Starting phenix.real_space_refine on Sun Mar 17 10:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/03_2024/7rzy_24783_updated.pdb" } resolution = 3.5 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= 0.021 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 21 5.49 5 S 77 5.16 5 C 11032 2.51 5 N 3017 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 37": "OD1" <-> "OD2" Residue "1 GLU 83": "OE1" <-> "OE2" Residue "1 ASP 86": "OD1" <-> "OD2" Residue "1 GLU 135": "OE1" <-> "OE2" Residue "1 GLU 141": "OE1" <-> "OE2" Residue "1 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 255": "OE1" <-> "OE2" Residue "1 GLU 267": "OE1" <-> "OE2" Residue "1 ASP 279": "OD1" <-> "OD2" Residue "1 GLU 296": "OE1" <-> "OE2" Residue "1 GLU 309": "OE1" <-> "OE2" Residue "2 GLU 41": "OE1" <-> "OE2" Residue "2 ASP 103": "OD1" <-> "OD2" Residue "2 GLU 267": "OE1" <-> "OE2" Residue "2 ASP 310": "OD1" <-> "OD2" Residue "3 ASP 30": "OD1" <-> "OD2" Residue "3 ASP 37": "OD1" <-> "OD2" Residue "3 GLU 96": "OE1" <-> "OE2" Residue "3 ASP 134": "OD1" <-> "OD2" Residue "3 PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 267": "OE1" <-> "OE2" Residue "3 GLU 296": "OE1" <-> "OE2" Residue "4 ASP 34": "OD1" <-> "OD2" Residue "4 ASP 37": "OD1" <-> "OD2" Residue "4 GLU 41": "OE1" <-> "OE2" Residue "4 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 83": "OE1" <-> "OE2" Residue "4 GLU 100": "OE1" <-> "OE2" Residue "4 GLU 141": "OE1" <-> "OE2" Residue "4 ASP 305": "OD1" <-> "OD2" Residue "4 GLU 309": "OE1" <-> "OE2" Residue "5 ASP 37": "OD1" <-> "OD2" Residue "5 GLU 39": "OE1" <-> "OE2" Residue "5 GLU 41": "OE1" <-> "OE2" Residue "5 GLU 83": "OE1" <-> "OE2" Residue "5 GLU 96": "OE1" <-> "OE2" Residue "5 GLU 100": "OE1" <-> "OE2" Residue "5 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 214": "OD1" <-> "OD2" Residue "5 GLU 266": "OE1" <-> "OE2" Residue "6 ASP 37": "OD1" <-> "OD2" Residue "6 GLU 41": "OE1" <-> "OE2" Residue "6 ASP 111": "OD1" <-> "OD2" Residue "6 GLU 135": "OE1" <-> "OE2" Residue "6 GLU 141": "OE1" <-> "OE2" Residue "6 PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 193": "OE1" <-> "OE2" Residue "6 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 220": "OE1" <-> "OE2" Residue "6 GLU 296": "OE1" <-> "OE2" Residue "6 ASP 310": "OD1" <-> "OD2" Residue "7 GLU 266": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17458 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "2" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "3" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "4" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "5" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "6" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "7" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2463 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 294} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "1" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Time building chain proxies: 9.03, per 1000 atoms: 0.52 Number of scatterers: 17458 At special positions: 0 Unit cell: (154.057, 154.057, 68.1667, 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 21 15.00 O 3311 8.00 N 3017 7.00 C 11032 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 3.0 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: 95 helices and 2 sheets defined 46.2% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 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: 3.999A pdb=" N ARG 1 68 " --> pdb=" O ASN 1 64 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU 1 69 " --> pdb=" O GLN 1 65 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER 1 70 " --> pdb=" O ASN 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 90 through 99 Processing helix chain '1' and resid 115 through 126 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 150 through 161 Processing helix chain '1' and resid 172 through 180 removed outlier: 3.766A pdb=" N LYS 1 175 " --> pdb=" O PRO 1 172 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL 1 176 " --> pdb=" O TYR 1 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 1 180 " --> pdb=" O VAL 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 187 removed outlier: 3.604A pdb=" N ARG 1 187 " --> pdb=" O GLN 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 216 Processing helix chain '1' and resid 228 through 237 removed outlier: 4.059A pdb=" N LYS 1 232 " --> pdb=" O GLU 1 228 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS 1 233 " --> pdb=" O SER 1 229 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 257 Processing helix chain '1' and resid 269 through 275 Processing helix chain '1' and resid 309 through 313 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: 3.866A pdb=" N ARG 2 68 " --> pdb=" O ASN 2 64 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU 2 69 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER 2 70 " --> pdb=" O ASN 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 90 through 100 Processing helix chain '2' and resid 115 through 126 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 150 through 161 Processing helix chain '2' and resid 172 through 180 removed outlier: 3.806A pdb=" N LYS 2 175 " --> pdb=" O PRO 2 172 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL 2 176 " --> pdb=" O TYR 2 173 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA 2 180 " --> pdb=" O VAL 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 205 through 216 Processing helix chain '2' and resid 228 through 237 removed outlier: 4.029A pdb=" N LYS 2 232 " --> pdb=" O GLU 2 228 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS 2 233 " --> pdb=" O SER 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 242 through 257 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: 3.951A pdb=" N ARG 3 68 " --> pdb=" O ASN 3 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU 3 69 " --> pdb=" O GLN 3 65 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER 3 70 " --> pdb=" O ASN 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 90 through 100 Processing helix chain '3' and resid 115 through 126 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 150 through 161 Processing helix chain '3' and resid 172 through 180 removed outlier: 3.561A pdb=" N LYS 3 175 " --> pdb=" O PRO 3 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 3 176 " --> pdb=" O TYR 3 173 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA 3 180 " --> pdb=" O VAL 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 182 through 186 Processing helix chain '3' and resid 205 through 216 Processing helix chain '3' and resid 228 through 237 removed outlier: 4.112A pdb=" N LYS 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS 3 233 " --> pdb=" O SER 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 257 Processing helix chain '3' and resid 269 through 275 Processing helix chain '3' and resid 296 through 299 Processing helix chain '3' and resid 309 through 313 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: 3.946A pdb=" N ARG 4 68 " --> pdb=" O ASN 4 64 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU 4 69 " --> pdb=" O GLN 4 65 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER 4 70 " --> pdb=" O ASN 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 100 Processing helix chain '4' and resid 115 through 126 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 150 through 161 Processing helix chain '4' and resid 172 through 180 removed outlier: 3.708A pdb=" N ALA 4 180 " --> pdb=" O VAL 4 177 " (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: 4.260A pdb=" N LYS 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS 4 233 " --> pdb=" O SER 4 229 " (cutoff:3.500A) Processing helix chain '4' and resid 242 through 257 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: 3.961A pdb=" N ARG 5 68 " --> pdb=" O ASN 5 64 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU 5 69 " --> pdb=" O GLN 5 65 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER 5 70 " --> pdb=" O ASN 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 90 through 100 Processing helix chain '5' and resid 115 through 126 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 150 through 161 Processing helix chain '5' and resid 174 through 180 removed outlier: 3.865A pdb=" N ALA 5 180 " --> pdb=" O VAL 5 177 " (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: 4.182A pdb=" N LYS 5 232 " --> pdb=" O GLU 5 228 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS 5 233 " --> pdb=" O SER 5 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 5 234 " --> pdb=" O LEU 5 230 " (cutoff:3.500A) Processing helix chain '5' and resid 242 through 257 Processing helix chain '5' and resid 269 through 275 Processing helix chain '5' and resid 296 through 299 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: 3.951A pdb=" N ARG 6 68 " --> pdb=" O ASN 6 64 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU 6 69 " --> pdb=" O GLN 6 65 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 6 70 " --> pdb=" O ASN 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 90 through 100 Processing helix chain '6' and resid 115 through 126 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 150 through 161 Processing helix chain '6' and resid 172 through 180 removed outlier: 3.540A pdb=" N LYS 6 175 " --> pdb=" O PRO 6 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL 6 176 " --> pdb=" O TYR 6 173 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA 6 180 " --> pdb=" O VAL 6 177 " (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: 3.782A pdb=" N LYS 6 232 " --> pdb=" O GLU 6 228 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS 6 233 " --> pdb=" O SER 6 229 " (cutoff:3.500A) Processing helix chain '6' and resid 242 through 257 Processing helix chain '6' and resid 269 through 275 Processing helix chain '6' and resid 297 through 299 No H-bonds generated for 'chain '6' and resid 297 through 299' 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: 3.923A pdb=" N ARG 7 68 " --> pdb=" O ASN 7 64 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU 7 69 " --> pdb=" O GLN 7 65 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER 7 70 " --> pdb=" O ASN 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 90 through 100 Processing helix chain '7' and resid 115 through 126 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 150 through 161 Processing helix chain '7' and resid 172 through 180 removed outlier: 3.519A pdb=" N LYS 7 175 " --> pdb=" O PRO 7 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL 7 176 " --> pdb=" O TYR 7 173 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 7 180 " --> pdb=" O VAL 7 177 " (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: 3.732A pdb=" N LYS 7 232 " --> pdb=" O GLU 7 228 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS 7 233 " --> pdb=" O SER 7 229 " (cutoff:3.500A) Processing helix chain '7' and resid 242 through 257 Processing helix chain '7' and resid 269 through 275 Processing helix chain '7' and resid 297 through 299 No H-bonds generated for 'chain '7' and resid 297 through 299' 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 79 through 82 removed outlier: 7.551A pdb=" N LEU 1 130 " --> pdb=" O LEU 1 80 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE 1 82 " --> pdb=" O LEU 1 130 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE 1 132 " --> pdb=" O ILE 1 82 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '4' and resid 79 through 82 removed outlier: 7.655A pdb=" N LEU 4 130 " --> pdb=" O LEU 4 80 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE 4 82 " --> pdb=" O LEU 4 130 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE 4 132 " --> pdb=" O ILE 4 82 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 561 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3535 1.34 - 1.46: 3843 1.46 - 1.58: 10262 1.58 - 1.70: 35 1.70 - 1.81: 133 Bond restraints: 17808 Sorted by residual: bond pdb=" N LYS 1 89 " pdb=" CA LYS 1 89 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N VAL 5 79 " pdb=" CA VAL 5 79 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL 7 79 " pdb=" CA VAL 7 79 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N VAL 2 17 " pdb=" CA VAL 2 17 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.21e+01 bond pdb=" N ILE 1 131 " pdb=" CA ILE 1 131 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.14e-02 7.69e+03 1.21e+01 ... (remaining 17803 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.41: 626 106.41 - 113.74: 9367 113.74 - 121.08: 8513 121.08 - 128.41: 5518 128.41 - 135.75: 105 Bond angle restraints: 24129 Sorted by residual: angle pdb=" PB ATP 1 402 " pdb=" O3B ATP 1 402 " pdb=" PG ATP 1 402 " ideal model delta sigma weight residual 139.87 132.00 7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" PA ATP 6 401 " pdb=" O3A ATP 6 401 " pdb=" PB ATP 6 401 " ideal model delta sigma weight residual 136.83 131.12 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" PB ATP 1 401 " pdb=" O3B ATP 1 401 " pdb=" PG ATP 1 401 " ideal model delta sigma weight residual 139.87 134.43 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" PA ATP 2 401 " pdb=" O3A ATP 2 401 " pdb=" PB ATP 2 401 " ideal model delta sigma weight residual 136.83 131.52 5.31 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASN 2 200 " pdb=" N GLY 2 201 " pdb=" CA GLY 2 201 " ideal model delta sigma weight residual 119.99 125.93 -5.94 1.13e+00 7.83e-01 2.76e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9817 17.95 - 35.90: 890 35.90 - 53.85: 282 53.85 - 71.79: 34 71.79 - 89.74: 16 Dihedral angle restraints: 11039 sinusoidal: 4697 harmonic: 6342 Sorted by residual: dihedral pdb=" CA MET 4 171 " pdb=" C MET 4 171 " pdb=" N PRO 4 172 " pdb=" CA PRO 4 172 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLN 4 191 " pdb=" C GLN 4 191 " pdb=" N VAL 4 192 " pdb=" CA VAL 4 192 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN 1 191 " pdb=" C GLN 1 191 " pdb=" N VAL 1 192 " pdb=" CA VAL 1 192 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 11036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 805 0.041 - 0.081: 796 0.081 - 0.121: 738 0.121 - 0.162: 261 0.162 - 0.202: 95 Chirality restraints: 2695 Sorted by residual: chirality pdb=" CA ILE 1 82 " pdb=" N ILE 1 82 " pdb=" C ILE 1 82 " pdb=" CB ILE 1 82 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE 6 82 " pdb=" N ILE 6 82 " pdb=" C ILE 6 82 " pdb=" CB ILE 6 82 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL 6 292 " pdb=" N VAL 6 292 " pdb=" C VAL 6 292 " pdb=" CB VAL 6 292 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 2692 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN 7 191 " 0.024 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C GLN 7 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 7 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 7 192 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 6 191 " 0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C GLN 6 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 6 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 6 192 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN 5 191 " 0.024 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C GLN 5 191 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN 5 191 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL 5 192 " 0.029 2.00e-02 2.50e+03 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6911 2.97 - 3.45: 18490 3.45 - 3.94: 27869 3.94 - 4.42: 29827 4.42 - 4.90: 51646 Nonbonded interactions: 134743 Sorted by model distance: nonbonded pdb=" O ILE 1 133 " pdb=" N PHE 1 169 " model vdw 2.491 2.520 nonbonded pdb=" NH1 ARG 4 14 " pdb=" OG SER 5 40 " model vdw 2.501 2.520 nonbonded pdb=" O ILE 3 133 " pdb=" N PHE 3 169 " model vdw 2.550 2.520 nonbonded pdb=" O MET 4 171 " pdb=" OG SER 4 174 " model vdw 2.558 2.440 nonbonded pdb=" O MET 7 101 " pdb=" N ASP 7 103 " model vdw 2.559 2.520 ... (remaining 134738 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' and resid 4 through 314) selection = (chain '2' and resid 4 through 314) selection = (chain '3' and resid 4 through 314) selection = (chain '4' and resid 4 through 314) selection = (chain '5' and resid 4 through 314) selection = (chain '6' and resid 4 through 314) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.410 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3956 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 : 0.014 0.045 17808 Z= 0.930 Angle : 1.827 7.866 24129 Z= 1.373 Chirality : 0.083 0.202 2695 Planarity : 0.003 0.050 3080 Dihedral : 15.463 89.743 6937 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 1.43 % Allowed : 10.17 % Favored : 88.40 % Rotamer: Outliers : 0.80 % Allowed : 4.83 % Favored : 94.37 % 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: -2.89 (0.15), residues: 2163 helix: -1.28 (0.13), residues: 1113 sheet: -4.06 (0.36), residues: 70 loop : -2.47 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 4 308 HIS 0.004 0.001 HIS 7 185 PHE 0.014 0.001 PHE 5 136 TYR 0.019 0.001 TYR 4 173 ARG 0.003 0.001 ARG 6 187 *********************** 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 415 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 400 time to evaluate : 1.764 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 36 SER cc_start: 0.6845 (m) cc_final: 0.6412 (p) REVERT: 1 89 LYS cc_start: 0.6656 (mtmm) cc_final: 0.6249 (mtmm) REVERT: 1 132 ILE cc_start: 0.5961 (mt) cc_final: 0.5152 (mt) REVERT: 1 192 VAL cc_start: 0.3705 (OUTLIER) cc_final: 0.2872 (m) REVERT: 2 44 CYS cc_start: 0.7151 (m) cc_final: 0.6803 (p) REVERT: 2 58 VAL cc_start: 0.2918 (t) cc_final: 0.2636 (t) REVERT: 2 147 VAL cc_start: 0.5963 (p) cc_final: 0.5743 (p) REVERT: 3 192 VAL cc_start: 0.6004 (OUTLIER) cc_final: 0.5636 (t) REVERT: 4 211 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5998 (mm-30) REVERT: 6 190 ILE cc_start: 0.2580 (mt) cc_final: 0.2361 (mt) REVERT: 7 89 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7604 (mtmm) REVERT: 7 190 ILE cc_start: 0.4252 (mt) cc_final: 0.3754 (pt) REVERT: 7 253 SER cc_start: 0.6332 (t) cc_final: 0.5461 (p) outliers start: 15 outliers final: 3 residues processed: 411 average time/residue: 0.3348 time to fit residues: 196.0922 Evaluate side-chains 311 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 192 VAL Chi-restraints excluded: chain 1 residue 259 ASN Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 7 residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.0370 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 81 HIS ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 65 GLN ** 2 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 247 ASN 5 261 HIS ** 6 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17808 Z= 0.284 Angle : 0.727 12.807 24129 Z= 0.373 Chirality : 0.044 0.188 2695 Planarity : 0.005 0.076 3080 Dihedral : 10.522 89.389 2617 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.47 % Favored : 93.07 % Rotamer: Outliers : 2.39 % Allowed : 12.11 % Favored : 85.50 % 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: -1.51 (0.17), residues: 2163 helix: 0.11 (0.15), residues: 1141 sheet: -3.52 (0.32), residues: 168 loop : -1.92 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 4 284 HIS 0.012 0.002 HIS 5 185 PHE 0.022 0.003 PHE 3 288 TYR 0.020 0.002 TYR 4 173 ARG 0.016 0.001 ARG 7 187 *********************** 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 418 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 373 time to evaluate : 1.973 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 24 LYS cc_start: 0.6582 (ttmm) cc_final: 0.6318 (tttp) REVERT: 1 89 LYS cc_start: 0.6674 (mtmm) cc_final: 0.6324 (mtmm) REVERT: 1 132 ILE cc_start: 0.6445 (mt) cc_final: 0.5745 (mt) REVERT: 1 261 HIS cc_start: 0.4595 (m170) cc_final: 0.4244 (m170) REVERT: 2 43 THR cc_start: 0.7031 (p) cc_final: 0.6763 (m) REVERT: 2 182 SER cc_start: 0.7490 (t) cc_final: 0.6832 (m) REVERT: 2 192 VAL cc_start: 0.6557 (OUTLIER) cc_final: 0.6295 (m) REVERT: 2 254 ILE cc_start: 0.5750 (mm) cc_final: 0.5545 (mm) REVERT: 2 266 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5392 (tp30) REVERT: 3 192 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7507 (m) REVERT: 4 61 LYS cc_start: 0.7950 (tppt) cc_final: 0.7732 (tptp) REVERT: 4 101 MET cc_start: 0.5672 (tmm) cc_final: 0.5396 (ppp) REVERT: 4 169 PHE cc_start: 0.5797 (m-80) cc_final: 0.5494 (m-10) REVERT: 5 101 MET cc_start: 0.6113 (tmm) cc_final: 0.5895 (tmm) REVERT: 5 168 ILE cc_start: 0.5470 (pt) cc_final: 0.4091 (pt) REVERT: 5 249 ILE cc_start: 0.7257 (mm) cc_final: 0.7054 (mm) REVERT: 6 79 VAL cc_start: 0.3654 (m) cc_final: 0.3355 (p) REVERT: 6 141 GLU cc_start: 0.4815 (mm-30) cc_final: 0.3371 (mp0) REVERT: 6 246 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6326 (tpt90) REVERT: 7 41 GLU cc_start: 0.6472 (tt0) cc_final: 0.6165 (tt0) REVERT: 7 59 ILE cc_start: 0.6750 (mt) cc_final: 0.6432 (mt) REVERT: 7 100 GLU cc_start: 0.7006 (tp30) cc_final: 0.6793 (mm-30) REVERT: 7 246 ARG cc_start: 0.5344 (mmm-85) cc_final: 0.4686 (mmm160) REVERT: 7 253 SER cc_start: 0.6879 (t) cc_final: 0.6053 (p) outliers start: 45 outliers final: 18 residues processed: 396 average time/residue: 0.3412 time to fit residues: 192.2163 Evaluate side-chains 355 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 335 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 174 SER Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 112 LEU Chi-restraints excluded: chain 5 residue 174 SER Chi-restraints excluded: chain 5 residue 247 ASN Chi-restraints excluded: chain 6 residue 29 MET Chi-restraints excluded: chain 6 residue 45 MET Chi-restraints excluded: chain 6 residue 282 ASN Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 138 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 HIS ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5350 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 17808 Z= 0.278 Angle : 0.740 11.273 24129 Z= 0.376 Chirality : 0.044 0.199 2695 Planarity : 0.006 0.142 3080 Dihedral : 10.218 89.694 2613 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.63 % Favored : 91.86 % Rotamer: Outliers : 3.66 % Allowed : 14.23 % Favored : 82.10 % 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: -1.46 (0.18), residues: 2163 helix: 0.11 (0.15), residues: 1141 sheet: -3.34 (0.34), residues: 168 loop : -1.88 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 4 284 HIS 0.009 0.002 HIS 6 185 PHE 0.027 0.002 PHE 1 188 TYR 0.023 0.002 TYR 4 48 ARG 0.032 0.001 ARG 6 187 *********************** 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 477 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 408 time to evaluate : 1.794 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 36 SER cc_start: 0.7625 (m) cc_final: 0.7284 (p) REVERT: 1 89 LYS cc_start: 0.6545 (mtmm) cc_final: 0.6233 (mtmm) REVERT: 1 100 GLU cc_start: 0.6036 (mp0) cc_final: 0.5744 (mp0) REVERT: 1 132 ILE cc_start: 0.6185 (mt) cc_final: 0.5691 (mt) REVERT: 1 135 GLU cc_start: 0.4607 (tp30) cc_final: 0.4382 (tp30) REVERT: 1 261 HIS cc_start: 0.4426 (m170) cc_final: 0.4169 (m170) REVERT: 2 13 LYS cc_start: 0.7952 (tppt) cc_final: 0.6818 (tppt) REVERT: 2 32 CYS cc_start: 0.5744 (m) cc_final: 0.5448 (m) REVERT: 2 182 SER cc_start: 0.7764 (t) cc_final: 0.7214 (m) REVERT: 2 191 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6565 (mp10) REVERT: 2 192 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7271 (m) REVERT: 3 121 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7257 (pp20) REVERT: 3 195 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6626 (mtp85) REVERT: 4 43 THR cc_start: 0.5980 (OUTLIER) cc_final: 0.5611 (p) REVERT: 4 61 LYS cc_start: 0.8077 (tppt) cc_final: 0.7676 (tptp) REVERT: 4 169 PHE cc_start: 0.6989 (m-80) cc_final: 0.6727 (m-10) REVERT: 4 255 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6586 (mm-30) REVERT: 5 46 MET cc_start: 0.5388 (tpt) cc_final: 0.4724 (tpp) REVERT: 5 101 MET cc_start: 0.6420 (tmm) cc_final: 0.5709 (tmm) REVERT: 5 136 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5753 (m-80) REVERT: 5 249 ILE cc_start: 0.7724 (mm) cc_final: 0.7460 (mm) REVERT: 6 16 PHE cc_start: 0.7556 (t80) cc_final: 0.7297 (t80) REVERT: 6 29 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5896 (mtm) REVERT: 6 45 MET cc_start: 0.7035 (ttp) cc_final: 0.6827 (ttt) REVERT: 6 81 HIS cc_start: 0.6940 (t-170) cc_final: 0.6531 (t-90) REVERT: 6 141 GLU cc_start: 0.5026 (mm-30) cc_final: 0.3545 (mp0) REVERT: 6 253 SER cc_start: 0.6903 (t) cc_final: 0.6609 (p) REVERT: 7 41 GLU cc_start: 0.6595 (tt0) cc_final: 0.6226 (tt0) REVERT: 7 45 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5584 (ttm) REVERT: 7 59 ILE cc_start: 0.7786 (mt) cc_final: 0.7525 (mt) REVERT: 7 89 LYS cc_start: 0.7556 (mtmm) cc_final: 0.7346 (mtmm) REVERT: 7 193 GLU cc_start: 0.5656 (mm-30) cc_final: 0.5289 (tm-30) REVERT: 7 246 ARG cc_start: 0.6393 (mmm-85) cc_final: 0.5995 (mmm160) outliers start: 69 outliers final: 21 residues processed: 446 average time/residue: 0.3199 time to fit residues: 205.8803 Evaluate side-chains 397 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 370 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 149 THR Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 29 MET Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 271 PHE Chi-restraints excluded: chain 7 residue 45 MET Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN ** 1 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 227 ASN ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 185 HIS ** 4 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 137 GLN 6 181 ASN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17808 Z= 0.262 Angle : 0.715 9.777 24129 Z= 0.360 Chirality : 0.043 0.171 2695 Planarity : 0.006 0.223 3080 Dihedral : 10.538 88.991 2612 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.43 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 16.36 % Favored : 79.39 % 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: -1.37 (0.18), residues: 2163 helix: 0.25 (0.16), residues: 1099 sheet: -3.30 (0.35), residues: 168 loop : -1.86 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 4 154 HIS 0.007 0.002 HIS 1 185 PHE 0.031 0.002 PHE 6 288 TYR 0.023 0.002 TYR 4 173 ARG 0.016 0.001 ARG 5 187 *********************** 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 485 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 405 time to evaluate : 1.920 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 23 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.7808 (ttp-170) REVERT: 1 36 SER cc_start: 0.7668 (m) cc_final: 0.7103 (p) REVERT: 1 89 LYS cc_start: 0.6537 (mtmm) cc_final: 0.6261 (mtmm) REVERT: 1 100 GLU cc_start: 0.6233 (mp0) cc_final: 0.5946 (mp0) REVERT: 1 132 ILE cc_start: 0.6368 (mt) cc_final: 0.5895 (mt) REVERT: 1 135 GLU cc_start: 0.4924 (tp30) cc_final: 0.4649 (tp30) REVERT: 1 193 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6544 (mm-30) REVERT: 1 207 LYS cc_start: 0.7684 (tttm) cc_final: 0.7276 (tptt) REVERT: 1 208 THR cc_start: 0.6912 (t) cc_final: 0.6576 (t) REVERT: 1 215 LYS cc_start: 0.7758 (tppp) cc_final: 0.7557 (tptp) REVERT: 1 239 GLN cc_start: 0.7160 (mp10) cc_final: 0.6670 (mp10) REVERT: 1 261 HIS cc_start: 0.4325 (m170) cc_final: 0.4118 (m170) REVERT: 2 182 SER cc_start: 0.8130 (t) cc_final: 0.7598 (m) REVERT: 2 191 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: 2 206 PHE cc_start: 0.6737 (t80) cc_final: 0.6501 (t80) REVERT: 2 266 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6455 (mm-30) REVERT: 2 298 MET cc_start: 0.2776 (ptm) cc_final: 0.2214 (ptp) REVERT: 3 61 LYS cc_start: 0.8142 (tptt) cc_final: 0.7704 (tptp) REVERT: 3 195 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6684 (mtp85) REVERT: 3 212 TYR cc_start: 0.5319 (OUTLIER) cc_final: 0.4136 (t80) REVERT: 3 255 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6689 (mm-30) REVERT: 4 43 THR cc_start: 0.5936 (p) cc_final: 0.5586 (p) REVERT: 4 146 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.3822 (ttp80) REVERT: 4 214 ASP cc_start: 0.6866 (m-30) cc_final: 0.6483 (m-30) REVERT: 4 255 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7072 (mm-30) REVERT: 4 280 LYS cc_start: 0.6707 (mmtm) cc_final: 0.6423 (mptt) REVERT: 5 101 MET cc_start: 0.6662 (tmm) cc_final: 0.5686 (tmm) REVERT: 5 136 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: 5 168 ILE cc_start: 0.7751 (pt) cc_final: 0.7160 (mt) REVERT: 5 211 GLU cc_start: 0.6213 (tt0) cc_final: 0.5846 (tt0) REVERT: 5 227 ASN cc_start: 0.7031 (p0) cc_final: 0.6736 (p0) REVERT: 5 249 ILE cc_start: 0.7980 (mm) cc_final: 0.7759 (mm) REVERT: 6 14 ARG cc_start: 0.7149 (mpp80) cc_final: 0.6683 (mtm180) REVERT: 6 16 PHE cc_start: 0.7975 (t80) cc_final: 0.7668 (t80) REVERT: 6 140 VAL cc_start: 0.6273 (t) cc_final: 0.6048 (t) REVERT: 6 141 GLU cc_start: 0.5454 (mm-30) cc_final: 0.3871 (mp0) REVERT: 6 253 SER cc_start: 0.7291 (t) cc_final: 0.7035 (p) REVERT: 7 14 ARG cc_start: 0.7593 (ptp90) cc_final: 0.7375 (ptp-170) REVERT: 7 45 MET cc_start: 0.6726 (ttp) cc_final: 0.6328 (ttm) REVERT: 7 153 ASN cc_start: 0.7069 (m110) cc_final: 0.6230 (m110) REVERT: 7 193 GLU cc_start: 0.6138 (mm-30) cc_final: 0.5781 (tm-30) REVERT: 7 246 ARG cc_start: 0.6318 (mmm-85) cc_final: 0.6013 (mmm160) REVERT: 7 255 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6167 (mm-30) outliers start: 80 outliers final: 39 residues processed: 453 average time/residue: 0.3214 time to fit residues: 210.1568 Evaluate side-chains 420 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 377 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 116 THR Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 133 ILE Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 205 VAL Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 168 ILE Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 238 SER Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 146 ARG Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 234 LEU Chi-restraints excluded: chain 4 residue 244 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 137 GLN Chi-restraints excluded: chain 5 residue 174 SER Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 275 LEU Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 188 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 181 ASN ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 185 HIS ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 247 ASN 7 153 ASN 7 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17808 Z= 0.259 Angle : 0.710 12.958 24129 Z= 0.349 Chirality : 0.043 0.266 2695 Planarity : 0.005 0.111 3080 Dihedral : 10.291 89.111 2611 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.40 % Favored : 91.96 % Rotamer: Outliers : 3.88 % Allowed : 18.22 % Favored : 77.91 % 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: -1.36 (0.18), residues: 2163 helix: 0.34 (0.16), residues: 1092 sheet: -3.35 (0.36), residues: 168 loop : -1.94 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 4 284 HIS 0.011 0.002 HIS 3 138 PHE 0.024 0.002 PHE 6 288 TYR 0.023 0.002 TYR 3 173 ARG 0.011 0.001 ARG 2 203 *********************** 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 499 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 426 time to evaluate : 1.961 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 36 SER cc_start: 0.7758 (m) cc_final: 0.7179 (p) REVERT: 1 100 GLU cc_start: 0.6348 (mp0) cc_final: 0.6034 (mp0) REVERT: 1 132 ILE cc_start: 0.6023 (mt) cc_final: 0.5491 (mt) REVERT: 1 135 GLU cc_start: 0.4755 (tp30) cc_final: 0.4458 (tp30) REVERT: 1 157 MET cc_start: 0.6534 (mtt) cc_final: 0.6194 (mtt) REVERT: 1 239 GLN cc_start: 0.7213 (mp10) cc_final: 0.6774 (mp10) REVERT: 1 255 GLU cc_start: 0.4841 (mt-10) cc_final: 0.4511 (mt-10) REVERT: 1 261 HIS cc_start: 0.4445 (m170) cc_final: 0.4239 (m170) REVERT: 2 23 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7794 (ttp-110) REVERT: 2 60 LYS cc_start: 0.6947 (tppt) cc_final: 0.6677 (mppt) REVERT: 2 182 SER cc_start: 0.8265 (t) cc_final: 0.7642 (m) REVERT: 2 225 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4674 (pt) REVERT: 2 298 MET cc_start: 0.3003 (ptm) cc_final: 0.2676 (ptp) REVERT: 3 195 ARG cc_start: 0.7629 (mtp85) cc_final: 0.6887 (mtp85) REVERT: 4 212 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6049 (t80) REVERT: 4 214 ASP cc_start: 0.7121 (m-30) cc_final: 0.6788 (m-30) REVERT: 5 101 MET cc_start: 0.6173 (tmm) cc_final: 0.5158 (tmm) REVERT: 5 136 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.5649 (m-80) REVERT: 5 227 ASN cc_start: 0.7107 (p0) cc_final: 0.6721 (p0) REVERT: 5 243 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: 5 288 PHE cc_start: 0.5714 (m-10) cc_final: 0.5494 (m-80) REVERT: 6 141 GLU cc_start: 0.5927 (mm-30) cc_final: 0.4417 (mp0) REVERT: 6 156 LYS cc_start: 0.6940 (ttpp) cc_final: 0.6476 (ttmm) REVERT: 6 171 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.4460 (mmm) REVERT: 6 211 GLU cc_start: 0.6438 (tt0) cc_final: 0.6037 (tt0) REVERT: 7 60 LYS cc_start: 0.7620 (tptp) cc_final: 0.7060 (tppt) REVERT: 7 193 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6225 (tm-30) REVERT: 7 255 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6485 (mm-30) outliers start: 73 outliers final: 40 residues processed: 464 average time/residue: 0.3523 time to fit residues: 229.5161 Evaluate side-chains 448 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 403 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 263 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 225 LEU Chi-restraints excluded: chain 2 residue 248 LEU Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 238 SER Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 200 ASN Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 243 ARG Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 247 ASN Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 282 ASN ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.8977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17808 Z= 0.259 Angle : 0.695 9.497 24129 Z= 0.348 Chirality : 0.043 0.367 2695 Planarity : 0.006 0.127 3080 Dihedral : 10.260 82.879 2611 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.80 % Favored : 92.60 % Rotamer: Outliers : 4.83 % Allowed : 19.65 % Favored : 75.52 % 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: -1.42 (0.18), residues: 2163 helix: 0.26 (0.16), residues: 1099 sheet: -3.28 (0.37), residues: 168 loop : -1.97 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 154 HIS 0.008 0.001 HIS 2 81 PHE 0.017 0.002 PHE 4 136 TYR 0.024 0.002 TYR 3 173 ARG 0.014 0.001 ARG 5 195 *********************** 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 530 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 439 time to evaluate : 1.857 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: 1 36 SER cc_start: 0.7606 (m) cc_final: 0.7005 (p) REVERT: 1 100 GLU cc_start: 0.6344 (mp0) cc_final: 0.6012 (mp0) REVERT: 1 101 MET cc_start: 0.6566 (tmm) cc_final: 0.6250 (tmm) REVERT: 1 135 GLU cc_start: 0.4642 (tp30) cc_final: 0.4363 (tp30) REVERT: 1 166 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6836 (mt) REVERT: 1 183 GLN cc_start: 0.7825 (tp40) cc_final: 0.7600 (tp40) REVERT: 1 239 GLN cc_start: 0.7366 (mp10) cc_final: 0.6922 (mp10) REVERT: 2 60 LYS cc_start: 0.7523 (tppt) cc_final: 0.7270 (mmtm) REVERT: 2 130 LEU cc_start: 0.8403 (mp) cc_final: 0.8168 (mt) REVERT: 2 182 SER cc_start: 0.7834 (t) cc_final: 0.7490 (m) REVERT: 2 191 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: 2 212 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5341 (t80) REVERT: 2 298 MET cc_start: 0.3008 (ptm) cc_final: 0.2434 (ptp) REVERT: 3 30 ASP cc_start: 0.6857 (m-30) cc_final: 0.6627 (t0) REVERT: 3 121 GLU cc_start: 0.7303 (pp20) cc_final: 0.6804 (mp0) REVERT: 3 129 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7851 (mtpp) REVERT: 3 195 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7231 (mtp85) REVERT: 3 212 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4405 (t80) REVERT: 3 238 SER cc_start: 0.7495 (OUTLIER) cc_final: 0.7290 (p) REVERT: 4 61 LYS cc_start: 0.8452 (tptm) cc_final: 0.8133 (tptp) REVERT: 4 212 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6163 (t80) REVERT: 4 214 ASP cc_start: 0.7300 (m-30) cc_final: 0.7042 (m-30) REVERT: 4 273 SER cc_start: 0.8080 (t) cc_final: 0.7442 (t) REVERT: 5 101 MET cc_start: 0.6345 (tmm) cc_final: 0.5204 (tmm) REVERT: 5 136 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: 5 153 ASN cc_start: 0.6662 (m110) cc_final: 0.6393 (m-40) REVERT: 5 227 ASN cc_start: 0.7053 (p0) cc_final: 0.6639 (p0) REVERT: 6 14 ARG cc_start: 0.7423 (mpp80) cc_final: 0.6926 (mtm180) REVERT: 6 19 THR cc_start: 0.7117 (m) cc_final: 0.6848 (m) REVERT: 6 29 MET cc_start: 0.7196 (mtt) cc_final: 0.6987 (mtm) REVERT: 6 156 LYS cc_start: 0.7154 (ttpp) cc_final: 0.6483 (tppp) REVERT: 6 171 MET cc_start: 0.4368 (OUTLIER) cc_final: 0.3801 (mtt) REVERT: 6 195 ARG cc_start: 0.7557 (mmp80) cc_final: 0.7202 (tpp-160) REVERT: 7 60 LYS cc_start: 0.7702 (tptp) cc_final: 0.7182 (tppt) REVERT: 7 129 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7712 (mtmt) REVERT: 7 195 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6270 (ttp80) REVERT: 7 255 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6642 (mm-30) outliers start: 91 outliers final: 51 residues processed: 486 average time/residue: 0.3488 time to fit residues: 237.4587 Evaluate side-chains 471 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 411 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 187 ARG Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 116 THR Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 200 ASN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 2 residue 225 LEU Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 59 ILE Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 238 SER Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 176 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 242 MET Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 193 GLU Chi-restraints excluded: chain 7 residue 23 ARG Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 0.0670 chunk 118 optimal weight: 0.4980 chunk 176 optimal weight: 0.0980 chunk 117 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 127 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 231 GLN ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN 7 65 GLN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.9262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17808 Z= 0.184 Angle : 0.679 13.819 24129 Z= 0.333 Chirality : 0.041 0.240 2695 Planarity : 0.007 0.241 3080 Dihedral : 10.112 86.395 2611 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.93 % Favored : 92.46 % Rotamer: Outliers : 3.13 % Allowed : 21.67 % Favored : 75.20 % 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: -1.12 (0.18), residues: 2163 helix: 0.46 (0.16), residues: 1092 sheet: -2.91 (0.54), residues: 84 loop : -1.96 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 154 HIS 0.014 0.001 HIS 1 261 PHE 0.019 0.002 PHE 5 288 TYR 0.026 0.001 TYR 5 235 ARG 0.010 0.001 ARG 1 187 *********************** 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 486 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 427 time to evaluate : 1.860 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: 1 60 LYS cc_start: 0.7325 (tptt) cc_final: 0.7096 (tppt) REVERT: 1 100 GLU cc_start: 0.6277 (mp0) cc_final: 0.5991 (mp0) REVERT: 1 101 MET cc_start: 0.6523 (tmm) cc_final: 0.6236 (tmm) REVERT: 1 132 ILE cc_start: 0.6594 (mp) cc_final: 0.6285 (mt) REVERT: 1 136 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: 1 166 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6873 (mt) REVERT: 1 183 GLN cc_start: 0.7651 (tp40) cc_final: 0.7401 (tp40) REVERT: 1 239 GLN cc_start: 0.7440 (mp10) cc_final: 0.6947 (mp10) REVERT: 2 60 LYS cc_start: 0.7651 (tppt) cc_final: 0.7402 (mmtm) REVERT: 2 62 TYR cc_start: 0.7639 (t80) cc_final: 0.7288 (t80) REVERT: 2 130 LEU cc_start: 0.8392 (mp) cc_final: 0.8167 (mt) REVERT: 2 136 PHE cc_start: 0.6086 (m-10) cc_final: 0.5535 (m-10) REVERT: 2 195 ARG cc_start: 0.6609 (ptp-110) cc_final: 0.6373 (mtm110) REVERT: 2 248 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6744 (tt) REVERT: 2 298 MET cc_start: 0.3017 (ptm) cc_final: 0.2464 (ptp) REVERT: 3 30 ASP cc_start: 0.6879 (m-30) cc_final: 0.6666 (t0) REVERT: 3 121 GLU cc_start: 0.7260 (pp20) cc_final: 0.6827 (mp0) REVERT: 3 129 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7847 (mtpp) REVERT: 3 195 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7192 (mtp85) REVERT: 3 212 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4626 (t80) REVERT: 3 274 LYS cc_start: 0.7088 (mtmm) cc_final: 0.6877 (mtmm) REVERT: 4 41 GLU cc_start: 0.6440 (tp30) cc_final: 0.5993 (tp30) REVERT: 4 61 LYS cc_start: 0.8436 (tptm) cc_final: 0.8222 (tptp) REVERT: 4 132 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6718 (mp) REVERT: 4 212 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6092 (t80) REVERT: 4 214 ASP cc_start: 0.7330 (m-30) cc_final: 0.7096 (m-30) REVERT: 4 273 SER cc_start: 0.8085 (t) cc_final: 0.7434 (t) REVERT: 5 101 MET cc_start: 0.6258 (tmm) cc_final: 0.5126 (tmm) REVERT: 5 136 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: 5 153 ASN cc_start: 0.6706 (m110) cc_final: 0.6426 (m-40) REVERT: 5 227 ASN cc_start: 0.7167 (p0) cc_final: 0.6817 (p0) REVERT: 6 14 ARG cc_start: 0.7301 (mpp80) cc_final: 0.6843 (mtm180) REVERT: 6 171 MET cc_start: 0.4192 (OUTLIER) cc_final: 0.3674 (mtm) REVERT: 7 14 ARG cc_start: 0.7946 (ptp90) cc_final: 0.7678 (ptp90) REVERT: 7 33 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8035 (ptm-80) REVERT: 7 60 LYS cc_start: 0.7584 (tptp) cc_final: 0.7230 (tppt) REVERT: 7 101 MET cc_start: 0.5998 (tpt) cc_final: 0.5690 (tpt) REVERT: 7 129 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7639 (mtmm) REVERT: 7 137 GLN cc_start: 0.6203 (mp10) cc_final: 0.5769 (mp10) REVERT: 7 195 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.6181 (ttp80) REVERT: 7 255 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6544 (tp30) outliers start: 59 outliers final: 38 residues processed: 460 average time/residue: 0.3417 time to fit residues: 221.0483 Evaluate side-chains 457 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 410 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 136 PHE Chi-restraints excluded: chain 1 residue 166 ILE Chi-restraints excluded: chain 1 residue 187 ARG Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 263 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 225 LEU Chi-restraints excluded: chain 2 residue 248 LEU Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 235 TYR Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 195 ARG Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 153 ASN ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 179 GLN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN 6 259 ASN 6 261 HIS ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.9813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17808 Z= 0.218 Angle : 0.690 10.321 24129 Z= 0.345 Chirality : 0.042 0.259 2695 Planarity : 0.008 0.348 3080 Dihedral : 10.348 126.725 2611 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.21 % Favored : 92.19 % Rotamer: Outliers : 4.14 % Allowed : 21.67 % Favored : 74.19 % 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: -1.05 (0.18), residues: 2163 helix: 0.48 (0.16), residues: 1092 sheet: -2.65 (0.62), residues: 70 loop : -1.93 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 154 HIS 0.006 0.001 HIS 7 138 PHE 0.020 0.002 PHE 4 288 TYR 0.025 0.002 TYR 3 173 ARG 0.040 0.001 ARG 6 187 *********************** 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 503 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 425 time to evaluate : 1.868 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: 1 48 TYR cc_start: 0.7271 (m-80) cc_final: 0.6857 (m-10) REVERT: 1 100 GLU cc_start: 0.6282 (mp0) cc_final: 0.5983 (mp0) REVERT: 1 101 MET cc_start: 0.6525 (tmm) cc_final: 0.6203 (tmm) REVERT: 1 136 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: 1 183 GLN cc_start: 0.7641 (tp40) cc_final: 0.7374 (tp40) REVERT: 1 239 GLN cc_start: 0.7382 (mp10) cc_final: 0.6923 (mp10) REVERT: 2 60 LYS cc_start: 0.7734 (tppt) cc_final: 0.7390 (mmtm) REVERT: 2 130 LEU cc_start: 0.8393 (mp) cc_final: 0.8186 (mt) REVERT: 2 239 GLN cc_start: 0.7539 (mt0) cc_final: 0.7312 (mt0) REVERT: 2 248 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6726 (tt) REVERT: 2 298 MET cc_start: 0.2365 (ptm) cc_final: 0.1743 (ptp) REVERT: 3 5 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6161 (ttm170) REVERT: 3 30 ASP cc_start: 0.6969 (m-30) cc_final: 0.6734 (t0) REVERT: 3 64 ASN cc_start: 0.6178 (t0) cc_final: 0.5872 (t0) REVERT: 3 121 GLU cc_start: 0.7225 (pp20) cc_final: 0.6883 (mp0) REVERT: 3 129 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7896 (mtpp) REVERT: 3 212 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.4697 (t80) REVERT: 4 40 SER cc_start: 0.7611 (t) cc_final: 0.7272 (m) REVERT: 4 41 GLU cc_start: 0.6622 (tp30) cc_final: 0.6188 (tp30) REVERT: 4 61 LYS cc_start: 0.8450 (tptm) cc_final: 0.8244 (tptt) REVERT: 4 212 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6048 (t80) REVERT: 4 273 SER cc_start: 0.8032 (t) cc_final: 0.7420 (t) REVERT: 5 11 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7783 (tmm-80) REVERT: 5 101 MET cc_start: 0.6329 (tmm) cc_final: 0.5175 (tmm) REVERT: 5 227 ASN cc_start: 0.6482 (p0) cc_final: 0.6042 (m110) REVERT: 6 14 ARG cc_start: 0.7274 (mpp80) cc_final: 0.7006 (mtm180) REVERT: 6 141 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6919 (mm-30) REVERT: 6 171 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.4132 (mtt) REVERT: 6 211 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6901 (mm-30) REVERT: 7 14 ARG cc_start: 0.7909 (ptp90) cc_final: 0.7650 (ptp90) REVERT: 7 33 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8064 (ptm-80) REVERT: 7 60 LYS cc_start: 0.7611 (tptp) cc_final: 0.7304 (tppt) REVERT: 7 116 THR cc_start: 0.6325 (m) cc_final: 0.6077 (p) REVERT: 7 129 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7810 (mtmm) REVERT: 7 179 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6325 (mp10) REVERT: 7 231 GLN cc_start: 0.6870 (tt0) cc_final: 0.6399 (pt0) outliers start: 78 outliers final: 55 residues processed: 464 average time/residue: 0.3384 time to fit residues: 221.9176 Evaluate side-chains 467 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 407 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 136 PHE Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 187 ARG Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 133 ILE Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 248 LEU Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 191 GLN Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 200 ASN Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 274 LYS Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 194 LEU Chi-restraints excluded: chain 5 residue 235 TYR Chi-restraints excluded: chain 5 residue 244 SER Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 257 ILE Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 5 residue 305 ASP Chi-restraints excluded: chain 6 residue 86 ASP Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 181 ASN Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 153 optimal weight: 0.0770 chunk 59 optimal weight: 0.0980 chunk 176 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 127 optimal weight: 0.0010 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN 7 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 1.0213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17808 Z= 0.196 Angle : 0.689 15.489 24129 Z= 0.343 Chirality : 0.042 0.239 2695 Planarity : 0.005 0.102 3080 Dihedral : 10.658 179.032 2611 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.12 % Favored : 92.28 % Rotamer: Outliers : 3.77 % Allowed : 22.41 % Favored : 73.82 % 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: -1.06 (0.18), residues: 2163 helix: 0.59 (0.16), residues: 1085 sheet: -2.81 (0.43), residues: 140 loop : -1.93 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 154 HIS 0.007 0.001 HIS 7 138 PHE 0.022 0.002 PHE 4 288 TYR 0.042 0.002 TYR 4 250 ARG 0.009 0.001 ARG 2 203 *********************** REFINEMENT MACRO_CYCLE 9 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 497 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 426 time to evaluate : 1.689 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: symmetry clash REVERT: 1 48 TYR cc_start: 0.7386 (m-80) cc_final: 0.6930 (m-10) REVERT: 1 100 GLU cc_start: 0.6247 (mp0) cc_final: 0.5916 (mp0) REVERT: 1 101 MET cc_start: 0.6550 (tmm) cc_final: 0.6179 (tmm) REVERT: 1 183 GLN cc_start: 0.7611 (tp40) cc_final: 0.7294 (tp40) REVERT: 1 279 ASP cc_start: 0.6838 (p0) cc_final: 0.6387 (p0) REVERT: 2 30 ASP cc_start: 0.7447 (t0) cc_final: 0.7213 (t0) REVERT: 2 60 LYS cc_start: 0.7744 (tppt) cc_final: 0.7250 (mppt) REVERT: 2 239 GLN cc_start: 0.7578 (mt0) cc_final: 0.7375 (mt0) REVERT: 2 266 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7256 (mm-30) REVERT: 2 298 MET cc_start: 0.2722 (ptm) cc_final: 0.2200 (ptp) REVERT: 3 25 ILE cc_start: 0.8047 (tp) cc_final: 0.7843 (tt) REVERT: 3 30 ASP cc_start: 0.7003 (m-30) cc_final: 0.6788 (t0) REVERT: 3 48 TYR cc_start: 0.5679 (m-10) cc_final: 0.5287 (m-10) REVERT: 3 129 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7912 (mtpp) REVERT: 3 212 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.4777 (t80) REVERT: 4 27 SER cc_start: 0.8039 (t) cc_final: 0.7598 (t) REVERT: 4 40 SER cc_start: 0.7801 (t) cc_final: 0.7433 (m) REVERT: 4 41 GLU cc_start: 0.6663 (tp30) cc_final: 0.6044 (tp30) REVERT: 4 61 LYS cc_start: 0.8439 (tptm) cc_final: 0.8213 (tptt) REVERT: 4 101 MET cc_start: 0.5397 (ppp) cc_final: 0.5171 (tmm) REVERT: 4 182 SER cc_start: 0.7167 (p) cc_final: 0.6937 (m) REVERT: 4 200 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5244 (p0) REVERT: 4 212 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.5988 (t80) REVERT: 4 273 SER cc_start: 0.8090 (t) cc_final: 0.7482 (t) REVERT: 4 279 ASP cc_start: 0.6897 (t0) cc_final: 0.6667 (t0) REVERT: 5 101 MET cc_start: 0.6300 (tmm) cc_final: 0.5424 (tmm) REVERT: 5 227 ASN cc_start: 0.6483 (p0) cc_final: 0.5561 (m-40) REVERT: 6 14 ARG cc_start: 0.7409 (mpp80) cc_final: 0.7032 (mtm180) REVERT: 6 101 MET cc_start: 0.6322 (tpt) cc_final: 0.5787 (tmm) REVERT: 6 129 LYS cc_start: 0.7580 (mmmt) cc_final: 0.7214 (mmmm) REVERT: 6 141 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7007 (mm-30) REVERT: 6 171 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4307 (mtp) REVERT: 6 211 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7028 (mm-30) REVERT: 6 242 MET cc_start: 0.7867 (tpp) cc_final: 0.7644 (tpp) REVERT: 7 14 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7632 (ptp90) REVERT: 7 60 LYS cc_start: 0.7643 (tptp) cc_final: 0.7359 (tppt) REVERT: 7 116 THR cc_start: 0.6369 (m) cc_final: 0.6103 (p) REVERT: 7 129 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7883 (mtpp) REVERT: 7 255 GLU cc_start: 0.7131 (tp30) cc_final: 0.6257 (tp30) outliers start: 71 outliers final: 51 residues processed: 462 average time/residue: 0.3320 time to fit residues: 219.6878 Evaluate side-chains 469 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 414 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 79 VAL Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 59 ILE Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 130 LEU Chi-restraints excluded: chain 3 residue 191 GLN Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 200 ASN Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 194 LEU Chi-restraints excluded: chain 5 residue 244 SER Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 271 PHE Chi-restraints excluded: chain 6 residue 295 THR Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 225 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 216 optimal weight: 0.0060 chunk 198 optimal weight: 0.0170 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 183 GLN ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 179 GLN ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 1.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17808 Z= 0.238 Angle : 0.724 15.394 24129 Z= 0.361 Chirality : 0.043 0.259 2695 Planarity : 0.006 0.152 3080 Dihedral : 10.667 165.208 2611 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.63 % Favored : 91.77 % Rotamer: Outliers : 3.13 % Allowed : 23.47 % Favored : 73.39 % 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: -1.12 (0.18), residues: 2163 helix: 0.51 (0.16), residues: 1085 sheet: -2.93 (0.42), residues: 140 loop : -1.89 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 154 HIS 0.009 0.001 HIS 7 81 PHE 0.025 0.002 PHE 5 271 TYR 0.035 0.002 TYR 4 250 ARG 0.025 0.001 ARG 1 187 ********************** REFINEMENT MACRO_CYCLE 10 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 487 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 428 time to evaluate : 1.894 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 23 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7316 (mtp180) REVERT: 1 48 TYR cc_start: 0.7576 (m-80) cc_final: 0.7115 (m-10) REVERT: 1 100 GLU cc_start: 0.6299 (mp0) cc_final: 0.5963 (mp0) REVERT: 1 239 GLN cc_start: 0.7439 (mp10) cc_final: 0.6975 (mp10) REVERT: 1 279 ASP cc_start: 0.6882 (p0) cc_final: 0.6469 (p0) REVERT: 2 60 LYS cc_start: 0.7965 (tppt) cc_final: 0.7455 (mppt) REVERT: 2 239 GLN cc_start: 0.7812 (mt0) cc_final: 0.7582 (mt0) REVERT: 2 255 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6207 (mt-10) REVERT: 2 266 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7249 (mm-30) REVERT: 2 298 MET cc_start: 0.2743 (ptm) cc_final: 0.2366 (ptp) REVERT: 3 29 MET cc_start: 0.7805 (tpp) cc_final: 0.7192 (mtm) REVERT: 3 48 TYR cc_start: 0.5927 (m-10) cc_final: 0.5475 (m-10) REVERT: 3 129 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7947 (mtpp) REVERT: 3 212 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.4842 (t80) REVERT: 4 27 SER cc_start: 0.8133 (t) cc_final: 0.7649 (t) REVERT: 4 40 SER cc_start: 0.8027 (t) cc_final: 0.7686 (m) REVERT: 4 41 GLU cc_start: 0.6902 (tp30) cc_final: 0.6246 (tp30) REVERT: 4 81 HIS cc_start: 0.6666 (t-170) cc_final: 0.6439 (t-90) REVERT: 4 161 LYS cc_start: 0.7744 (mptt) cc_final: 0.7516 (mppt) REVERT: 4 200 ASN cc_start: 0.6289 (OUTLIER) cc_final: 0.5847 (p0) REVERT: 4 212 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6001 (t80) REVERT: 5 31 ARG cc_start: 0.7596 (ttm170) cc_final: 0.7323 (ttm170) REVERT: 5 101 MET cc_start: 0.6353 (tmm) cc_final: 0.5376 (tmm) REVERT: 5 227 ASN cc_start: 0.6091 (p0) cc_final: 0.5542 (m-40) REVERT: 5 230 LEU cc_start: 0.5813 (tp) cc_final: 0.5581 (tp) REVERT: 5 244 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7940 (t) REVERT: 5 284 TRP cc_start: 0.7551 (t60) cc_final: 0.6700 (t60) REVERT: 6 14 ARG cc_start: 0.7427 (mpp80) cc_final: 0.6931 (mtm180) REVERT: 6 101 MET cc_start: 0.6309 (tpt) cc_final: 0.5804 (tmm) REVERT: 6 129 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7466 (mmmm) REVERT: 6 141 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7140 (mm-30) REVERT: 6 171 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4953 (mtp) REVERT: 6 211 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7136 (mm-30) REVERT: 7 14 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7615 (ptp90) REVERT: 7 60 LYS cc_start: 0.7672 (tptp) cc_final: 0.7378 (tppt) REVERT: 7 116 THR cc_start: 0.6452 (m) cc_final: 0.6176 (p) REVERT: 7 129 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7960 (mtmm) REVERT: 7 135 GLU cc_start: 0.8111 (mp0) cc_final: 0.7821 (mp0) REVERT: 7 255 GLU cc_start: 0.7185 (tp30) cc_final: 0.6304 (tp30) outliers start: 59 outliers final: 42 residues processed: 458 average time/residue: 0.3532 time to fit residues: 228.5088 Evaluate side-chains 468 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 420 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 107 LEU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 147 VAL Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 265 THR Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 191 GLN Chi-restraints excluded: chain 3 residue 193 GLU Chi-restraints excluded: chain 3 residue 212 TYR Chi-restraints excluded: chain 3 residue 261 HIS Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 200 ASN Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 238 SER Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 282 ASN Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 46 MET Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 147 VAL Chi-restraints excluded: chain 5 residue 194 LEU Chi-restraints excluded: chain 5 residue 244 SER Chi-restraints excluded: chain 5 residue 254 ILE Chi-restraints excluded: chain 5 residue 264 ILE Chi-restraints excluded: chain 6 residue 19 THR Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 192 VAL Chi-restraints excluded: chain 6 residue 295 THR Chi-restraints excluded: chain 7 residue 115 LEU Chi-restraints excluded: chain 7 residue 263 THR Chi-restraints excluded: chain 7 residue 267 GLU Chi-restraints excluded: chain 7 residue 298 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.3980 chunk 52 optimal weight: 0.3980 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 191 GLN ** 3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 HIS ** 5 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 179 GLN ** 5 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.177571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157748 restraints weight = 26940.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.162303 restraints weight = 14622.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165292 restraints weight = 9345.265| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 1.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17808 Z= 0.261 Angle : 0.744 12.414 24129 Z= 0.369 Chirality : 0.044 0.240 2695 Planarity : 0.006 0.221 3080 Dihedral : 10.851 176.805 2611 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.49 % Favored : 91.91 % Rotamer: Outliers : 3.08 % Allowed : 23.95 % Favored : 72.97 % 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: -1.20 (0.18), residues: 2163 helix: 0.44 (0.16), residues: 1085 sheet: -2.94 (0.41), residues: 140 loop : -1.94 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 5 154 HIS 0.007 0.001 HIS 2 81 PHE 0.022 0.002 PHE 4 288 TYR 0.041 0.002 TYR 5 48 ARG 0.024 0.001 ARG 1 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4230.33 seconds wall clock time: 76 minutes 47.56 seconds (4607.56 seconds total)