 1 101 MET cc_start: 0.8123 (ttp) cc_final: 0.7650 (ttp) REVERT: 1 109 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6514 (tt0) REVERT: 1 114 ARG cc_start: 0.7318 (ptp90) cc_final: 0.7057 (mtm-85) REVERT: 1 129 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7981 (mtpt) REVERT: 1 134 ASP cc_start: 0.7326 (t0) cc_final: 0.6833 (t0) REVERT: 1 150 GLN cc_start: 0.7921 (mt0) cc_final: 0.7649 (mt0) REVERT: 1 163 LYS cc_start: 0.8383 (mptt) cc_final: 0.8182 (mmtp) REVERT: 1 168 ILE cc_start: 0.8187 (pt) cc_final: 0.7926 (pt) REVERT: 1 175 LYS cc_start: 0.7490 (ttmt) cc_final: 0.7270 (ttpp) REVERT: 1 187 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7427 (mtt-85) REVERT: 1 192 VAL cc_start: 0.8239 (t) cc_final: 0.7946 (m) REVERT: 1 193 GLU cc_start: 0.8003 (tp30) cc_final: 0.7501 (tp30) REVERT: 1 261 HIS cc_start: 0.6306 (m170) cc_final: 0.5947 (m90) REVERT: 1 271 PHE cc_start: 0.7163 (t80) cc_final: 0.6910 (t80) REVERT: 1 274 LYS cc_start: 0.8022 (mttt) cc_final: 0.7739 (mtpp) REVERT: 1 280 LYS cc_start: 0.7348 (mmtm) cc_final: 0.7112 (mmmt) REVERT: 1 285 LYS cc_start: 0.7315 (tppt) cc_final: 0.6813 (tppt) REVERT: 1 300 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7421 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7405 (m-30) cc_final: 0.7108 (m-30) REVERT: 2 6 GLU cc_start: 0.7244 (pm20) cc_final: 0.6346 (tm-30) REVERT: 2 23 ARG cc_start: 0.7235 (mtm180) cc_final: 0.6935 (mtm-85) REVERT: 2 33 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7432 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6061 (mp0) cc_final: 0.5611 (mp0) REVERT: 2 40 SER cc_start: 0.7193 (m) cc_final: 0.6714 (t) REVERT: 2 41 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: 2 46 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: 2 89 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7199 (mmmt) REVERT: 2 96 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7214 (tp30) REVERT: 2 100 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7370 (tm-30) REVERT: 2 101 MET cc_start: 0.7001 (ttp) cc_final: 0.6770 (ttp) REVERT: 2 122 LEU cc_start: 0.7565 (tp) cc_final: 0.7271 (tp) REVERT: 2 129 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7946 (mmpt) REVERT: 2 141 GLU cc_start: 0.7048 (tt0) cc_final: 0.6420 (tm-30) REVERT: 2 150 GLN cc_start: 0.7711 (mt0) cc_final: 0.6739 (mm110) REVERT: 2 163 LYS cc_start: 0.8011 (mppt) cc_final: 0.7599 (mmtm) REVERT: 2 181 ASN cc_start: 0.7211 (t0) cc_final: 0.6506 (t0) REVERT: 2 262 GLU cc_start: 0.6517 (mp0) cc_final: 0.6157 (mp0) REVERT: 2 286 ASN cc_start: 0.8676 (t0) cc_final: 0.8182 (t0) REVERT: 3 34 ASP cc_start: 0.7482 (m-30) cc_final: 0.6970 (m-30) REVERT: 3 38 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7632 (mm) REVERT: 3 39 GLU cc_start: 0.7105 (mp0) cc_final: 0.6603 (mp0) REVERT: 3 46 MET cc_start: 0.8138 (tpt) cc_final: 0.7708 (tpp) REVERT: 3 61 LYS cc_start: 0.7994 (tptp) cc_final: 0.7625 (tptp) REVERT: 3 89 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7806 (mmmt) REVERT: 3 118 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7559 (ttt180) REVERT: 3 143 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7441 (ppt170) REVERT: 3 157 MET cc_start: 0.7821 (ttm) cc_final: 0.7121 (tpp) REVERT: 3 171 MET cc_start: 0.7865 (mtp) cc_final: 0.7641 (mtm) REVERT: 3 173 TYR cc_start: 0.8448 (p90) cc_final: 0.8013 (p90) REVERT: 3 175 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7557 (ttmm) REVERT: 3 195 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7336 (mtp-110) REVERT: 3 207 LYS cc_start: 0.8114 (tttt) cc_final: 0.7537 (ttmt) REVERT: 3 233 LYS cc_start: 0.7526 (mtpt) cc_final: 0.7029 (mtmm) REVERT: 3 241 ASN cc_start: 0.7513 (m-40) cc_final: 0.7087 (t0) REVERT: 3 247 ASN cc_start: 0.8210 (m-40) cc_final: 0.7919 (m-40) REVERT: 3 259 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6478 (p0) REVERT: 3 268 ASP cc_start: 0.7043 (p0) cc_final: 0.6647 (p0) REVERT: 3 279 ASP cc_start: 0.7343 (p0) cc_final: 0.7138 (p0) REVERT: 3 282 ASN cc_start: 0.8003 (t0) cc_final: 0.7688 (t0) REVERT: 3 300 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7994 (ptp90) REVERT: 4 19 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7332 (p) REVERT: 4 23 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6585 (mtm110) REVERT: 4 24 LYS cc_start: 0.7216 (tttt) cc_final: 0.6852 (tptp) REVERT: 4 29 MET cc_start: 0.7566 (mtt) cc_final: 0.7092 (mmp) REVERT: 4 46 MET cc_start: 0.7682 (tpt) cc_final: 0.7268 (tpt) REVERT: 4 62 TYR cc_start: 0.7797 (t80) cc_final: 0.7450 (t80) REVERT: 4 83 GLU cc_start: 0.7561 (tt0) cc_final: 0.6592 (tt0) REVERT: 4 114 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7331 (ttp80) REVERT: 4 118 ARG cc_start: 0.7011 (ttm170) cc_final: 0.6775 (mtp180) REVERT: 4 137 GLN cc_start: 0.7791 (pm20) cc_final: 0.6721 (pt0) REVERT: 4 149 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.5004 (t) REVERT: 4 154 TRP cc_start: 0.7498 (t60) cc_final: 0.7137 (t60) REVERT: 4 155 LEU cc_start: 0.8259 (mt) cc_final: 0.8018 (mm) REVERT: 4 168 ILE cc_start: 0.6595 (pt) cc_final: 0.6374 (pt) REVERT: 4 171 MET cc_start: 0.8266 (mtp) cc_final: 0.7828 (mtp) REVERT: 4 194 LEU cc_start: 0.7524 (tt) cc_final: 0.7307 (tt) REVERT: 4 242 MET cc_start: 0.7810 (tpp) cc_final: 0.7466 (tpt) REVERT: 4 247 ASN cc_start: 0.7575 (m-40) cc_final: 0.7205 (t0) REVERT: 4 253 SER cc_start: 0.7701 (p) cc_final: 0.7482 (p) REVERT: 4 262 GLU cc_start: 0.6897 (mp0) cc_final: 0.6512 (mp0) REVERT: 4 271 PHE cc_start: 0.7584 (t80) cc_final: 0.7378 (t80) REVERT: 4 286 ASN cc_start: 0.7854 (t0) cc_final: 0.7591 (t0) REVERT: 4 295 THR cc_start: 0.8092 (p) cc_final: 0.7875 (t) REVERT: 4 298 MET cc_start: 0.6394 (mtt) cc_final: 0.6173 (mtt) REVERT: 4 304 LYS cc_start: 0.7199 (tppt) cc_final: 0.6891 (tppt) REVERT: 5 55 LYS cc_start: 0.6385 (mtmm) cc_final: 0.5913 (mtmm) REVERT: 5 60 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6862 (mmtt) REVERT: 5 84 LEU cc_start: 0.6959 (mp) cc_final: 0.6728 (mt) REVERT: 5 105 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6355 (mm) REVERT: 5 118 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7592 (ttm170) REVERT: 5 129 LYS cc_start: 0.7102 (mtpt) cc_final: 0.6365 (mptt) REVERT: 5 171 MET cc_start: 0.7590 (mtp) cc_final: 0.6834 (mtp) REVERT: 5 215 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7005 (tmtt) REVERT: 5 241 ASN cc_start: 0.6981 (t0) cc_final: 0.6470 (t0) REVERT: 6 19 THR cc_start: 0.7474 (p) cc_final: 0.7258 (p) REVERT: 6 30 ASP cc_start: 0.6703 (m-30) cc_final: 0.6442 (m-30) REVERT: 6 41 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7823 (mm-30) REVERT: 6 64 ASN cc_start: 0.5842 (m-40) cc_final: 0.5622 (m110) REVERT: 6 111 ASP cc_start: 0.7464 (t70) cc_final: 0.6854 (t0) REVERT: 6 134 ASP cc_start: 0.6916 (t0) cc_final: 0.6507 (t0) REVERT: 6 135 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7258 (mm-30) REVERT: 6 141 GLU cc_start: 0.6914 (tt0) cc_final: 0.6394 (tt0) REVERT: 6 143 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7428 (ppt170) REVERT: 6 146 ARG cc_start: 0.7498 (ptm160) cc_final: 0.7265 (ptm-80) REVERT: 6 149 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7497 (p) REVERT: 6 150 GLN cc_start: 0.7619 (mt0) cc_final: 0.7321 (mt0) REVERT: 6 175 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7387 (ttmm) REVERT: 6 188 PHE cc_start: 0.8249 (m-80) cc_final: 0.7924 (m-80) REVERT: 6 189 SER cc_start: 0.8626 (p) cc_final: 0.8125 (m) REVERT: 6 198 SER cc_start: 0.7866 (p) cc_final: 0.7662 (p) REVERT: 6 255 GLU cc_start: 0.7171 (tp30) cc_final: 0.6894 (tt0) REVERT: 6 268 ASP cc_start: 0.7928 (p0) cc_final: 0.6562 (p0) REVERT: 6 283 SER cc_start: 0.8240 (p) cc_final: 0.8030 (t) REVERT: 7 24 LYS cc_start: 0.7582 (tttt) cc_final: 0.7245 (ttpp) REVERT: 7 39 GLU cc_start: 0.7654 (mp0) cc_final: 0.6839 (mp0) REVERT: 7 41 GLU cc_start: 0.7465 (tt0) cc_final: 0.7233 (tt0) REVERT: 7 43 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7377 (m) REVERT: 7 44 CYS cc_start: 0.8098 (m) cc_final: 0.7791 (m) REVERT: 7 48 TYR cc_start: 0.8068 (m-80) cc_final: 0.7857 (m-80) REVERT: 7 60 LYS cc_start: 0.7461 (mtpp) cc_final: 0.7212 (mttp) REVERT: 7 83 GLU cc_start: 0.7039 (tt0) cc_final: 0.6787 (mt-10) REVERT: 7 86 ASP cc_start: 0.8263 (t70) cc_final: 0.7911 (t0) REVERT: 7 95 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7160 (ptm160) REVERT: 7 107 LEU cc_start: 0.7844 (pt) cc_final: 0.7604 (pt) REVERT: 7 111 ASP cc_start: 0.7218 (t70) cc_final: 0.6915 (t70) REVERT: 7 129 LYS cc_start: 0.7696 (mmmm) cc_final: 0.7370 (mttp) REVERT: 7 146 ARG cc_start: 0.7629 (ptm160) cc_final: 0.7336 (ptm160) REVERT: 7 156 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7360 (tttp) REVERT: 7 166 ILE cc_start: 0.8217 (mt) cc_final: 0.7905 (tp) REVERT: 7 181 ASN cc_start: 0.7435 (t0) cc_final: 0.7149 (t0) REVERT: 7 232 LYS cc_start: 0.7457 (ttmm) cc_final: 0.6840 (ttpp) REVERT: 7 271 PHE cc_start: 0.7993 (t80) cc_final: 0.7748 (t80) outliers start: 116 outliers final: 63 residues processed: 722 average time/residue: 0.3868 time to fit residues: 385.1739 Evaluate side-chains 719 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 641 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 92 ASP Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 61 LYS Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 211 GLU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 2 residue 314 HIS Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 199 TYR Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 149 THR Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 6 residue 6 GLU Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 118 ARG Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 143 ARG Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 241 ASN Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 77 ILE Chi-restraints excluded: chain 7 residue 99 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 199 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN 1 179 GLN ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 GLN 3 138 HIS 4 160 ASN 4 259 ASN 6 160 ASN ** 6 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 87 ASN ** 7 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 247 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18772 Z= 0.206 Angle : 0.615 10.360 25612 Z= 0.309 Chirality : 0.040 0.161 2863 Planarity : 0.004 0.040 3122 Dihedral : 17.008 89.067 3140 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.56 % Allowed : 25.53 % Favored : 67.91 % 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: -1.64 (0.18), residues: 2163 helix: 0.05 (0.15), residues: 1183 sheet: -2.68 (0.34), residues: 238 loop : -2.31 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 6 154 HIS 0.003 0.001 HIS 1 261 PHE 0.016 0.001 PHE 1 237 TYR 0.016 0.001 TYR 6 199 ARG 0.007 0.001 ARG 1 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 637 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 19 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.6605 (t) REVERT: 1 23 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7059 (mtm-85) REVERT: 1 30 ASP cc_start: 0.7069 (m-30) cc_final: 0.6787 (m-30) REVERT: 1 37 ASP cc_start: 0.7936 (p0) cc_final: 0.7153 (p0) REVERT: 1 39 GLU cc_start: 0.6495 (mp0) cc_final: 0.5305 (mp0) REVERT: 1 45 MET cc_start: 0.8546 (ttm) cc_final: 0.8294 (ttp) REVERT: 1 46 MET cc_start: 0.7975 (tpt) cc_final: 0.7775 (tpt) REVERT: 1 57 THR cc_start: 0.7606 (t) cc_final: 0.7351 (t) REVERT: 1 65 GLN cc_start: 0.7416 (pt0) cc_final: 0.7106 (pp30) REVERT: 1 83 GLU cc_start: 0.7876 (tt0) cc_final: 0.7442 (mt-10) REVERT: 1 100 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7127 (tm-30) REVERT: 1 101 MET cc_start: 0.8135 (ttp) cc_final: 0.7794 (ttp) REVERT: 1 109 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: 1 129 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7939 (mtpt) REVERT: 1 150 GLN cc_start: 0.7914 (mt0) cc_final: 0.7614 (mt0) REVERT: 1 163 LYS cc_start: 0.8258 (mptt) cc_final: 0.7902 (mmtm) REVERT: 1 168 ILE cc_start: 0.8152 (pt) cc_final: 0.7835 (pt) REVERT: 1 175 LYS cc_start: 0.7493 (ttmt) cc_final: 0.7249 (ttpp) REVERT: 1 179 GLN cc_start: 0.7350 (mt0) cc_final: 0.7149 (mt0) REVERT: 1 192 VAL cc_start: 0.8264 (t) cc_final: 0.7995 (m) REVERT: 1 193 GLU cc_start: 0.7998 (tp30) cc_final: 0.7510 (tp30) REVERT: 1 242 MET cc_start: 0.7573 (tpt) cc_final: 0.7250 (tpt) REVERT: 1 274 LYS cc_start: 0.8023 (mttt) cc_final: 0.7739 (mtpp) REVERT: 1 285 LYS cc_start: 0.7406 (tppt) cc_final: 0.6893 (tppt) REVERT: 1 300 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: 1 310 ASP cc_start: 0.7440 (m-30) cc_final: 0.7135 (m-30) REVERT: 2 6 GLU cc_start: 0.7186 (pm20) cc_final: 0.6283 (tm-30) REVERT: 2 23 ARG cc_start: 0.7243 (mtm180) cc_final: 0.6952 (mtm-85) REVERT: 2 33 ARG cc_start: 0.7821 (ttp80) cc_final: 0.7606 (ttp-170) REVERT: 2 41 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: 2 46 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7693 (ttt) REVERT: 2 89 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7199 (mmmt) REVERT: 2 96 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7207 (tp30) REVERT: 2 100 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7474 (tm-30) REVERT: 2 101 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6768 (ptm) REVERT: 2 122 LEU cc_start: 0.7583 (tp) cc_final: 0.7299 (tp) REVERT: 2 129 LYS cc_start: 0.8173 (mmpt) cc_final: 0.7946 (mmpt) REVERT: 2 150 GLN cc_start: 0.7716 (mt0) cc_final: 0.6905 (mt0) REVERT: 2 162 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7968 (p) REVERT: 2 163 LYS cc_start: 0.7996 (mppt) cc_final: 0.7566 (mmtm) REVERT: 2 171 MET cc_start: 0.8763 (mtp) cc_final: 0.8512 (mmm) REVERT: 2 181 ASN cc_start: 0.7102 (t0) cc_final: 0.6355 (t0) REVERT: 2 235 TYR cc_start: 0.7597 (t80) cc_final: 0.7131 (t80) REVERT: 2 242 MET cc_start: 0.7022 (mmm) cc_final: 0.6674 (tmm) REVERT: 2 262 GLU cc_start: 0.6587 (mp0) cc_final: 0.6209 (mp0) REVERT: 2 286 ASN cc_start: 0.8682 (t0) cc_final: 0.8328 (t0) REVERT: 2 309 GLU cc_start: 0.6640 (pm20) cc_final: 0.6348 (tm-30) REVERT: 2 313 ARG cc_start: 0.7270 (ttp-170) cc_final: 0.6863 (ttp-110) REVERT: 3 30 ASP cc_start: 0.7858 (m-30) cc_final: 0.7479 (m-30) REVERT: 3 34 ASP cc_start: 0.7522 (m-30) cc_final: 0.6966 (m-30) REVERT: 3 38 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7576 (mm) REVERT: 3 39 GLU cc_start: 0.6999 (mp0) cc_final: 0.6508 (mp0) REVERT: 3 46 MET cc_start: 0.8114 (tpt) cc_final: 0.7625 (tpp) REVERT: 3 61 LYS cc_start: 0.7998 (tptp) cc_final: 0.7653 (tptp) REVERT: 3 87 ASN cc_start: 0.7923 (t0) cc_final: 0.7480 (t0) REVERT: 3 89 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7847 (mmtt) REVERT: 3 92 ASP cc_start: 0.7542 (t0) cc_final: 0.7238 (t0) REVERT: 3 121 GLU cc_start: 0.6319 (mt-10) cc_final: 0.6048 (mt-10) REVERT: 3 157 MET cc_start: 0.7806 (ttm) cc_final: 0.7198 (tpp) REVERT: 3 171 MET cc_start: 0.7853 (mtp) cc_final: 0.7645 (mtm) REVERT: 3 173 TYR cc_start: 0.8591 (p90) cc_final: 0.8112 (p90) REVERT: 3 175 LYS cc_start: 0.7793 (ttmt) cc_final: 0.7432 (ttmm) REVERT: 3 207 LYS cc_start: 0.8104 (tttt) cc_final: 0.7382 (ttmm) REVERT: 3 233 LYS cc_start: 0.7591 (mtpt) cc_final: 0.7107 (mtmm) REVERT: 3 241 ASN cc_start: 0.7530 (m-40) cc_final: 0.7005 (t0) REVERT: 3 242 MET cc_start: 0.7948 (mmm) cc_final: 0.7671 (tmm) REVERT: 3 247 ASN cc_start: 0.8184 (m-40) cc_final: 0.7942 (m-40) REVERT: 3 250 TYR cc_start: 0.7515 (t80) cc_final: 0.6937 (t80) REVERT: 3 259 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6857 (p0) REVERT: 3 268 ASP cc_start: 0.7170 (p0) cc_final: 0.6658 (p0) REVERT: 3 269 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.4922 (t80) REVERT: 3 282 ASN cc_start: 0.8134 (t0) cc_final: 0.7860 (t0) REVERT: 4 14 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7477 (ptp90) REVERT: 4 19 THR cc_start: 0.7709 (p) cc_final: 0.7330 (p) REVERT: 4 23 ARG cc_start: 0.6708 (mtm180) cc_final: 0.6268 (mtm110) REVERT: 4 25 ILE cc_start: 0.7145 (mm) cc_final: 0.6938 (tp) REVERT: 4 29 MET cc_start: 0.7539 (mtt) cc_final: 0.7058 (mmp) REVERT: 4 33 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7405 (ttp80) REVERT: 4 46 MET cc_start: 0.7786 (tpt) cc_final: 0.7310 (tpt) REVERT: 4 62 TYR cc_start: 0.7792 (t80) cc_final: 0.7393 (t80) REVERT: 4 83 GLU cc_start: 0.7522 (tt0) cc_final: 0.6517 (tt0) REVERT: 4 114 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7408 (ptt90) REVERT: 4 118 ARG cc_start: 0.7059 (ttm170) cc_final: 0.6743 (mtp180) REVERT: 4 121 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7312 (mt-10) REVERT: 4 150 GLN cc_start: 0.8005 (mt0) cc_final: 0.7558 (mp10) REVERT: 4 154 TRP cc_start: 0.7537 (t60) cc_final: 0.7150 (t60) REVERT: 4 155 LEU cc_start: 0.8246 (mt) cc_final: 0.8044 (mm) REVERT: 4 168 ILE cc_start: 0.6633 (pt) cc_final: 0.6418 (pt) REVERT: 4 193 GLU cc_start: 0.7507 (tp30) cc_final: 0.7009 (tp30) REVERT: 4 194 LEU cc_start: 0.7424 (tt) cc_final: 0.7111 (tt) REVERT: 4 195 ARG cc_start: 0.6909 (ptm160) cc_final: 0.6596 (ptp-110) REVERT: 4 247 ASN cc_start: 0.7563 (m-40) cc_final: 0.7268 (t0) REVERT: 4 262 GLU cc_start: 0.6913 (mp0) cc_final: 0.6543 (mp0) REVERT: 4 271 PHE cc_start: 0.7544 (t80) cc_final: 0.7245 (t80) REVERT: 4 274 LYS cc_start: 0.7780 (mttt) cc_final: 0.7294 (mtmm) REVERT: 4 279 ASP cc_start: 0.7854 (p0) cc_final: 0.7376 (t70) REVERT: 4 286 ASN cc_start: 0.7870 (t0) cc_final: 0.7585 (t0) REVERT: 4 304 LYS cc_start: 0.7351 (tppt) cc_final: 0.6830 (tppt) REVERT: 5 55 LYS cc_start: 0.6365 (mtmm) cc_final: 0.5903 (mtmm) REVERT: 5 60 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6898 (mmtt) REVERT: 5 105 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6319 (mm) REVERT: 5 129 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6389 (mptt) REVERT: 5 171 MET cc_start: 0.7592 (mtp) cc_final: 0.6871 (mtp) REVERT: 5 215 LYS cc_start: 0.7408 (mmtt) cc_final: 0.6989 (tmtt) REVERT: 5 241 ASN cc_start: 0.6975 (t0) cc_final: 0.6521 (t0) REVERT: 6 5 ARG cc_start: 0.5640 (tpp80) cc_final: 0.5414 (tpp-160) REVERT: 6 30 ASP cc_start: 0.6630 (m-30) cc_final: 0.6406 (m-30) REVERT: 6 41 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8003 (mm-30) REVERT: 6 46 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7630 (tpt) REVERT: 6 64 ASN cc_start: 0.5876 (m-40) cc_final: 0.5648 (m-40) REVERT: 6 107 LEU cc_start: 0.7198 (pt) cc_final: 0.6887 (tp) REVERT: 6 111 ASP cc_start: 0.7481 (t70) cc_final: 0.7246 (t0) REVERT: 6 115 LEU cc_start: 0.6815 (pp) cc_final: 0.6446 (tp) REVERT: 6 134 ASP cc_start: 0.6869 (t0) cc_final: 0.6462 (t0) REVERT: 6 135 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7069 (mm-30) REVERT: 6 146 ARG cc_start: 0.7536 (ptm160) cc_final: 0.7280 (ptm160) REVERT: 6 149 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7214 (p) REVERT: 6 150 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: 6 162 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7722 (p) REVERT: 6 164 CYS cc_start: 0.7853 (t) cc_final: 0.7385 (p) REVERT: 6 171 MET cc_start: 0.8167 (mtp) cc_final: 0.7890 (mmt) REVERT: 6 175 LYS cc_start: 0.7562 (ttmt) cc_final: 0.7310 (ttmm) REVERT: 6 188 PHE cc_start: 0.8281 (m-80) cc_final: 0.7926 (m-80) REVERT: 6 189 SER cc_start: 0.8557 (p) cc_final: 0.8149 (m) REVERT: 6 192 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8276 (t) REVERT: 6 198 SER cc_start: 0.7579 (p) cc_final: 0.6996 (t) REVERT: 6 242 MET cc_start: 0.8186 (tpp) cc_final: 0.7948 (mmm) REVERT: 6 255 GLU cc_start: 0.6954 (tp30) cc_final: 0.6227 (mm-30) REVERT: 7 24 LYS cc_start: 0.7572 (tttt) cc_final: 0.7309 (ttpp) REVERT: 7 33 ARG cc_start: 0.7444 (ttp80) cc_final: 0.6776 (ttm170) REVERT: 7 39 GLU cc_start: 0.7581 (mp0) cc_final: 0.6818 (mp0) REVERT: 7 41 GLU cc_start: 0.7479 (tt0) cc_final: 0.7247 (tt0) REVERT: 7 43 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7211 (m) REVERT: 7 44 CYS cc_start: 0.7987 (m) cc_final: 0.7639 (m) REVERT: 7 45 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: 7 48 TYR cc_start: 0.8043 (m-80) cc_final: 0.7630 (m-80) REVERT: 7 83 GLU cc_start: 0.7228 (tt0) cc_final: 0.6918 (mt-10) REVERT: 7 86 ASP cc_start: 0.7992 (t70) cc_final: 0.7744 (t0) REVERT: 7 111 ASP cc_start: 0.7249 (t70) cc_final: 0.6975 (t70) REVERT: 7 129 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7499 (mttp) REVERT: 7 146 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7401 (ptm160) REVERT: 7 156 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7344 (tttp) REVERT: 7 162 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7585 (p) REVERT: 7 166 ILE cc_start: 0.8225 (mt) cc_final: 0.7927 (tp) REVERT: 7 175 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7270 (ttmt) REVERT: 7 181 ASN cc_start: 0.7699 (t0) cc_final: 0.7403 (t0) REVERT: 7 193 GLU cc_start: 0.8126 (tp30) cc_final: 0.7869 (tp30) REVERT: 7 232 LYS cc_start: 0.7472 (ttmm) cc_final: 0.6817 (ttpp) REVERT: 7 247 ASN cc_start: 0.7644 (m-40) cc_final: 0.7306 (m-40) REVERT: 7 271 PHE cc_start: 0.7965 (t80) cc_final: 0.7765 (t80) outliers start: 123 outliers final: 69 residues processed: 698 average time/residue: 0.3827 time to fit residues: 370.4471 Evaluate side-chains 704 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 616 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 109 GLU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 149 THR Chi-restraints excluded: chain 1 residue 261 HIS Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 273 SER Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 156 LYS Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 149 THR Chi-restraints excluded: chain 6 residue 150 GLN Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 179 GLN Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 241 ASN Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 40 SER Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 45 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 261 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.0870 chunk 151 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.0170 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 GLN 3 259 ASN 6 160 ASN 6 183 GLN 7 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18772 Z= 0.209 Angle : 0.607 10.746 25612 Z= 0.304 Chirality : 0.041 0.368 2863 Planarity : 0.004 0.043 3122 Dihedral : 16.444 89.752 3118 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 6.24 % Allowed : 26.12 % Favored : 67.64 % 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: -1.27 (0.19), residues: 2163 helix: 0.32 (0.15), residues: 1183 sheet: -2.43 (0.35), residues: 238 loop : -2.12 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 6 154 HIS 0.003 0.001 HIS 3 185 PHE 0.017 0.001 PHE 1 269 TYR 0.022 0.002 TYR 5 62 ARG 0.009 0.001 ARG 4 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 626 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 30 ASP cc_start: 0.7234 (m-30) cc_final: 0.6999 (m-30) REVERT: 1 33 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7759 (tmm-80) REVERT: 1 37 ASP cc_start: 0.7891 (p0) cc_final: 0.7141 (p0) REVERT: 1 38 LEU cc_start: 0.7794 (mt) cc_final: 0.7520 (mt) REVERT: 1 39 GLU cc_start: 0.6501 (mp0) cc_final: 0.5405 (mp0) REVERT: 1 57 THR cc_start: 0.7594 (t) cc_final: 0.7378 (t) REVERT: 1 65 GLN cc_start: 0.7397 (pt0) cc_final: 0.7101 (pp30) REVERT: 1 83 GLU cc_start: 0.7903 (tt0) cc_final: 0.7439 (mt-10) REVERT: 1 92 ASP cc_start: 0.7263 (t0) cc_final: 0.6926 (t0) REVERT: 1 100 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7114 (tm-30) REVERT: 1 101 MET cc_start: 0.8126 (ttp) cc_final: 0.7815 (ttp) REVERT: 1 105 LEU cc_start: 0.7708 (pp) cc_final: 0.7335 (mp) REVERT: 1 129 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7977 (mtpt) REVERT: 1 163 LYS cc_start: 0.8236 (mptt) cc_final: 0.7956 (mmtm) REVERT: 1 168 ILE cc_start: 0.8205 (pt) cc_final: 0.7940 (pt) REVERT: 1 171 MET cc_start: 0.8150 (mtp) cc_final: 0.7631 (mmm) REVERT: 1 175 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7115 (ttpp) REVERT: 1 179 GLN cc_start: 0.7376 (mt0) cc_final: 0.7117 (mt0) REVERT: 1 192 VAL cc_start: 0.8266 (t) cc_final: 0.7995 (m) REVERT: 1 193 GLU cc_start: 0.7982 (tp30) cc_final: 0.7531 (tp30) REVERT: 1 274 LYS cc_start: 0.8010 (mttt) cc_final: 0.7717 (mtpp) REVERT: 1 285 LYS cc_start: 0.7464 (tppt) cc_final: 0.6941 (tppt) REVERT: 1 297 ASP cc_start: 0.7708 (t0) cc_final: 0.7445 (t0) REVERT: 1 300 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7438 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7409 (m-30) cc_final: 0.7131 (m-30) REVERT: 2 6 GLU cc_start: 0.7188 (pm20) cc_final: 0.6272 (tm-30) REVERT: 2 23 ARG cc_start: 0.7228 (mtm180) cc_final: 0.6474 (mtm-85) REVERT: 2 33 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7626 (ttp-170) REVERT: 2 41 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: 2 46 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7676 (ttt) REVERT: 2 89 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7185 (mmmt) REVERT: 2 96 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: 2 100 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7451 (tm-30) REVERT: 2 122 LEU cc_start: 0.7442 (tp) cc_final: 0.7172 (tp) REVERT: 2 129 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7823 (mmpt) REVERT: 2 141 GLU cc_start: 0.7226 (tp30) cc_final: 0.7013 (tp30) REVERT: 2 150 GLN cc_start: 0.7695 (mt0) cc_final: 0.6925 (mt0) REVERT: 2 162 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7953 (p) REVERT: 2 163 LYS cc_start: 0.7995 (mppt) cc_final: 0.7529 (mmtm) REVERT: 2 171 MET cc_start: 0.8771 (mtp) cc_final: 0.8510 (mmm) REVERT: 2 181 ASN cc_start: 0.7213 (t0) cc_final: 0.6474 (t0) REVERT: 2 235 TYR cc_start: 0.7683 (t80) cc_final: 0.7279 (t80) REVERT: 2 262 GLU cc_start: 0.6478 (mp0) cc_final: 0.6056 (pm20) REVERT: 2 274 LYS cc_start: 0.7059 (mttm) cc_final: 0.6818 (mttm) REVERT: 2 286 ASN cc_start: 0.8667 (t0) cc_final: 0.8221 (t0) REVERT: 2 309 GLU cc_start: 0.6660 (pm20) cc_final: 0.6248 (pm20) REVERT: 2 313 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.7083 (ttp-110) REVERT: 3 30 ASP cc_start: 0.7875 (m-30) cc_final: 0.7484 (m-30) REVERT: 3 34 ASP cc_start: 0.7619 (m-30) cc_final: 0.7038 (m-30) REVERT: 3 39 GLU cc_start: 0.7009 (mp0) cc_final: 0.6502 (mp0) REVERT: 3 46 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7578 (tpp) REVERT: 3 61 LYS cc_start: 0.7985 (tptp) cc_final: 0.7358 (tptp) REVERT: 3 65 GLN cc_start: 0.8233 (pt0) cc_final: 0.7264 (pp30) REVERT: 3 87 ASN cc_start: 0.7986 (t0) cc_final: 0.7714 (t0) REVERT: 3 89 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7734 (mmmt) REVERT: 3 92 ASP cc_start: 0.7588 (t0) cc_final: 0.7248 (t0) REVERT: 3 109 GLU cc_start: 0.7802 (tt0) cc_final: 0.7483 (tt0) REVERT: 3 121 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6118 (mt-10) REVERT: 3 143 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7386 (ppt170) REVERT: 3 149 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7226 (p) REVERT: 3 150 GLN cc_start: 0.7665 (mt0) cc_final: 0.7285 (mm-40) REVERT: 3 157 MET cc_start: 0.7809 (ttm) cc_final: 0.7127 (tpp) REVERT: 3 173 TYR cc_start: 0.8594 (p90) cc_final: 0.8113 (p90) REVERT: 3 175 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7490 (ttmm) REVERT: 3 207 LYS cc_start: 0.8122 (tttt) cc_final: 0.7389 (ttmm) REVERT: 3 233 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7063 (mtmm) REVERT: 3 239 GLN cc_start: 0.7682 (mp10) cc_final: 0.7411 (mm-40) REVERT: 3 241 ASN cc_start: 0.7264 (m-40) cc_final: 0.6817 (t0) REVERT: 3 255 GLU cc_start: 0.7625 (tp30) cc_final: 0.7180 (tp30) REVERT: 3 259 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6731 (p0) REVERT: 3 268 ASP cc_start: 0.7214 (p0) cc_final: 0.6737 (p0) REVERT: 3 269 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.4929 (t80) REVERT: 3 282 ASN cc_start: 0.8149 (t0) cc_final: 0.7855 (t0) REVERT: 3 300 ARG cc_start: 0.8541 (ptp90) cc_final: 0.7925 (ptp90) REVERT: 4 14 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7415 (ptp90) REVERT: 4 19 THR cc_start: 0.7714 (p) cc_final: 0.7387 (p) REVERT: 4 23 ARG cc_start: 0.6790 (mtm180) cc_final: 0.6346 (mtm110) REVERT: 4 24 LYS cc_start: 0.7200 (tttp) cc_final: 0.6833 (tptp) REVERT: 4 25 ILE cc_start: 0.6907 (mm) cc_final: 0.6662 (mm) REVERT: 4 29 MET cc_start: 0.7559 (mtt) cc_final: 0.7067 (mmp) REVERT: 4 46 MET cc_start: 0.7698 (tpt) cc_final: 0.7190 (tpt) REVERT: 4 62 TYR cc_start: 0.7804 (t80) cc_final: 0.7411 (t80) REVERT: 4 83 GLU cc_start: 0.7553 (tt0) cc_final: 0.6550 (tt0) REVERT: 4 109 GLU cc_start: 0.7795 (pm20) cc_final: 0.7564 (pm20) REVERT: 4 114 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7462 (ptt90) REVERT: 4 121 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7417 (mt-10) REVERT: 4 137 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: 4 146 ARG cc_start: 0.6817 (ptm160) cc_final: 0.6171 (ptm160) REVERT: 4 154 TRP cc_start: 0.7611 (t60) cc_final: 0.7212 (t60) REVERT: 4 155 LEU cc_start: 0.8290 (mt) cc_final: 0.8089 (mm) REVERT: 4 168 ILE cc_start: 0.6733 (pt) cc_final: 0.6489 (pt) REVERT: 4 187 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7499 (mtm-85) REVERT: 4 190 ILE cc_start: 0.8021 (mt) cc_final: 0.7646 (pt) REVERT: 4 193 GLU cc_start: 0.7524 (tp30) cc_final: 0.6993 (tp30) REVERT: 4 194 LEU cc_start: 0.7411 (tt) cc_final: 0.7035 (tt) REVERT: 4 195 ARG cc_start: 0.6852 (ptm160) cc_final: 0.6543 (ptp-110) REVERT: 4 221 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7606 (ptpt) REVERT: 4 247 ASN cc_start: 0.7596 (m-40) cc_final: 0.7263 (t0) REVERT: 4 262 GLU cc_start: 0.6958 (mp0) cc_final: 0.6638 (mp0) REVERT: 4 274 LYS cc_start: 0.7810 (mttt) cc_final: 0.7340 (mtmt) REVERT: 4 286 ASN cc_start: 0.7860 (t0) cc_final: 0.7568 (t0) REVERT: 4 295 THR cc_start: 0.8429 (t) cc_final: 0.7821 (t) REVERT: 4 298 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6185 (mpp) REVERT: 4 304 LYS cc_start: 0.7335 (tppt) cc_final: 0.6846 (tppt) REVERT: 5 45 MET cc_start: 0.8290 (ttm) cc_final: 0.8069 (ttp) REVERT: 5 55 LYS cc_start: 0.6203 (mtmm) cc_final: 0.5767 (mtmm) REVERT: 5 60 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6806 (tppt) REVERT: 5 105 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6281 (mp) REVERT: 5 114 ARG cc_start: 0.7138 (ttp-110) cc_final: 0.6867 (ttp-110) REVERT: 5 171 MET cc_start: 0.7500 (mtp) cc_final: 0.6895 (mtp) REVERT: 5 215 LYS cc_start: 0.7383 (mmtt) cc_final: 0.6980 (tmtt) REVERT: 5 241 ASN cc_start: 0.6969 (t0) cc_final: 0.6544 (t0) REVERT: 6 5 ARG cc_start: 0.5672 (tpp80) cc_final: 0.5402 (tpp-160) REVERT: 6 30 ASP cc_start: 0.6640 (m-30) cc_final: 0.6407 (m-30) REVERT: 6 41 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7949 (mm-30) REVERT: 6 46 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7565 (tpt) REVERT: 6 64 ASN cc_start: 0.5803 (m-40) cc_final: 0.5587 (m-40) REVERT: 6 107 LEU cc_start: 0.7240 (pt) cc_final: 0.6507 (tp) REVERT: 6 111 ASP cc_start: 0.7477 (t70) cc_final: 0.7259 (t0) REVERT: 6 115 LEU cc_start: 0.6692 (pp) cc_final: 0.6267 (tp) REVERT: 6 134 ASP cc_start: 0.6883 (t0) cc_final: 0.6600 (t0) REVERT: 6 135 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6997 (mm-30) REVERT: 6 143 ARG cc_start: 0.8126 (ppt170) cc_final: 0.7618 (ppt170) REVERT: 6 146 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7418 (ptm160) REVERT: 6 149 THR cc_start: 0.7556 (p) cc_final: 0.7174 (p) REVERT: 6 150 GLN cc_start: 0.7548 (mt0) cc_final: 0.7106 (mt0) REVERT: 6 162 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7614 (p) REVERT: 6 164 CYS cc_start: 0.7820 (t) cc_final: 0.7383 (p) REVERT: 6 171 MET cc_start: 0.8159 (mtp) cc_final: 0.7897 (mmt) REVERT: 6 175 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7270 (ttmm) REVERT: 6 188 PHE cc_start: 0.8287 (m-80) cc_final: 0.7930 (m-80) REVERT: 6 189 SER cc_start: 0.8514 (p) cc_final: 0.8081 (m) REVERT: 6 198 SER cc_start: 0.7526 (p) cc_final: 0.6941 (t) REVERT: 6 219 PHE cc_start: 0.5788 (m-80) cc_final: 0.5510 (m-80) REVERT: 6 242 MET cc_start: 0.8220 (tpp) cc_final: 0.7527 (mmm) REVERT: 6 255 GLU cc_start: 0.6949 (tp30) cc_final: 0.6164 (mm-30) REVERT: 7 24 LYS cc_start: 0.7568 (tttt) cc_final: 0.7308 (ttpp) REVERT: 7 44 CYS cc_start: 0.7920 (m) cc_final: 0.7637 (m) REVERT: 7 45 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7908 (tmm) REVERT: 7 48 TYR cc_start: 0.8094 (m-80) cc_final: 0.7694 (m-10) REVERT: 7 83 GLU cc_start: 0.7298 (tt0) cc_final: 0.6974 (mt-10) REVERT: 7 86 ASP cc_start: 0.7996 (t70) cc_final: 0.7731 (t0) REVERT: 7 129 LYS cc_start: 0.7699 (mmmm) cc_final: 0.7488 (mttp) REVERT: 7 146 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7594 (ptm160) REVERT: 7 156 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7355 (tttp) REVERT: 7 162 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7630 (p) REVERT: 7 163 LYS cc_start: 0.8401 (mppt) cc_final: 0.8136 (mttp) REVERT: 7 166 ILE cc_start: 0.8227 (mt) cc_final: 0.7907 (tp) REVERT: 7 181 ASN cc_start: 0.7610 (t0) cc_final: 0.7159 (t0) REVERT: 7 193 GLU cc_start: 0.8111 (tp30) cc_final: 0.7699 (tp30) REVERT: 7 232 LYS cc_start: 0.7442 (ttmm) cc_final: 0.6790 (ttpp) REVERT: 7 247 ASN cc_start: 0.7608 (m-40) cc_final: 0.7266 (m-40) REVERT: 7 271 PHE cc_start: 0.7776 (t80) cc_final: 0.7518 (t80) outliers start: 117 outliers final: 70 residues processed: 684 average time/residue: 0.3786 time to fit residues: 361.0999 Evaluate side-chains 697 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 610 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 46 MET Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 162 THR Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 253 SER Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 162 THR Chi-restraints excluded: chain 6 residue 179 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 241 ASN Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 40 SER Chi-restraints excluded: chain 7 residue 45 MET Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 3 optimal weight: 30.0000 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 191 GLN ** 2 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 GLN ** 3 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 261 HIS 5 150 GLN ** 5 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18772 Z= 0.329 Angle : 0.648 9.346 25612 Z= 0.327 Chirality : 0.043 0.302 2863 Planarity : 0.004 0.039 3122 Dihedral : 16.269 89.853 3107 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 7.04 % Allowed : 26.44 % Favored : 66.52 % 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: -1.31 (0.18), residues: 2163 helix: 0.25 (0.15), residues: 1183 sheet: -2.13 (0.37), residues: 224 loop : -2.19 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 6 154 HIS 0.007 0.001 HIS 3 261 PHE 0.014 0.002 PHE 4 209 TYR 0.023 0.002 TYR 3 199 ARG 0.006 0.001 ARG 1 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 633 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7261 (ttp-170) REVERT: 1 14 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6810 (ptp90) REVERT: 1 23 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7278 (mtm110) REVERT: 1 37 ASP cc_start: 0.7915 (p0) cc_final: 0.7191 (p0) REVERT: 1 38 LEU cc_start: 0.7693 (mt) cc_final: 0.7322 (mt) REVERT: 1 39 GLU cc_start: 0.6700 (mp0) cc_final: 0.5517 (mp0) REVERT: 1 65 GLN cc_start: 0.7401 (pt0) cc_final: 0.7073 (pp30) REVERT: 1 83 GLU cc_start: 0.7928 (tt0) cc_final: 0.7470 (mt-10) REVERT: 1 87 ASN cc_start: 0.8227 (m-40) cc_final: 0.7716 (m110) REVERT: 1 92 ASP cc_start: 0.7330 (t0) cc_final: 0.7010 (t0) REVERT: 1 100 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7329 (tm-30) REVERT: 1 101 MET cc_start: 0.8207 (ttp) cc_final: 0.7892 (ttp) REVERT: 1 105 LEU cc_start: 0.7692 (pp) cc_final: 0.7322 (mp) REVERT: 1 109 GLU cc_start: 0.7478 (tt0) cc_final: 0.7057 (tt0) REVERT: 1 129 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7919 (mtpt) REVERT: 1 150 GLN cc_start: 0.7900 (mt0) cc_final: 0.7672 (mt0) REVERT: 1 163 LYS cc_start: 0.8155 (mptt) cc_final: 0.7833 (mmtm) REVERT: 1 171 MET cc_start: 0.8169 (mtp) cc_final: 0.7698 (mmm) REVERT: 1 175 LYS cc_start: 0.7419 (ttmt) cc_final: 0.7121 (ttpp) REVERT: 1 193 GLU cc_start: 0.7962 (tp30) cc_final: 0.7564 (tp30) REVERT: 1 242 MET cc_start: 0.7472 (tpt) cc_final: 0.7154 (tpp) REVERT: 1 268 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7501 (p0) REVERT: 1 274 LYS cc_start: 0.8026 (mttt) cc_final: 0.7690 (mtpp) REVERT: 1 279 ASP cc_start: 0.7684 (p0) cc_final: 0.7323 (p0) REVERT: 1 285 LYS cc_start: 0.7687 (tppt) cc_final: 0.7089 (tppt) REVERT: 1 297 ASP cc_start: 0.7774 (t0) cc_final: 0.7549 (t0) REVERT: 1 300 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7568 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7386 (m-30) cc_final: 0.7093 (m-30) REVERT: 2 33 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7581 (ttp-170) REVERT: 2 41 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: 2 46 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7688 (ttt) REVERT: 2 96 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: 2 100 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7401 (tm-30) REVERT: 2 121 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7107 (mt-10) REVERT: 2 129 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7566 (mmmm) REVERT: 2 141 GLU cc_start: 0.7384 (tp30) cc_final: 0.7128 (tp30) REVERT: 2 146 ARG cc_start: 0.7316 (ptm160) cc_final: 0.6994 (tmm-80) REVERT: 2 150 GLN cc_start: 0.7726 (mt0) cc_final: 0.7220 (mt0) REVERT: 2 162 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (p) REVERT: 2 163 LYS cc_start: 0.8010 (mppt) cc_final: 0.7487 (mmtm) REVERT: 2 175 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7918 (ttmm) REVERT: 2 181 ASN cc_start: 0.7358 (t0) cc_final: 0.6572 (t0) REVERT: 2 242 MET cc_start: 0.6898 (mmm) cc_final: 0.6600 (tpp) REVERT: 2 262 GLU cc_start: 0.6726 (mp0) cc_final: 0.6288 (pm20) REVERT: 2 286 ASN cc_start: 0.8642 (t0) cc_final: 0.8200 (t0) REVERT: 2 309 GLU cc_start: 0.6782 (pm20) cc_final: 0.6277 (pm20) REVERT: 2 313 ARG cc_start: 0.7324 (ttp-170) cc_final: 0.7095 (ttp-110) REVERT: 3 30 ASP cc_start: 0.7884 (m-30) cc_final: 0.7478 (m-30) REVERT: 3 34 ASP cc_start: 0.7788 (m-30) cc_final: 0.7284 (m-30) REVERT: 3 39 GLU cc_start: 0.6752 (mp0) cc_final: 0.6115 (mp0) REVERT: 3 61 LYS cc_start: 0.7978 (tptp) cc_final: 0.7310 (tptp) REVERT: 3 65 GLN cc_start: 0.8216 (pt0) cc_final: 0.7565 (pp30) REVERT: 3 92 ASP cc_start: 0.7612 (t0) cc_final: 0.7267 (t0) REVERT: 3 109 GLU cc_start: 0.7891 (tt0) cc_final: 0.7564 (tt0) REVERT: 3 121 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6403 (mt-10) REVERT: 3 143 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7443 (ppt170) REVERT: 3 149 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7471 (p) REVERT: 3 150 GLN cc_start: 0.7660 (mt0) cc_final: 0.7289 (mm-40) REVERT: 3 157 MET cc_start: 0.7836 (ttm) cc_final: 0.7149 (tpp) REVERT: 3 173 TYR cc_start: 0.8693 (p90) cc_final: 0.8376 (p90) REVERT: 3 175 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7460 (ttmm) REVERT: 3 207 LYS cc_start: 0.8149 (tttt) cc_final: 0.7420 (ttmm) REVERT: 3 220 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: 3 241 ASN cc_start: 0.7291 (m-40) cc_final: 0.6801 (t0) REVERT: 3 242 MET cc_start: 0.7856 (mmm) cc_final: 0.7609 (tmm) REVERT: 3 255 GLU cc_start: 0.7743 (tp30) cc_final: 0.7513 (tp30) REVERT: 3 259 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6415 (p0) REVERT: 3 268 ASP cc_start: 0.7309 (p0) cc_final: 0.6826 (p0) REVERT: 3 269 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.4981 (t80) REVERT: 4 19 THR cc_start: 0.7778 (p) cc_final: 0.7385 (p) REVERT: 4 23 ARG cc_start: 0.6839 (mtm180) cc_final: 0.6527 (mtm180) REVERT: 4 29 MET cc_start: 0.7582 (mtt) cc_final: 0.7159 (mmm) REVERT: 4 45 MET cc_start: 0.7640 (ttp) cc_final: 0.7437 (ttp) REVERT: 4 46 MET cc_start: 0.7747 (tpt) cc_final: 0.7136 (tpt) REVERT: 4 62 TYR cc_start: 0.7825 (t80) cc_final: 0.7576 (t80) REVERT: 4 83 GLU cc_start: 0.7562 (tt0) cc_final: 0.6597 (tt0) REVERT: 4 84 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6225 (mt) REVERT: 4 105 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6203 (pp) REVERT: 4 115 LEU cc_start: 0.8247 (pp) cc_final: 0.7819 (pp) REVERT: 4 118 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6685 (mtp180) REVERT: 4 121 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7489 (mt-10) REVERT: 4 137 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7101 (pt0) REVERT: 4 146 ARG cc_start: 0.6805 (ptm160) cc_final: 0.6207 (ptm160) REVERT: 4 154 TRP cc_start: 0.7692 (t60) cc_final: 0.7198 (t60) REVERT: 4 168 ILE cc_start: 0.6941 (pt) cc_final: 0.6580 (pt) REVERT: 4 171 MET cc_start: 0.8440 (mtp) cc_final: 0.7838 (mtp) REVERT: 4 187 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7510 (mtm-85) REVERT: 4 193 GLU cc_start: 0.7628 (tp30) cc_final: 0.7075 (tp30) REVERT: 4 194 LEU cc_start: 0.7483 (tt) cc_final: 0.7052 (tt) REVERT: 4 221 LYS cc_start: 0.8069 (ptpt) cc_final: 0.7764 (ptpt) REVERT: 4 228 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7586 (tm-30) REVERT: 4 247 ASN cc_start: 0.7566 (m-40) cc_final: 0.7247 (t0) REVERT: 4 262 GLU cc_start: 0.7066 (mp0) cc_final: 0.6729 (mp0) REVERT: 4 286 ASN cc_start: 0.7878 (t0) cc_final: 0.7579 (t0) REVERT: 4 295 THR cc_start: 0.8391 (t) cc_final: 0.7797 (t) REVERT: 4 298 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6171 (mpp) REVERT: 4 300 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7691 (ttm-80) REVERT: 5 23 ARG cc_start: 0.6412 (mtm180) cc_final: 0.6053 (mpp80) REVERT: 5 55 LYS cc_start: 0.6054 (mtmm) cc_final: 0.5668 (mtmm) REVERT: 5 105 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6163 (mt) REVERT: 5 157 MET cc_start: 0.6125 (tmm) cc_final: 0.5900 (tmm) REVERT: 5 171 MET cc_start: 0.7518 (mtp) cc_final: 0.6941 (mtp) REVERT: 5 215 LYS cc_start: 0.7411 (mmtt) cc_final: 0.6946 (tmtt) REVERT: 5 241 ASN cc_start: 0.6956 (t0) cc_final: 0.6454 (t0) REVERT: 6 41 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8042 (mm-30) REVERT: 6 46 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7484 (tpt) REVERT: 6 107 LEU cc_start: 0.7409 (pt) cc_final: 0.6884 (tp) REVERT: 6 134 ASP cc_start: 0.6890 (t0) cc_final: 0.6605 (t0) REVERT: 6 135 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7088 (mm-30) REVERT: 6 143 ARG cc_start: 0.8078 (ppt170) cc_final: 0.7577 (ppt170) REVERT: 6 146 ARG cc_start: 0.7756 (ptm160) cc_final: 0.7418 (ptm160) REVERT: 6 149 THR cc_start: 0.7781 (p) cc_final: 0.7387 (p) REVERT: 6 150 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: 6 164 CYS cc_start: 0.7802 (t) cc_final: 0.7498 (m) REVERT: 6 171 MET cc_start: 0.8242 (mtp) cc_final: 0.7991 (mmt) REVERT: 6 175 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7357 (ttmm) REVERT: 6 189 SER cc_start: 0.8553 (p) cc_final: 0.8140 (m) REVERT: 6 198 SER cc_start: 0.7442 (p) cc_final: 0.6843 (t) REVERT: 6 209 PHE cc_start: 0.7585 (t80) cc_final: 0.7093 (t80) REVERT: 6 219 PHE cc_start: 0.5886 (m-80) cc_final: 0.5566 (m-80) REVERT: 6 231 GLN cc_start: 0.8717 (tt0) cc_final: 0.8201 (mt0) REVERT: 6 242 MET cc_start: 0.8272 (tpp) cc_final: 0.7423 (mmm) REVERT: 6 243 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6660 (ttm-80) REVERT: 6 255 GLU cc_start: 0.6901 (tp30) cc_final: 0.6176 (mm-30) REVERT: 6 266 GLU cc_start: 0.7808 (tp30) cc_final: 0.7018 (tp30) REVERT: 7 24 LYS cc_start: 0.7599 (tttt) cc_final: 0.7308 (ttpp) REVERT: 7 39 GLU cc_start: 0.7617 (mp0) cc_final: 0.6976 (mp0) REVERT: 7 48 TYR cc_start: 0.8248 (m-80) cc_final: 0.7553 (m-10) REVERT: 7 83 GLU cc_start: 0.7410 (tt0) cc_final: 0.7094 (mt-10) REVERT: 7 98 LEU cc_start: 0.6648 (mt) cc_final: 0.6374 (mm) REVERT: 7 111 ASP cc_start: 0.7282 (t70) cc_final: 0.6787 (t70) REVERT: 7 129 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7541 (mttp) REVERT: 7 146 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7592 (ptm160) REVERT: 7 156 LYS cc_start: 0.7608 (ttpt) cc_final: 0.7383 (tttp) REVERT: 7 162 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (p) REVERT: 7 166 ILE cc_start: 0.8286 (mt) cc_final: 0.7947 (tp) REVERT: 7 175 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7243 (ttmt) REVERT: 7 181 ASN cc_start: 0.7685 (t0) cc_final: 0.7194 (t0) REVERT: 7 193 GLU cc_start: 0.7996 (tp30) cc_final: 0.7545 (tp30) REVERT: 7 232 LYS cc_start: 0.7449 (ttmm) cc_final: 0.6797 (ttpp) REVERT: 7 271 PHE cc_start: 0.7967 (t80) cc_final: 0.7684 (t80) outliers start: 132 outliers final: 82 residues processed: 701 average time/residue: 0.3834 time to fit residues: 378.5131 Evaluate side-chains 726 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 625 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 158 ILE Chi-restraints excluded: chain 1 residue 176 VAL Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 268 ASP Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 107 LEU Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 117 LYS Chi-restraints excluded: chain 2 residue 162 THR Chi-restraints excluded: chain 2 residue 208 THR Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 2 residue 294 VAL Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 149 THR Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 105 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 211 GLU Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 253 SER Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 300 ARG Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 120 THR Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 211 GLU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 150 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 241 ASN Chi-restraints excluded: chain 6 residue 268 ASP Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 191 GLN 3 259 ASN ** 5 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18772 Z= 0.213 Angle : 0.621 10.253 25612 Z= 0.307 Chirality : 0.041 0.279 2863 Planarity : 0.004 0.046 3122 Dihedral : 15.957 88.694 3106 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.08 % Allowed : 27.51 % Favored : 66.42 % 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: -1.10 (0.19), residues: 2163 helix: 0.35 (0.15), residues: 1183 sheet: -1.96 (0.37), residues: 224 loop : -2.01 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 154 HIS 0.004 0.001 HIS 3 185 PHE 0.013 0.001 PHE 4 271 TYR 0.018 0.001 TYR 6 199 ARG 0.009 0.001 ARG 1 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 614 time to evaluate : 2.046 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: 1 11 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7268 (ttp-170) REVERT: 1 23 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7190 (mtm110) REVERT: 1 30 ASP cc_start: 0.7264 (m-30) cc_final: 0.7036 (m-30) REVERT: 1 31 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6446 (ttm110) REVERT: 1 37 ASP cc_start: 0.7907 (p0) cc_final: 0.7225 (p0) REVERT: 1 38 LEU cc_start: 0.7685 (mt) cc_final: 0.7381 (mm) REVERT: 1 39 GLU cc_start: 0.6547 (mp0) cc_final: 0.5446 (mp0) REVERT: 1 48 TYR cc_start: 0.8461 (m-80) cc_final: 0.7862 (m-80) REVERT: 1 57 THR cc_start: 0.7926 (t) cc_final: 0.7712 (t) REVERT: 1 65 GLN cc_start: 0.7408 (pt0) cc_final: 0.7076 (pp30) REVERT: 1 83 GLU cc_start: 0.7926 (tt0) cc_final: 0.7483 (mt-10) REVERT: 1 87 ASN cc_start: 0.8131 (m-40) cc_final: 0.7657 (m110) REVERT: 1 92 ASP cc_start: 0.7345 (t0) cc_final: 0.6951 (t0) REVERT: 1 100 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7258 (tm-30) REVERT: 1 101 MET cc_start: 0.8210 (ttp) cc_final: 0.7938 (ttp) REVERT: 1 105 LEU cc_start: 0.7616 (pp) cc_final: 0.7268 (mp) REVERT: 1 109 GLU cc_start: 0.7446 (tt0) cc_final: 0.7040 (tt0) REVERT: 1 129 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7921 (mtpt) REVERT: 1 149 THR cc_start: 0.7558 (p) cc_final: 0.7222 (p) REVERT: 1 163 LYS cc_start: 0.8146 (mptt) cc_final: 0.7865 (mmtm) REVERT: 1 171 MET cc_start: 0.8148 (mtp) cc_final: 0.7763 (mmm) REVERT: 1 182 SER cc_start: 0.8315 (t) cc_final: 0.7775 (p) REVERT: 1 192 VAL cc_start: 0.8229 (t) cc_final: 0.7979 (m) REVERT: 1 193 GLU cc_start: 0.7853 (tp30) cc_final: 0.7510 (tp30) REVERT: 1 242 MET cc_start: 0.7375 (tpt) cc_final: 0.7137 (tpp) REVERT: 1 261 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6030 (m170) REVERT: 1 269 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: 1 274 LYS cc_start: 0.8032 (mttt) cc_final: 0.7649 (mtpp) REVERT: 1 279 ASP cc_start: 0.7680 (p0) cc_final: 0.7354 (p0) REVERT: 1 285 LYS cc_start: 0.7640 (tppt) cc_final: 0.7056 (tppt) REVERT: 1 297 ASP cc_start: 0.7778 (t0) cc_final: 0.7574 (t0) REVERT: 1 300 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7582 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7473 (m-30) cc_final: 0.7182 (m-30) REVERT: 2 33 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7712 (ttp-110) REVERT: 2 39 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6624 (tm-30) REVERT: 2 41 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: 2 46 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7597 (ttt) REVERT: 2 89 LYS cc_start: 0.7768 (mmmm) cc_final: 0.7442 (mmmm) REVERT: 2 96 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: 2 121 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7112 (mt-10) REVERT: 2 122 LEU cc_start: 0.7162 (tp) cc_final: 0.6932 (tp) REVERT: 2 129 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7562 (mmpt) REVERT: 2 146 ARG cc_start: 0.7312 (ptm160) cc_final: 0.6988 (tmm-80) REVERT: 2 150 GLN cc_start: 0.7672 (mt0) cc_final: 0.7149 (mt0) REVERT: 2 163 LYS cc_start: 0.8036 (mppt) cc_final: 0.7476 (mmtm) REVERT: 2 181 ASN cc_start: 0.7384 (t0) cc_final: 0.6580 (t0) REVERT: 2 235 TYR cc_start: 0.7492 (t80) cc_final: 0.6997 (t80) REVERT: 2 242 MET cc_start: 0.7057 (mmm) cc_final: 0.6491 (tmm) REVERT: 2 262 GLU cc_start: 0.6842 (mp0) cc_final: 0.6382 (pm20) REVERT: 2 286 ASN cc_start: 0.8592 (t0) cc_final: 0.8074 (t0) REVERT: 2 309 GLU cc_start: 0.7010 (pm20) cc_final: 0.6490 (pm20) REVERT: 2 313 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7089 (ttp-110) REVERT: 3 30 ASP cc_start: 0.7889 (m-30) cc_final: 0.7326 (m-30) REVERT: 3 34 ASP cc_start: 0.7661 (m-30) cc_final: 0.6752 (m-30) REVERT: 3 39 GLU cc_start: 0.6777 (mp0) cc_final: 0.6111 (mp0) REVERT: 3 46 MET cc_start: 0.7739 (tpt) cc_final: 0.7400 (tpp) REVERT: 3 61 LYS cc_start: 0.7934 (tptp) cc_final: 0.7626 (tptp) REVERT: 3 65 GLN cc_start: 0.8201 (pt0) cc_final: 0.7456 (pp30) REVERT: 3 109 GLU cc_start: 0.7836 (tt0) cc_final: 0.7515 (tt0) REVERT: 3 143 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7401 (ppt170) REVERT: 3 149 THR cc_start: 0.8109 (p) cc_final: 0.7521 (p) REVERT: 3 150 GLN cc_start: 0.7703 (mt0) cc_final: 0.7310 (mm-40) REVERT: 3 157 MET cc_start: 0.7831 (ttm) cc_final: 0.7136 (tpp) REVERT: 3 173 TYR cc_start: 0.8678 (p90) cc_final: 0.8306 (p90) REVERT: 3 175 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7430 (ttmm) REVERT: 3 207 LYS cc_start: 0.8180 (tttt) cc_final: 0.7443 (ttmm) REVERT: 3 220 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: 3 237 PHE cc_start: 0.7063 (t80) cc_final: 0.6618 (t80) REVERT: 3 241 ASN cc_start: 0.7193 (m-40) cc_final: 0.6700 (m-40) REVERT: 3 255 GLU cc_start: 0.7831 (tp30) cc_final: 0.7466 (tp30) REVERT: 3 259 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6875 (p0) REVERT: 3 268 ASP cc_start: 0.7158 (p0) cc_final: 0.6651 (p0) REVERT: 3 269 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5061 (t80) REVERT: 3 300 ARG cc_start: 0.8503 (ptp90) cc_final: 0.7868 (ptp90) REVERT: 4 11 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8380 (ttm170) REVERT: 4 19 THR cc_start: 0.7724 (p) cc_final: 0.7379 (p) REVERT: 4 23 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6400 (mtm110) REVERT: 4 24 LYS cc_start: 0.7355 (tttp) cc_final: 0.6984 (tptp) REVERT: 4 29 MET cc_start: 0.7618 (mtt) cc_final: 0.7189 (mmp) REVERT: 4 46 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6911 (tpt) REVERT: 4 62 TYR cc_start: 0.7810 (t80) cc_final: 0.7544 (t80) REVERT: 4 83 GLU cc_start: 0.7564 (tt0) cc_final: 0.6545 (tt0) REVERT: 4 84 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6115 (mp) REVERT: 4 115 LEU cc_start: 0.8223 (pp) cc_final: 0.7796 (pp) REVERT: 4 118 ARG cc_start: 0.7026 (ttm170) cc_final: 0.6799 (mtp180) REVERT: 4 131 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7527 (tp) REVERT: 4 137 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: 4 146 ARG cc_start: 0.6832 (ptm160) cc_final: 0.6266 (ptm160) REVERT: 4 154 TRP cc_start: 0.7704 (t60) cc_final: 0.7254 (t60) REVERT: 4 168 ILE cc_start: 0.6957 (pt) cc_final: 0.6546 (pt) REVERT: 4 171 MET cc_start: 0.8446 (mtp) cc_final: 0.7833 (mtp) REVERT: 4 190 ILE cc_start: 0.7971 (mt) cc_final: 0.7598 (pt) REVERT: 4 193 GLU cc_start: 0.7543 (tp30) cc_final: 0.7031 (tp30) REVERT: 4 194 LEU cc_start: 0.7601 (tt) cc_final: 0.7137 (tt) REVERT: 4 221 LYS cc_start: 0.8025 (ptpt) cc_final: 0.7675 (ptpt) REVERT: 4 228 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7457 (tm-30) REVERT: 4 242 MET cc_start: 0.8383 (tpt) cc_final: 0.8166 (tpp) REVERT: 4 247 ASN cc_start: 0.7560 (m-40) cc_final: 0.7186 (t0) REVERT: 4 262 GLU cc_start: 0.7077 (mp0) cc_final: 0.6737 (mp0) REVERT: 4 286 ASN cc_start: 0.7864 (t0) cc_final: 0.7551 (t0) REVERT: 5 55 LYS cc_start: 0.6035 (mtmm) cc_final: 0.5663 (mtmm) REVERT: 5 62 TYR cc_start: 0.8032 (t80) cc_final: 0.7603 (t80) REVERT: 5 105 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6173 (mp) REVERT: 5 142 GLU cc_start: 0.4457 (OUTLIER) cc_final: 0.3945 (mm-30) REVERT: 5 171 MET cc_start: 0.7442 (mtp) cc_final: 0.6920 (mtp) REVERT: 5 215 LYS cc_start: 0.7374 (mmtt) cc_final: 0.6976 (tmtt) REVERT: 5 241 ASN cc_start: 0.6975 (t0) cc_final: 0.6467 (t0) REVERT: 6 41 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8047 (mm-30) REVERT: 6 46 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7415 (tpt) REVERT: 6 107 LEU cc_start: 0.7092 (pt) cc_final: 0.6683 (tp) REVERT: 6 134 ASP cc_start: 0.6835 (t0) cc_final: 0.6487 (t0) REVERT: 6 135 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7082 (mm-30) REVERT: 6 143 ARG cc_start: 0.8096 (ppt170) cc_final: 0.7647 (ppt170) REVERT: 6 146 ARG cc_start: 0.7827 (ptm160) cc_final: 0.7496 (ptm160) REVERT: 6 149 THR cc_start: 0.7762 (p) cc_final: 0.7397 (p) REVERT: 6 150 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: 6 164 CYS cc_start: 0.7740 (t) cc_final: 0.7527 (m) REVERT: 6 175 LYS cc_start: 0.7516 (ttmt) cc_final: 0.7279 (ttmm) REVERT: 6 189 SER cc_start: 0.8677 (p) cc_final: 0.8271 (m) REVERT: 6 219 PHE cc_start: 0.5847 (m-80) cc_final: 0.5521 (m-80) REVERT: 6 231 GLN cc_start: 0.8735 (tt0) cc_final: 0.8120 (mt0) REVERT: 6 242 MET cc_start: 0.8280 (tpp) cc_final: 0.7383 (mmm) REVERT: 6 243 ARG cc_start: 0.6882 (ttm-80) cc_final: 0.6602 (ttm-80) REVERT: 6 255 GLU cc_start: 0.6862 (tp30) cc_final: 0.6037 (mm-30) REVERT: 6 266 GLU cc_start: 0.7800 (tp30) cc_final: 0.7057 (tp30) REVERT: 7 24 LYS cc_start: 0.7554 (tttt) cc_final: 0.7274 (ttpp) REVERT: 7 39 GLU cc_start: 0.7605 (mp0) cc_final: 0.7018 (mp0) REVERT: 7 48 TYR cc_start: 0.8111 (m-80) cc_final: 0.7399 (m-10) REVERT: 7 83 GLU cc_start: 0.7332 (tt0) cc_final: 0.7065 (mt-10) REVERT: 7 98 LEU cc_start: 0.6655 (mt) cc_final: 0.6397 (mm) REVERT: 7 111 ASP cc_start: 0.7297 (t70) cc_final: 0.7055 (t70) REVERT: 7 129 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7449 (mttp) REVERT: 7 145 ASN cc_start: 0.7729 (m-40) cc_final: 0.7447 (m-40) REVERT: 7 146 ARG cc_start: 0.7820 (ptm160) cc_final: 0.7606 (ptm160) REVERT: 7 156 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7577 (tttp) REVERT: 7 162 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7710 (p) REVERT: 7 175 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7185 (ttmt) REVERT: 7 181 ASN cc_start: 0.7656 (t0) cc_final: 0.7176 (t0) REVERT: 7 193 GLU cc_start: 0.8067 (tp30) cc_final: 0.7513 (tp30) REVERT: 7 232 LYS cc_start: 0.7437 (ttmm) cc_final: 0.6781 (ttpp) REVERT: 7 271 PHE cc_start: 0.7730 (t80) cc_final: 0.7434 (t80) outliers start: 114 outliers final: 69 residues processed: 667 average time/residue: 0.3779 time to fit residues: 349.9220 Evaluate side-chains 684 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 596 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 261 HIS Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 SER Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 269 PHE Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 150 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 121 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 191 GLN ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 227 ASN 4 160 ASN ** 5 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18772 Z= 0.206 Angle : 0.622 10.876 25612 Z= 0.306 Chirality : 0.040 0.256 2863 Planarity : 0.004 0.036 3122 Dihedral : 15.723 87.422 3097 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.65 % Allowed : 28.25 % Favored : 66.10 % 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: -0.98 (0.19), residues: 2163 helix: 0.42 (0.15), residues: 1183 sheet: -1.83 (0.37), residues: 224 loop : -1.91 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 154 HIS 0.003 0.000 HIS 3 185 PHE 0.010 0.001 PHE 4 219 TYR 0.049 0.002 TYR 5 62 ARG 0.008 0.000 ARG 1 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 608 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7432 (ttp-170) REVERT: 1 23 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7068 (mtm110) REVERT: 1 30 ASP cc_start: 0.7263 (m-30) cc_final: 0.7014 (m-30) REVERT: 1 31 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6624 (ttm170) REVERT: 1 37 ASP cc_start: 0.7898 (p0) cc_final: 0.7569 (p0) REVERT: 1 38 LEU cc_start: 0.7683 (mt) cc_final: 0.7440 (mm) REVERT: 1 39 GLU cc_start: 0.6528 (mp0) cc_final: 0.5921 (mp0) REVERT: 1 48 TYR cc_start: 0.8396 (m-80) cc_final: 0.7792 (m-80) REVERT: 1 57 THR cc_start: 0.7925 (t) cc_final: 0.7683 (t) REVERT: 1 65 GLN cc_start: 0.7406 (pt0) cc_final: 0.7075 (pp30) REVERT: 1 83 GLU cc_start: 0.7908 (tt0) cc_final: 0.7444 (mt-10) REVERT: 1 87 ASN cc_start: 0.8141 (m-40) cc_final: 0.7662 (m110) REVERT: 1 92 ASP cc_start: 0.7332 (t0) cc_final: 0.6935 (t0) REVERT: 1 100 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7285 (tm-30) REVERT: 1 101 MET cc_start: 0.8233 (ttp) cc_final: 0.7993 (ttp) REVERT: 1 105 LEU cc_start: 0.7585 (pp) cc_final: 0.7227 (mp) REVERT: 1 109 GLU cc_start: 0.7295 (tt0) cc_final: 0.6878 (tt0) REVERT: 1 129 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7876 (mtpt) REVERT: 1 149 THR cc_start: 0.7628 (p) cc_final: 0.6866 (p) REVERT: 1 163 LYS cc_start: 0.8133 (mptt) cc_final: 0.7871 (mmtm) REVERT: 1 171 MET cc_start: 0.8160 (mtp) cc_final: 0.7781 (mmm) REVERT: 1 182 SER cc_start: 0.8177 (t) cc_final: 0.7648 (p) REVERT: 1 192 VAL cc_start: 0.8150 (t) cc_final: 0.7941 (m) REVERT: 1 193 GLU cc_start: 0.7863 (tp30) cc_final: 0.7508 (tp30) REVERT: 1 261 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6028 (m170) REVERT: 1 274 LYS cc_start: 0.7962 (mttt) cc_final: 0.7586 (mtpp) REVERT: 1 279 ASP cc_start: 0.7767 (p0) cc_final: 0.7342 (p0) REVERT: 1 285 LYS cc_start: 0.7654 (tppt) cc_final: 0.7060 (tppt) REVERT: 1 296 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6901 (tm-30) REVERT: 1 297 ASP cc_start: 0.7797 (t0) cc_final: 0.7457 (t0) REVERT: 1 300 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7521 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7487 (m-30) cc_final: 0.7198 (m-30) REVERT: 2 33 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7620 (ttp-170) REVERT: 2 41 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: 2 46 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7591 (ttt) REVERT: 2 89 LYS cc_start: 0.7698 (mmmm) cc_final: 0.7405 (mmmm) REVERT: 2 96 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: 2 100 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7532 (tm-30) REVERT: 2 121 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7104 (mt-10) REVERT: 2 122 LEU cc_start: 0.7160 (tp) cc_final: 0.6910 (tp) REVERT: 2 129 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7641 (mmpt) REVERT: 2 143 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.6007 (ppt-90) REVERT: 2 146 ARG cc_start: 0.7372 (ptm160) cc_final: 0.6997 (tmm-80) REVERT: 2 150 GLN cc_start: 0.7649 (mt0) cc_final: 0.7158 (mt0) REVERT: 2 163 LYS cc_start: 0.7988 (mppt) cc_final: 0.7417 (mmtm) REVERT: 2 181 ASN cc_start: 0.7430 (t0) cc_final: 0.6640 (t0) REVERT: 2 235 TYR cc_start: 0.7569 (t80) cc_final: 0.7000 (t80) REVERT: 2 242 MET cc_start: 0.7124 (mmm) cc_final: 0.6419 (tmm) REVERT: 2 262 GLU cc_start: 0.6864 (mp0) cc_final: 0.6391 (pm20) REVERT: 2 286 ASN cc_start: 0.8558 (t0) cc_final: 0.7958 (t0) REVERT: 2 309 GLU cc_start: 0.7114 (pm20) cc_final: 0.6493 (pm20) REVERT: 2 313 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.7111 (ttp-110) REVERT: 3 39 GLU cc_start: 0.6772 (mp0) cc_final: 0.6102 (mp0) REVERT: 3 44 CYS cc_start: 0.7926 (m) cc_final: 0.7241 (p) REVERT: 3 46 MET cc_start: 0.7756 (tpt) cc_final: 0.7458 (tpp) REVERT: 3 61 LYS cc_start: 0.7930 (tptp) cc_final: 0.7274 (tptp) REVERT: 3 65 GLN cc_start: 0.8189 (pt0) cc_final: 0.7217 (pp30) REVERT: 3 109 GLU cc_start: 0.7846 (tt0) cc_final: 0.7519 (tt0) REVERT: 3 131 ILE cc_start: 0.7607 (mt) cc_final: 0.7402 (mp) REVERT: 3 143 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7383 (ppt170) REVERT: 3 157 MET cc_start: 0.7830 (ttm) cc_final: 0.7125 (tpp) REVERT: 3 173 TYR cc_start: 0.8682 (p90) cc_final: 0.8294 (p90) REVERT: 3 175 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7422 (ttmm) REVERT: 3 207 LYS cc_start: 0.8184 (tttt) cc_final: 0.7472 (ttmm) REVERT: 3 220 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: 3 237 PHE cc_start: 0.7061 (t80) cc_final: 0.6551 (t80) REVERT: 3 241 ASN cc_start: 0.7191 (m-40) cc_final: 0.6696 (t0) REVERT: 3 242 MET cc_start: 0.7688 (mmm) cc_final: 0.7465 (tmm) REVERT: 3 255 GLU cc_start: 0.7967 (tp30) cc_final: 0.7611 (tp30) REVERT: 3 259 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6946 (p0) REVERT: 3 268 ASP cc_start: 0.7116 (p0) cc_final: 0.6627 (p0) REVERT: 3 269 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.5077 (t80) REVERT: 3 300 ARG cc_start: 0.8456 (ptp90) cc_final: 0.7822 (ptp90) REVERT: 4 11 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8354 (ttp80) REVERT: 4 23 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6399 (mtm110) REVERT: 4 29 MET cc_start: 0.7616 (mtt) cc_final: 0.7181 (mmp) REVERT: 4 46 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6916 (tpt) REVERT: 4 62 TYR cc_start: 0.7803 (t80) cc_final: 0.7538 (t80) REVERT: 4 83 GLU cc_start: 0.7578 (tt0) cc_final: 0.6510 (tt0) REVERT: 4 84 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6133 (mp) REVERT: 4 115 LEU cc_start: 0.8231 (pp) cc_final: 0.7807 (pp) REVERT: 4 118 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6780 (mtp180) REVERT: 4 131 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7405 (tp) REVERT: 4 137 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: 4 146 ARG cc_start: 0.6773 (ptm160) cc_final: 0.6203 (ptm160) REVERT: 4 154 TRP cc_start: 0.7641 (t60) cc_final: 0.7221 (t60) REVERT: 4 168 ILE cc_start: 0.6952 (pt) cc_final: 0.6521 (pt) REVERT: 4 171 MET cc_start: 0.8456 (mtp) cc_final: 0.7852 (mtp) REVERT: 4 190 ILE cc_start: 0.7975 (mt) cc_final: 0.7594 (pt) REVERT: 4 193 GLU cc_start: 0.7498 (tp30) cc_final: 0.7007 (tp30) REVERT: 4 194 LEU cc_start: 0.7601 (tt) cc_final: 0.7139 (tt) REVERT: 4 247 ASN cc_start: 0.7548 (m-40) cc_final: 0.7168 (t0) REVERT: 4 262 GLU cc_start: 0.6942 (mp0) cc_final: 0.6574 (mp0) REVERT: 4 286 ASN cc_start: 0.7884 (t0) cc_final: 0.7557 (t0) REVERT: 4 298 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6622 (mpp) REVERT: 5 23 ARG cc_start: 0.6367 (mtm180) cc_final: 0.6011 (mpp80) REVERT: 5 55 LYS cc_start: 0.6036 (mtmm) cc_final: 0.5672 (mtmm) REVERT: 5 105 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6015 (mt) REVERT: 5 142 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3965 (mm-30) REVERT: 5 157 MET cc_start: 0.6715 (tmm) cc_final: 0.6509 (ppp) REVERT: 5 171 MET cc_start: 0.7468 (mtp) cc_final: 0.6959 (mtp) REVERT: 5 215 LYS cc_start: 0.7370 (mmtt) cc_final: 0.6938 (tmtt) REVERT: 5 241 ASN cc_start: 0.6955 (t0) cc_final: 0.6458 (t0) REVERT: 6 41 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8062 (mm-30) REVERT: 6 46 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7272 (tpt) REVERT: 6 60 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7392 (ttpp) REVERT: 6 101 MET cc_start: 0.7226 (ttm) cc_final: 0.7000 (ttm) REVERT: 6 107 LEU cc_start: 0.7152 (pt) cc_final: 0.6837 (tp) REVERT: 6 134 ASP cc_start: 0.6816 (t0) cc_final: 0.6475 (t0) REVERT: 6 135 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7098 (mm-30) REVERT: 6 143 ARG cc_start: 0.8109 (ppt170) cc_final: 0.7655 (ppt170) REVERT: 6 146 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7519 (ptm160) REVERT: 6 149 THR cc_start: 0.7759 (p) cc_final: 0.7413 (p) REVERT: 6 150 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: 6 175 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7328 (ttmm) REVERT: 6 189 SER cc_start: 0.8667 (p) cc_final: 0.8266 (m) REVERT: 6 209 PHE cc_start: 0.7483 (t80) cc_final: 0.7047 (t80) REVERT: 6 219 PHE cc_start: 0.5817 (m-80) cc_final: 0.5504 (m-80) REVERT: 6 231 GLN cc_start: 0.8695 (tt0) cc_final: 0.8019 (mt0) REVERT: 6 242 MET cc_start: 0.8282 (tpp) cc_final: 0.7378 (mmm) REVERT: 6 243 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6608 (ttm-80) REVERT: 6 255 GLU cc_start: 0.6823 (tp30) cc_final: 0.6224 (tp30) REVERT: 6 266 GLU cc_start: 0.7702 (tp30) cc_final: 0.7006 (tp30) REVERT: 7 24 LYS cc_start: 0.7552 (tttt) cc_final: 0.7280 (ttpp) REVERT: 7 39 GLU cc_start: 0.7601 (mp0) cc_final: 0.7030 (mp0) REVERT: 7 48 TYR cc_start: 0.8104 (m-80) cc_final: 0.7347 (m-10) REVERT: 7 83 GLU cc_start: 0.7204 (tt0) cc_final: 0.6927 (mt-10) REVERT: 7 98 LEU cc_start: 0.6659 (mt) cc_final: 0.6406 (mm) REVERT: 7 111 ASP cc_start: 0.7240 (t70) cc_final: 0.7032 (t70) REVERT: 7 129 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7467 (mttp) REVERT: 7 145 ASN cc_start: 0.7752 (m-40) cc_final: 0.7469 (m-40) REVERT: 7 146 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7612 (ptm160) REVERT: 7 156 LYS cc_start: 0.7793 (ttpt) cc_final: 0.7573 (tttp) REVERT: 7 162 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7549 (p) REVERT: 7 175 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7231 (ttmt) REVERT: 7 181 ASN cc_start: 0.7647 (t0) cc_final: 0.7163 (t0) REVERT: 7 193 GLU cc_start: 0.8046 (tp30) cc_final: 0.7475 (tp30) REVERT: 7 232 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6765 (ttpp) REVERT: 7 271 PHE cc_start: 0.7722 (t80) cc_final: 0.7454 (t80) outliers start: 106 outliers final: 71 residues processed: 664 average time/residue: 0.3761 time to fit residues: 347.1130 Evaluate side-chains 693 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 602 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 119 LEU Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 261 HIS Chi-restraints excluded: chain 1 residue 295 THR Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 96 GLU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 259 ASN Chi-restraints excluded: chain 3 residue 263 THR Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 131 ILE Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 300 ARG Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 150 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 109 GLU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 142 GLU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.0020 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 64 ASN ** 1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN 2 191 GLN ** 3 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 227 ASN 3 259 ASN ** 5 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 231 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18772 Z= 0.200 Angle : 0.626 14.220 25612 Z= 0.306 Chirality : 0.040 0.241 2863 Planarity : 0.004 0.037 3122 Dihedral : 15.460 88.211 3097 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.12 % Allowed : 28.73 % Favored : 66.15 % 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: -0.84 (0.19), residues: 2163 helix: 0.49 (0.15), residues: 1183 sheet: -1.73 (0.38), residues: 224 loop : -1.78 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 6 154 HIS 0.003 0.001 HIS 3 185 PHE 0.011 0.001 PHE 6 219 TYR 0.032 0.001 TYR 5 62 ARG 0.007 0.000 ARG 7 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 600 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7432 (ttp-170) REVERT: 1 23 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7059 (mtm110) REVERT: 1 30 ASP cc_start: 0.7224 (m-30) cc_final: 0.6955 (m-30) REVERT: 1 31 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6565 (ttm170) REVERT: 1 33 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7808 (tmm-80) REVERT: 1 37 ASP cc_start: 0.8042 (p0) cc_final: 0.7273 (p0) REVERT: 1 38 LEU cc_start: 0.7658 (mt) cc_final: 0.7367 (mm) REVERT: 1 39 GLU cc_start: 0.6485 (mp0) cc_final: 0.5492 (mp0) REVERT: 1 48 TYR cc_start: 0.8384 (m-80) cc_final: 0.7700 (m-80) REVERT: 1 57 THR cc_start: 0.7939 (t) cc_final: 0.7689 (t) REVERT: 1 65 GLN cc_start: 0.7394 (pt0) cc_final: 0.7084 (pp30) REVERT: 1 81 HIS cc_start: 0.7950 (t70) cc_final: 0.7728 (t-170) REVERT: 1 83 GLU cc_start: 0.7922 (tt0) cc_final: 0.7551 (mt-10) REVERT: 1 87 ASN cc_start: 0.8138 (m-40) cc_final: 0.7573 (m110) REVERT: 1 92 ASP cc_start: 0.7324 (t0) cc_final: 0.6936 (t0) REVERT: 1 100 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7258 (tm-30) REVERT: 1 101 MET cc_start: 0.8265 (ttp) cc_final: 0.8050 (ttp) REVERT: 1 105 LEU cc_start: 0.7543 (pp) cc_final: 0.7186 (mp) REVERT: 1 109 GLU cc_start: 0.7320 (tt0) cc_final: 0.6902 (tt0) REVERT: 1 129 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7824 (mtpt) REVERT: 1 142 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: 1 163 LYS cc_start: 0.8146 (mptt) cc_final: 0.7895 (mmtm) REVERT: 1 171 MET cc_start: 0.8159 (mtp) cc_final: 0.7798 (mmm) REVERT: 1 182 SER cc_start: 0.8207 (t) cc_final: 0.7634 (p) REVERT: 1 192 VAL cc_start: 0.8185 (t) cc_final: 0.7932 (m) REVERT: 1 193 GLU cc_start: 0.7880 (tp30) cc_final: 0.7517 (tp30) REVERT: 1 261 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5976 (m170) REVERT: 1 269 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: 1 274 LYS cc_start: 0.7966 (mttt) cc_final: 0.7587 (mtpp) REVERT: 1 279 ASP cc_start: 0.7777 (p0) cc_final: 0.7362 (p0) REVERT: 1 285 LYS cc_start: 0.7637 (tppt) cc_final: 0.7080 (tppt) REVERT: 1 296 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6893 (tm-30) REVERT: 1 297 ASP cc_start: 0.7813 (t0) cc_final: 0.7495 (t0) REVERT: 1 300 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7535 (ttm-80) REVERT: 1 310 ASP cc_start: 0.7496 (m-30) cc_final: 0.7211 (m-30) REVERT: 2 33 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7643 (ttp-170) REVERT: 2 39 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6628 (tm-30) REVERT: 2 41 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: 2 46 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: 2 48 TYR cc_start: 0.7867 (m-80) cc_final: 0.7518 (m-80) REVERT: 2 89 LYS cc_start: 0.7727 (mmmm) cc_final: 0.7420 (mmmm) REVERT: 2 96 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7206 (tp30) REVERT: 2 100 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7576 (tm-30) REVERT: 2 121 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7119 (mt-10) REVERT: 2 129 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7609 (mmpt) REVERT: 2 143 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6029 (ppt-90) REVERT: 2 146 ARG cc_start: 0.7372 (ptm160) cc_final: 0.7001 (tmm-80) REVERT: 2 150 GLN cc_start: 0.7650 (mt0) cc_final: 0.7137 (mt0) REVERT: 2 163 LYS cc_start: 0.7977 (mppt) cc_final: 0.7408 (mmtm) REVERT: 2 181 ASN cc_start: 0.7406 (t0) cc_final: 0.6606 (t0) REVERT: 2 235 TYR cc_start: 0.7560 (t80) cc_final: 0.7012 (t80) REVERT: 2 262 GLU cc_start: 0.6879 (mp0) cc_final: 0.6402 (pm20) REVERT: 2 286 ASN cc_start: 0.8537 (t0) cc_final: 0.7975 (t0) REVERT: 2 300 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7472 (mtm-85) REVERT: 2 309 GLU cc_start: 0.7085 (pm20) cc_final: 0.6508 (pm20) REVERT: 2 313 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.7144 (ttp-110) REVERT: 3 39 GLU cc_start: 0.6875 (mp0) cc_final: 0.6193 (mp0) REVERT: 3 61 LYS cc_start: 0.7924 (tptp) cc_final: 0.7234 (tptp) REVERT: 3 65 GLN cc_start: 0.8179 (pt0) cc_final: 0.7359 (pp30) REVERT: 3 109 GLU cc_start: 0.7838 (tt0) cc_final: 0.7503 (tt0) REVERT: 3 143 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7345 (ppt170) REVERT: 3 157 MET cc_start: 0.7831 (ttm) cc_final: 0.7120 (tpp) REVERT: 3 173 TYR cc_start: 0.8673 (p90) cc_final: 0.8260 (p90) REVERT: 3 175 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7474 (ttmm) REVERT: 3 207 LYS cc_start: 0.8182 (tttt) cc_final: 0.7419 (ttmm) REVERT: 3 220 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: 3 237 PHE cc_start: 0.7084 (t80) cc_final: 0.6676 (t80) REVERT: 3 241 ASN cc_start: 0.7076 (m-40) cc_final: 0.6536 (t0) REVERT: 3 242 MET cc_start: 0.7693 (mmm) cc_final: 0.7369 (tmm) REVERT: 3 255 GLU cc_start: 0.7843 (tp30) cc_final: 0.7502 (tp30) REVERT: 3 268 ASP cc_start: 0.7148 (p0) cc_final: 0.6648 (p0) REVERT: 3 269 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.4936 (t80) REVERT: 3 300 ARG cc_start: 0.8433 (ptp90) cc_final: 0.7799 (ptp90) REVERT: 3 309 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6934 (mm-30) REVERT: 4 23 ARG cc_start: 0.6880 (mtm180) cc_final: 0.6411 (mtm110) REVERT: 4 24 LYS cc_start: 0.7367 (tttp) cc_final: 0.7070 (tptm) REVERT: 4 29 MET cc_start: 0.7644 (mtt) cc_final: 0.7185 (mmp) REVERT: 4 46 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7006 (tpt) REVERT: 4 62 TYR cc_start: 0.7796 (t80) cc_final: 0.7543 (t80) REVERT: 4 83 GLU cc_start: 0.7588 (tt0) cc_final: 0.6223 (tt0) REVERT: 4 84 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6433 (mp) REVERT: 4 115 LEU cc_start: 0.8243 (pp) cc_final: 0.7822 (pp) REVERT: 4 118 ARG cc_start: 0.6956 (ttm170) cc_final: 0.6749 (mtp180) REVERT: 4 137 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: 4 146 ARG cc_start: 0.6742 (ptm160) cc_final: 0.6082 (ptm160) REVERT: 4 154 TRP cc_start: 0.7647 (t60) cc_final: 0.7236 (t60) REVERT: 4 168 ILE cc_start: 0.6954 (pt) cc_final: 0.6500 (pt) REVERT: 4 171 MET cc_start: 0.8455 (mtp) cc_final: 0.7819 (mtp) REVERT: 4 190 ILE cc_start: 0.7966 (mt) cc_final: 0.7585 (pt) REVERT: 4 194 LEU cc_start: 0.7593 (tt) cc_final: 0.7291 (tt) REVERT: 4 262 GLU cc_start: 0.6989 (mp0) cc_final: 0.6573 (mp0) REVERT: 4 286 ASN cc_start: 0.7892 (t0) cc_final: 0.7539 (t0) REVERT: 4 298 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6425 (mpp) REVERT: 5 23 ARG cc_start: 0.6372 (mtm180) cc_final: 0.6005 (mpp80) REVERT: 5 55 LYS cc_start: 0.6035 (mtmm) cc_final: 0.5654 (mtmm) REVERT: 5 62 TYR cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: 5 105 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6095 (mt) REVERT: 5 142 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.3904 (mm-30) REVERT: 5 171 MET cc_start: 0.7481 (mtp) cc_final: 0.6961 (mtp) REVERT: 5 215 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6920 (tmtt) REVERT: 5 241 ASN cc_start: 0.6926 (t0) cc_final: 0.6341 (t0) REVERT: 6 41 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8068 (mm-30) REVERT: 6 46 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7442 (tpt) REVERT: 6 60 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7387 (ttpp) REVERT: 6 61 LYS cc_start: 0.7364 (tptm) cc_final: 0.6953 (tptm) REVERT: 6 107 LEU cc_start: 0.7072 (pt) cc_final: 0.6840 (tp) REVERT: 6 134 ASP cc_start: 0.6658 (t0) cc_final: 0.6395 (t70) REVERT: 6 135 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7115 (mm-30) REVERT: 6 143 ARG cc_start: 0.8117 (ppt170) cc_final: 0.7662 (ppt170) REVERT: 6 146 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7512 (ptm160) REVERT: 6 149 THR cc_start: 0.7777 (p) cc_final: 0.7423 (p) REVERT: 6 150 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: 6 175 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7284 (ttmm) REVERT: 6 189 SER cc_start: 0.8682 (p) cc_final: 0.8279 (m) REVERT: 6 209 PHE cc_start: 0.7493 (t80) cc_final: 0.7074 (t80) REVERT: 6 231 GLN cc_start: 0.8754 (tt0) cc_final: 0.8116 (mt0) REVERT: 6 242 MET cc_start: 0.8255 (tpp) cc_final: 0.7318 (mmm) REVERT: 6 243 ARG cc_start: 0.6833 (ttm-80) cc_final: 0.6590 (ttm-80) REVERT: 6 255 GLU cc_start: 0.7028 (tp30) cc_final: 0.6382 (tp30) REVERT: 6 266 GLU cc_start: 0.7680 (tp30) cc_final: 0.7081 (tp30) REVERT: 6 275 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5856 (mp) REVERT: 7 24 LYS cc_start: 0.7550 (tttt) cc_final: 0.7296 (ttpp) REVERT: 7 39 GLU cc_start: 0.7592 (mp0) cc_final: 0.7048 (mp0) REVERT: 7 83 GLU cc_start: 0.7216 (tt0) cc_final: 0.6947 (mt-10) REVERT: 7 98 LEU cc_start: 0.6666 (mt) cc_final: 0.6419 (mm) REVERT: 7 111 ASP cc_start: 0.7196 (t70) cc_final: 0.6872 (t70) REVERT: 7 129 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7455 (mttp) REVERT: 7 145 ASN cc_start: 0.7757 (m-40) cc_final: 0.7486 (m-40) REVERT: 7 146 ARG cc_start: 0.7824 (ptm160) cc_final: 0.7609 (ptm160) REVERT: 7 156 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7568 (tttp) REVERT: 7 162 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7568 (p) REVERT: 7 175 LYS cc_start: 0.7614 (ttmt) cc_final: 0.7256 (ttmt) REVERT: 7 181 ASN cc_start: 0.7639 (t0) cc_final: 0.7171 (t0) REVERT: 7 193 GLU cc_start: 0.8126 (tp30) cc_final: 0.7522 (tp30) REVERT: 7 232 LYS cc_start: 0.7409 (ttmm) cc_final: 0.6741 (ttpp) REVERT: 7 271 PHE cc_start: 0.7711 (t80) cc_final: 0.7476 (t80) outliers start: 96 outliers final: 65 residues processed: 649 average time/residue: 0.3896 time to fit residues: 348.7851 Evaluate side-chains 682 residues out of total 1876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 597 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 31 ARG Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 110 THR Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 148 LEU Chi-restraints excluded: chain 1 residue 215 LYS Chi-restraints excluded: chain 1 residue 261 HIS Chi-restraints excluded: chain 1 residue 269 PHE Chi-restraints excluded: chain 1 residue 309 GLU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 46 MET Chi-restraints excluded: chain 2 residue 101 MET Chi-restraints excluded: chain 2 residue 105 LEU Chi-restraints excluded: chain 2 residue 143 ARG Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 213 LEU Chi-restraints excluded: chain 2 residue 263 THR Chi-restraints excluded: chain 3 residue 10 SER Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 45 MET Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 99 VAL Chi-restraints excluded: chain 3 residue 110 THR Chi-restraints excluded: chain 3 residue 142 GLU Chi-restraints excluded: chain 3 residue 143 ARG Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 220 GLU Chi-restraints excluded: chain 3 residue 269 PHE Chi-restraints excluded: chain 3 residue 270 VAL Chi-restraints excluded: chain 3 residue 312 LEU Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 46 MET Chi-restraints excluded: chain 4 residue 60 LYS Chi-restraints excluded: chain 4 residue 79 VAL Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 110 THR Chi-restraints excluded: chain 4 residue 114 ARG Chi-restraints excluded: chain 4 residue 119 LEU Chi-restraints excluded: chain 4 residue 130 LEU Chi-restraints excluded: chain 4 residue 137 GLN Chi-restraints excluded: chain 4 residue 142 GLU Chi-restraints excluded: chain 4 residue 148 LEU Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 230 LEU Chi-restraints excluded: chain 4 residue 231 GLN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 298 MET Chi-restraints excluded: chain 4 residue 300 ARG Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 105 LEU Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 142 GLU Chi-restraints excluded: chain 5 residue 299 LEU Chi-restraints excluded: chain 6 residue 46 MET Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 82 ILE Chi-restraints excluded: chain 6 residue 99 VAL Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 142 GLU Chi-restraints excluded: chain 6 residue 148 LEU Chi-restraints excluded: chain 6 residue 150 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 269 PHE Chi-restraints excluded: chain 6 residue 275 LEU Chi-restraints excluded: chain 7 residue 107 LEU Chi-restraints excluded: chain 7 residue 117 LYS Chi-restraints excluded: chain 7 residue 119 LEU Chi-restraints excluded: chain 7 residue 148 LEU Chi-restraints excluded: chain 7 residue 149 THR Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 7 residue 231 GLN Chi-restraints excluded: chain 7 residue 269 PHE Chi-restraints excluded: chain 7 residue 305 ASP Chi-restraints excluded: chain 7 residue 309 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5 > 50: distance: 31 - 37: 31.454 distance: 37 - 38: 51.670 distance: 38 - 39: 56.981 distance: 38 - 41: 68.262 distance: 39 - 40: 39.090 distance: 39 - 46: 70.516 distance: 41 - 42: 40.860 distance: 42 - 43: 17.464 distance: 43 - 44: 46.882 distance: 43 - 45: 18.333 distance: 46 - 47: 57.284 distance: 47 - 48: 56.958 distance: 47 - 50: 38.554 distance: 48 - 49: 40.621 distance: 48 - 54: 58.506 distance: 50 - 51: 39.289 distance: 51 - 53: 40.036 distance: 54 - 55: 54.487 distance: 54 - 60: 55.183 distance: 55 - 56: 43.284 distance: 55 - 58: 51.768 distance: 56 - 57: 20.680 distance: 56 - 61: 60.739 distance: 58 - 59: 50.070 distance: 59 - 60: 56.406 distance: 61 - 62: 39.067 distance: 62 - 63: 58.091 distance: 62 - 65: 56.546 distance: 63 - 64: 40.640 distance: 63 - 69: 42.728 distance: 65 - 66: 32.753 distance: 66 - 67: 65.877 distance: 66 - 68: 41.151 distance: 69 - 70: 40.478 distance: 71 - 72: 40.161 distance: 71 - 77: 9.472 distance: 73 - 74: 41.493 distance: 74 - 75: 39.457 distance: 74 - 76: 40.251 distance: 77 - 78: 41.974 distance: 78 - 79: 56.564 distance: 78 - 81: 64.219 distance: 79 - 80: 52.261 distance: 79 - 82: 12.545 distance: 82 - 83: 20.196 distance: 83 - 84: 39.946 distance: 83 - 86: 38.699 distance: 84 - 85: 57.754 distance: 84 - 91: 69.168 distance: 87 - 88: 69.775 distance: 88 - 89: 57.253 distance: 89 - 90: 26.664 distance: 91 - 92: 38.792 distance: 91 - 97: 54.707 distance: 92 - 93: 39.915 distance: 92 - 95: 40.074 distance: 93 - 94: 39.035 distance: 93 - 98: 40.943 distance: 94 - 118: 34.520 distance: 95 - 96: 41.353 distance: 96 - 97: 39.036 distance: 98 - 99: 39.546 distance: 99 - 100: 38.565 distance: 99 - 102: 41.540 distance: 100 - 101: 56.725 distance: 100 - 105: 61.461 distance: 101 - 123: 35.624 distance: 102 - 103: 4.940 distance: 102 - 104: 37.734 distance: 105 - 106: 20.163 distance: 106 - 107: 27.288 distance: 106 - 109: 25.226 distance: 107 - 108: 41.295 distance: 107 - 113: 35.534 distance: 108 - 134: 20.960 distance: 109 - 110: 40.254 distance: 110 - 111: 54.387