Starting phenix.real_space_refine on Fri Sep 27 23:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/09_2024/7rzy_24783.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/09_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_24783/09_2024/7rzy_24783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/09_2024/7rzy_24783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/09_2024/7rzy_24783.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzy_24783/09_2024/7rzy_24783.cif" } 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. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.19, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 2.3 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... Secondary structure from input PDB file: 103 helices and 10 sheets defined 55.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain '1' and resid 5 through 14 removed outlier: 3.567A pdb=" N ILE 1 9 " --> pdb=" O ARG 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 19 through 36 removed outlier: 4.121A pdb=" N SER 1 36 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 54 through 74 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 89 through 100 Processing helix chain '1' and resid 114 through 127 Proline residue: 1 124 - end of helix Processing helix chain '1' and resid 136 through 140 Processing helix chain '1' and resid 149 through 162 Processing helix chain '1' and resid 171 through 173 No H-bonds generated for 'chain '1' and resid 171 through 173' Processing helix chain '1' and resid 174 through 181 removed outlier: 4.020A pdb=" N LEU 1 178 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN 1 181 " --> pdb=" O VAL 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 181 through 188 removed outlier: 3.604A pdb=" N ARG 1 187 " --> pdb=" O GLN 1 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 1 188 " --> pdb=" O LEU 1 184 " (cutoff:3.500A) Processing helix chain '1' and resid 204 through 217 removed outlier: 4.227A pdb=" N THR 1 208 " --> pdb=" O GLY 1 204 " (cutoff:3.500A) Processing helix chain '1' and resid 227 through 238 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 241 through 258 removed outlier: 3.541A pdb=" N LEU 1 245 " --> pdb=" O ASN 1 241 " (cutoff:3.500A) Processing helix chain '1' and resid 268 through 276 Processing helix chain '1' and resid 308 through 314 removed outlier: 4.298A pdb=" N HIS 1 314 " --> pdb=" O ASP 1 310 " (cutoff:3.500A) Processing helix chain '2' and resid 5 through 14 removed outlier: 3.606A pdb=" N ILE 2 9 " --> pdb=" O ARG 2 5 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 36 removed outlier: 3.983A pdb=" N SER 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 74 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 89 through 101 Processing helix chain '2' and resid 114 through 127 Proline residue: 2 124 - end of helix Processing helix chain '2' and resid 149 through 162 Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 174 through 181 removed outlier: 3.970A pdb=" N LEU 2 178 " --> pdb=" O SER 2 174 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN 2 181 " --> pdb=" O VAL 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 182 through 188 removed outlier: 3.586A pdb=" N PHE 2 188 " --> pdb=" O LEU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 217 Processing helix chain '2' and resid 227 through 238 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 241 through 258 removed outlier: 3.636A pdb=" N LEU 2 245 " --> pdb=" O ASN 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 268 through 276 Processing helix chain '2' and resid 308 through 313 Processing helix chain '3' and resid 5 through 14 removed outlier: 3.648A pdb=" N ILE 3 9 " --> pdb=" O ARG 3 5 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 36 removed outlier: 3.903A pdb=" N SER 3 36 " --> pdb=" O CYS 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 74 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) removed outlier: 3.609A pdb=" N GLY 3 74 " --> pdb=" O SER 3 70 " (cutoff:3.500A) Processing helix chain '3' and resid 89 through 101 Processing helix chain '3' and resid 114 through 127 Proline residue: 3 124 - end of helix Processing helix chain '3' and resid 149 through 162 Processing helix chain '3' and resid 171 through 173 No H-bonds generated for 'chain '3' and resid 171 through 173' Processing helix chain '3' and resid 174 through 181 removed outlier: 3.861A pdb=" N LEU 3 178 " --> pdb=" O SER 3 174 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN 3 181 " --> pdb=" O VAL 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 181 through 187 Processing helix chain '3' and resid 204 through 217 removed outlier: 3.942A pdb=" N THR 3 208 " --> pdb=" O GLY 3 204 " (cutoff:3.500A) Processing helix chain '3' and resid 227 through 238 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 241 through 258 removed outlier: 3.542A pdb=" N LEU 3 245 " --> pdb=" O ASN 3 241 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 276 Processing helix chain '3' and resid 295 through 300 removed outlier: 3.676A pdb=" N ARG 3 300 " --> pdb=" O ASP 3 297 " (cutoff:3.500A) Processing helix chain '3' and resid 308 through 314 removed outlier: 4.487A pdb=" N HIS 3 314 " --> pdb=" O ASP 3 310 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 14 removed outlier: 3.536A pdb=" N ILE 4 9 " --> pdb=" O ARG 4 5 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 36 removed outlier: 3.986A pdb=" N SER 4 36 " --> pdb=" O CYS 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 74 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 89 through 101 removed outlier: 3.743A pdb=" N MET 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) Processing helix chain '4' and resid 114 through 127 Proline residue: 4 124 - end of helix Processing helix chain '4' and resid 149 through 162 Processing helix chain '4' and resid 171 through 173 No H-bonds generated for 'chain '4' and resid 171 through 173' Processing helix chain '4' and resid 174 through 181 removed outlier: 3.811A pdb=" N LEU 4 178 " --> pdb=" O SER 4 174 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN 4 181 " --> pdb=" O VAL 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 181 through 188 Processing helix chain '4' and resid 204 through 217 Processing helix chain '4' and resid 227 through 238 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 241 through 258 removed outlier: 3.536A pdb=" N LEU 4 245 " --> pdb=" O ASN 4 241 " (cutoff:3.500A) Processing helix chain '4' and resid 268 through 276 Processing helix chain '4' and resid 308 through 313 Processing helix chain '5' and resid 5 through 14 Processing helix chain '5' and resid 19 through 36 removed outlier: 3.946A pdb=" N SER 5 36 " --> pdb=" O CYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 74 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) removed outlier: 3.572A pdb=" N GLY 5 74 " --> pdb=" O SER 5 70 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 101 Processing helix chain '5' and resid 114 through 127 Proline residue: 5 124 - end of helix Processing helix chain '5' and resid 149 through 162 Processing helix chain '5' and resid 171 through 173 No H-bonds generated for 'chain '5' and resid 171 through 173' Processing helix chain '5' and resid 174 through 181 removed outlier: 3.885A pdb=" N LEU 5 178 " --> pdb=" O SER 5 174 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN 5 181 " --> pdb=" O VAL 5 177 " (cutoff:3.500A) Processing helix chain '5' and resid 181 through 188 Processing helix chain '5' and resid 204 through 217 removed outlier: 3.926A pdb=" N THR 5 208 " --> pdb=" O GLY 5 204 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 238 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 241 through 258 removed outlier: 3.580A pdb=" N LEU 5 245 " --> pdb=" O ASN 5 241 " (cutoff:3.500A) Processing helix chain '5' and resid 268 through 276 Processing helix chain '5' and resid 295 through 300 removed outlier: 3.613A pdb=" N ARG 5 300 " --> pdb=" O ASP 5 297 " (cutoff:3.500A) Processing helix chain '5' and resid 308 through 313 Processing helix chain '6' and resid 5 through 14 removed outlier: 3.595A pdb=" N ILE 6 9 " --> pdb=" O ARG 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 36 removed outlier: 4.010A pdb=" N SER 6 36 " --> pdb=" O CYS 6 32 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 74 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) removed outlier: 3.657A pdb=" N GLY 6 74 " --> pdb=" O SER 6 70 " (cutoff:3.500A) Processing helix chain '6' and resid 89 through 101 removed outlier: 3.508A pdb=" N MET 6 101 " --> pdb=" O LEU 6 97 " (cutoff:3.500A) Processing helix chain '6' and resid 114 through 127 Proline residue: 6 124 - end of helix Processing helix chain '6' and resid 149 through 162 Processing helix chain '6' and resid 171 through 173 No H-bonds generated for 'chain '6' and resid 171 through 173' Processing helix chain '6' and resid 174 through 181 removed outlier: 3.978A pdb=" N LEU 6 178 " --> pdb=" O SER 6 174 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN 6 181 " --> pdb=" O VAL 6 177 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 188 removed outlier: 3.673A pdb=" N PHE 6 188 " --> pdb=" O LEU 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 204 through 217 removed outlier: 3.969A pdb=" N THR 6 208 " --> pdb=" O GLY 6 204 " (cutoff:3.500A) Processing helix chain '6' and resid 227 through 238 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 241 through 258 removed outlier: 3.641A pdb=" N LEU 6 245 " --> pdb=" O ASN 6 241 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 276 Processing helix chain '6' and resid 296 through 300 removed outlier: 3.743A pdb=" N ARG 6 300 " --> pdb=" O ASP 6 297 " (cutoff:3.500A) Processing helix chain '6' and resid 308 through 313 Processing helix chain '7' and resid 5 through 14 Processing helix chain '7' and resid 19 through 36 removed outlier: 4.082A pdb=" N SER 7 36 " --> pdb=" O CYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 74 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) removed outlier: 3.549A pdb=" N GLY 7 74 " --> pdb=" O SER 7 70 " (cutoff:3.500A) Processing helix chain '7' and resid 89 through 101 removed outlier: 3.529A pdb=" N MET 7 101 " --> pdb=" O LEU 7 97 " (cutoff:3.500A) Processing helix chain '7' and resid 114 through 127 Proline residue: 7 124 - end of helix Processing helix chain '7' and resid 149 through 162 Processing helix chain '7' and resid 171 through 173 No H-bonds generated for 'chain '7' and resid 171 through 173' Processing helix chain '7' and resid 174 through 181 removed outlier: 3.786A pdb=" N LEU 7 178 " --> pdb=" O SER 7 174 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN 7 181 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 188 Processing helix chain '7' and resid 204 through 217 removed outlier: 3.897A pdb=" N THR 7 208 " --> pdb=" O GLY 7 204 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 238 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 241 through 258 Processing helix chain '7' and resid 268 through 276 Processing helix chain '7' and resid 295 through 300 removed outlier: 3.705A pdb=" N ARG 7 300 " --> pdb=" O ASP 7 297 " (cutoff:3.500A) Processing helix chain '7' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain '1' and resid 46 through 47 removed outlier: 6.975A pdb=" N MET 1 46 " --> pdb=" O VAL 1 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '1' and resid 79 through 82 removed outlier: 3.636A pdb=" N LEU 1 80 " --> pdb=" O LEU 1 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 46 through 47 removed outlier: 7.121A pdb=" N MET 2 46 " --> pdb=" O VAL 2 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '2' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain '3' and resid 46 through 47 removed outlier: 6.917A pdb=" N MET 3 46 " --> pdb=" O VAL 3 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '4' and resid 46 through 47 removed outlier: 7.097A pdb=" N MET 4 46 " --> pdb=" O VAL 4 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '4' and resid 79 through 82 removed outlier: 3.621A pdb=" N LEU 4 80 " --> pdb=" O LEU 4 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 46 through 47 removed outlier: 6.978A pdb=" N MET 5 46 " --> pdb=" O VAL 5 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '6' and resid 46 through 47 removed outlier: 6.917A pdb=" N MET 6 46 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '7' and resid 46 through 47 removed outlier: 6.971A pdb=" N MET 7 46 " --> pdb=" O VAL 7 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 697 hydrogen bonds defined for protein. 2064 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: 4.93 Time building geometry restraints manager: 5.11 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: 0.00 - 1.57: 15504 1.57 - 3.15: 6490 3.15 - 4.72: 1689 4.72 - 6.29: 444 6.29 - 7.87: 2 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: 6862 2.97 - 3.45: 18411 3.45 - 3.94: 27711 3.94 - 4.42: 29585 4.42 - 4.90: 51630 Nonbonded interactions: 134199 Sorted by model distance: nonbonded pdb=" O ILE 1 133 " pdb=" N PHE 1 169 " model vdw 2.491 3.120 nonbonded pdb=" NH1 ARG 4 14 " pdb=" OG SER 5 40 " model vdw 2.501 3.120 nonbonded pdb=" O ILE 3 133 " pdb=" N PHE 3 169 " model vdw 2.550 3.120 nonbonded pdb=" O MET 4 171 " pdb=" OG SER 4 174 " model vdw 2.558 3.040 nonbonded pdb=" O MET 7 101 " pdb=" N ASP 7 103 " model vdw 2.559 3.120 ... (remaining 134194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 1.550 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.460 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- 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= 0.915 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 : 1.810 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: 0.3296 time to fit residues: 194.2691 Evaluate side-chains 311 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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: 0.8980 chunk 164 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 0.0170 chunk 87 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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** ** 1 160 ASN ** 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** 5 153 ASN 5 247 ASN 5 261 HIS 6 261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4787 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 17808 Z= 0.305 Angle : 0.763 14.231 24129 Z= 0.392 Chirality : 0.044 0.193 2695 Planarity : 0.005 0.048 3080 Dihedral : 10.504 88.576 2617 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.26 % Favored : 92.23 % Rotamer: Outliers : 2.12 % Allowed : 11.68 % Favored : 86.19 % 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: -1.27 (0.17), residues: 2163 helix: 0.35 (0.15), residues: 1134 sheet: -4.07 (0.40), residues: 84 loop : -2.04 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 4 284 HIS 0.010 0.002 HIS 4 185 PHE 0.020 0.003 PHE 3 237 TYR 0.018 0.002 TYR 4 173 ARG 0.013 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 408 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 368 time to evaluate : 1.918 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 14 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.6686 (ptp90) REVERT: 1 24 LYS cc_start: 0.6571 (ttmm) cc_final: 0.6259 (tttp) REVERT: 1 89 LYS cc_start: 0.6630 (mtmm) cc_final: 0.6260 (mtmm) REVERT: 1 132 ILE cc_start: 0.6246 (mt) cc_final: 0.5443 (mt) REVERT: 1 192 VAL cc_start: 0.5395 (OUTLIER) cc_final: 0.5120 (p) REVERT: 2 23 ARG cc_start: 0.7217 (ttm-80) cc_final: 0.6928 (ttp-110) REVERT: 2 43 THR cc_start: 0.7025 (p) cc_final: 0.6791 (m) REVERT: 2 192 VAL cc_start: 0.6455 (OUTLIER) cc_final: 0.6014 (t) REVERT: 2 266 GLU cc_start: 0.5978 (mm-30) cc_final: 0.5618 (mm-30) REVERT: 3 11 ARG cc_start: 0.6497 (tmm-80) cc_final: 0.6128 (ttp-170) REVERT: 3 192 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7448 (m) REVERT: 4 61 LYS cc_start: 0.7924 (tppt) cc_final: 0.7693 (tptp) REVERT: 4 169 PHE cc_start: 0.5544 (m-80) cc_final: 0.4974 (m-80) REVERT: 4 305 ASP cc_start: 0.5957 (p0) cc_final: 0.5531 (p0) REVERT: 5 169 PHE cc_start: 0.5769 (m-80) cc_final: 0.4900 (m-80) REVERT: 5 288 PHE cc_start: 0.4107 (m-80) cc_final: 0.3874 (m-80) REVERT: 6 79 VAL cc_start: 0.3512 (m) cc_final: 0.2980 (p) REVERT: 6 141 GLU cc_start: 0.4779 (mm-30) cc_final: 0.3366 (mp0) REVERT: 6 246 ARG cc_start: 0.6914 (mmm-85) cc_final: 0.6651 (tpt90) REVERT: 7 59 ILE cc_start: 0.6754 (mt) cc_final: 0.6445 (mt) REVERT: 7 100 GLU cc_start: 0.7012 (tp30) cc_final: 0.6811 (mm-30) REVERT: 7 101 MET cc_start: 0.5821 (tpt) cc_final: 0.5546 (tpt) REVERT: 7 246 ARG cc_start: 0.5271 (mmm-85) cc_final: 0.5024 (tpp-160) outliers start: 40 outliers final: 16 residues processed: 389 average time/residue: 0.3544 time to fit residues: 197.2455 Evaluate side-chains 349 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 330 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 192 VAL 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 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 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: 0.3980 chunk 61 optimal weight: 0.0170 chunk 164 optimal weight: 3.9990 chunk 134 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 overall best weight: 0.3628 ------------------------------------------------------------------------------- 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** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 160 ASN 1 261 HIS 2 138 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 HIS ** 5 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 247 ASN 6 181 ASN 7 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17808 Z= 0.211 Angle : 0.679 10.716 24129 Z= 0.339 Chirality : 0.041 0.242 2695 Planarity : 0.005 0.077 3080 Dihedral : 10.187 87.091 2614 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.40 % Favored : 92.05 % Rotamer: Outliers : 2.71 % Allowed : 13.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2163 helix: 0.69 (0.15), residues: 1141 sheet: -3.33 (0.34), residues: 154 loop : -1.86 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 4 284 HIS 0.006 0.001 HIS 1 261 PHE 0.017 0.002 PHE 5 206 TYR 0.019 0.001 TYR 3 173 ARG 0.012 0.001 ARG 4 146 *********************** 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 401 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 350 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8139 (tppt) cc_final: 0.7768 (tppt) REVERT: 1 14 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.6872 (ptp90) REVERT: 1 36 SER cc_start: 0.7094 (m) cc_final: 0.6670 (p) REVERT: 1 89 LYS cc_start: 0.6611 (mtmm) cc_final: 0.6253 (mtmm) REVERT: 1 132 ILE cc_start: 0.6108 (mt) cc_final: 0.5612 (mt) REVERT: 1 298 MET cc_start: 0.3911 (tmm) cc_final: 0.3663 (ptt) REVERT: 2 13 LYS cc_start: 0.7597 (tppt) cc_final: 0.6314 (tppt) REVERT: 2 43 THR cc_start: 0.7061 (p) cc_final: 0.6836 (m) REVERT: 2 192 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6490 (t) REVERT: 3 23 ARG cc_start: 0.6602 (ttm-80) cc_final: 0.6135 (ttm-80) REVERT: 3 105 LEU cc_start: 0.5155 (mm) cc_final: 0.4941 (mp) REVERT: 3 192 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7452 (t) REVERT: 3 195 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6489 (mtp85) REVERT: 4 43 THR cc_start: 0.5518 (OUTLIER) cc_final: 0.5083 (p) REVERT: 4 59 ILE cc_start: 0.7361 (mt) cc_final: 0.7150 (tt) REVERT: 4 61 LYS cc_start: 0.7981 (tppt) cc_final: 0.7594 (tptp) REVERT: 4 169 PHE cc_start: 0.6485 (m-80) cc_final: 0.5937 (m-80) REVERT: 4 305 ASP cc_start: 0.6108 (p0) cc_final: 0.5794 (p0) REVERT: 5 132 ILE cc_start: 0.7511 (mt) cc_final: 0.7176 (pt) REVERT: 5 168 ILE cc_start: 0.5978 (pt) cc_final: 0.5102 (pt) REVERT: 6 14 ARG cc_start: 0.6802 (mpp80) cc_final: 0.6470 (mtm180) REVERT: 6 16 PHE cc_start: 0.7402 (t80) cc_final: 0.7199 (t80) REVERT: 6 62 TYR cc_start: 0.5786 (t80) cc_final: 0.5377 (t80) REVERT: 6 79 VAL cc_start: 0.4594 (m) cc_final: 0.4172 (m) REVERT: 6 141 GLU cc_start: 0.4953 (mm-30) cc_final: 0.3487 (mp0) REVERT: 6 267 GLU cc_start: 0.5950 (tp30) cc_final: 0.5049 (pt0) REVERT: 6 289 GLU cc_start: 0.6338 (tp30) cc_final: 0.6040 (tp30) REVERT: 7 41 GLU cc_start: 0.6581 (tt0) cc_final: 0.5972 (tt0) REVERT: 7 45 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4436 (ttm) REVERT: 7 59 ILE cc_start: 0.7047 (mt) cc_final: 0.6499 (mt) REVERT: 7 101 MET cc_start: 0.5850 (tpt) cc_final: 0.5588 (tpt) REVERT: 7 193 GLU cc_start: 0.5325 (mm-30) cc_final: 0.4944 (tm-30) outliers start: 51 outliers final: 16 residues processed: 379 average time/residue: 0.3291 time to fit residues: 180.2460 Evaluate side-chains 348 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 115 LEU Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 41 GLU Chi-restraints excluded: chain 2 residue 192 VAL Chi-restraints excluded: chain 3 residue 192 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 63 LEU Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 146 ARG 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 151 VAL Chi-restraints excluded: chain 5 residue 174 SER Chi-restraints excluded: chain 5 residue 259 ASN Chi-restraints excluded: chain 7 residue 45 MET Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 0.8980 chunk 148 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 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** ** 1 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 239 GLN 5 137 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 17808 Z= 0.300 Angle : 0.795 16.087 24129 Z= 0.399 Chirality : 0.046 0.215 2695 Planarity : 0.005 0.056 3080 Dihedral : 10.367 85.812 2613 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.58 % Favored : 91.82 % Rotamer: Outliers : 4.09 % Allowed : 13.65 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -1.23 (0.18), residues: 2163 helix: 0.49 (0.15), residues: 1134 sheet: -3.49 (0.32), residues: 210 loop : -1.88 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 4 284 HIS 0.013 0.002 HIS 5 138 PHE 0.031 0.003 PHE 5 269 TYR 0.022 0.003 TYR 4 48 ARG 0.015 0.001 ARG 2 195 *********************** 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 496 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 419 time to evaluate : 1.884 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 14 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7394 (ptp90) REVERT: 1 36 SER cc_start: 0.7873 (m) cc_final: 0.7319 (p) REVERT: 1 89 LYS cc_start: 0.6517 (mtmm) cc_final: 0.6223 (mtmm) REVERT: 1 100 GLU cc_start: 0.6297 (mp0) cc_final: 0.6076 (mt-10) REVERT: 1 132 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5533 (mt) REVERT: 1 210 LEU cc_start: 0.5857 (tp) cc_final: 0.5616 (tp) REVERT: 1 239 GLN cc_start: 0.7200 (mp10) cc_final: 0.6767 (mp10) REVERT: 2 13 LYS cc_start: 0.8267 (tppt) cc_final: 0.7936 (tppt) REVERT: 2 41 GLU cc_start: 0.6626 (tt0) cc_final: 0.6386 (tp30) REVERT: 2 46 MET cc_start: 0.6598 (mmm) cc_final: 0.6318 (mmm) REVERT: 2 191 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6380 (mp10) REVERT: 2 266 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6498 (mm-30) REVERT: 2 298 MET cc_start: 0.2845 (ptm) cc_final: 0.2303 (ptp) REVERT: 3 23 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6487 (ttm-80) REVERT: 3 43 THR cc_start: 0.6947 (p) cc_final: 0.6700 (p) REVERT: 3 45 MET cc_start: 0.7239 (ptm) cc_final: 0.6943 (ptp) REVERT: 3 195 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6742 (ttm-80) REVERT: 4 29 MET cc_start: 0.6191 (tpp) cc_final: 0.5789 (tpp) REVERT: 4 43 THR cc_start: 0.6135 (OUTLIER) cc_final: 0.5736 (p) REVERT: 4 63 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7506 (tt) REVERT: 4 280 LYS cc_start: 0.6368 (mmtt) cc_final: 0.6018 (mmtm) REVERT: 4 305 ASP cc_start: 0.6601 (p0) cc_final: 0.6280 (p0) REVERT: 5 101 MET cc_start: 0.6446 (tmm) cc_final: 0.5538 (tmm) REVERT: 5 136 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: 6 14 ARG cc_start: 0.7172 (mpp80) cc_final: 0.6918 (mtm180) REVERT: 6 16 PHE cc_start: 0.7958 (t80) cc_final: 0.7468 (t80) REVERT: 6 60 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7587 (ttmm) REVERT: 6 86 ASP cc_start: 0.4338 (t0) cc_final: 0.4133 (t0) REVERT: 6 141 GLU cc_start: 0.5421 (mm-30) cc_final: 0.3827 (mp0) REVERT: 6 171 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3412 (mmm) REVERT: 6 253 SER cc_start: 0.7279 (t) cc_final: 0.7045 (p) REVERT: 7 41 GLU cc_start: 0.7173 (tt0) cc_final: 0.6930 (tt0) REVERT: 7 45 MET cc_start: 0.6820 (ttp) cc_final: 0.6359 (ttm) REVERT: 7 60 LYS cc_start: 0.7730 (tptp) cc_final: 0.7096 (tppt) REVERT: 7 100 GLU cc_start: 0.7247 (tp30) cc_final: 0.6954 (mm-30) REVERT: 7 153 ASN cc_start: 0.7183 (m110) cc_final: 0.6618 (m110) REVERT: 7 166 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7428 (mp) outliers start: 77 outliers final: 32 residues processed: 463 average time/residue: 0.3174 time to fit residues: 212.6346 Evaluate side-chains 423 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 384 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 116 THR Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 110 THR Chi-restraints excluded: chain 2 residue 133 ILE 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 205 VAL Chi-restraints excluded: chain 3 residue 58 VAL Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 63 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 190 ILE Chi-restraints excluded: chain 4 residue 192 VAL Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 45 MET Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 267 GLU Chi-restraints excluded: chain 5 residue 275 LEU Chi-restraints excluded: chain 5 residue 282 ASN Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 171 MET Chi-restraints excluded: chain 6 residue 190 ILE Chi-restraints excluded: chain 6 residue 271 PHE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR 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: 0.9980 chunk 3 optimal weight: 0.0040 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 144 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 1 183 GLN 2 81 HIS ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 153 ASN 7 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17808 Z= 0.218 Angle : 0.695 10.524 24129 Z= 0.345 Chirality : 0.043 0.341 2695 Planarity : 0.008 0.334 3080 Dihedral : 10.286 88.621 2611 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.75 % Favored : 92.65 % Rotamer: Outliers : 3.40 % Allowed : 16.99 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2163 helix: 0.67 (0.15), residues: 1148 sheet: -3.36 (0.36), residues: 168 loop : -1.80 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 284 HIS 0.006 0.001 HIS 2 81 PHE 0.034 0.002 PHE 4 269 TYR 0.023 0.002 TYR 3 173 ARG 0.022 0.001 ARG 6 187 *********************** 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 491 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 427 time to evaluate : 1.915 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 29 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6663 (mtm) REVERT: 1 36 SER cc_start: 0.7769 (m) cc_final: 0.7360 (p) REVERT: 1 100 GLU cc_start: 0.6387 (mp0) cc_final: 0.6171 (mt-10) REVERT: 1 132 ILE cc_start: 0.5888 (OUTLIER) cc_final: 0.5505 (mt) REVERT: 1 157 MET cc_start: 0.5763 (mtt) cc_final: 0.5484 (mtt) REVERT: 1 239 GLN cc_start: 0.7349 (mp10) cc_final: 0.6870 (mp10) REVERT: 2 60 LYS cc_start: 0.6988 (tppt) cc_final: 0.6733 (mppt) REVERT: 2 130 LEU cc_start: 0.7758 (tt) cc_final: 0.7519 (mt) REVERT: 2 191 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6408 (mp10) REVERT: 2 212 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.5136 (t80) REVERT: 2 298 MET cc_start: 0.2905 (ptm) cc_final: 0.2362 (ptp) REVERT: 3 43 THR cc_start: 0.6790 (p) cc_final: 0.6524 (p) REVERT: 3 45 MET cc_start: 0.7230 (ptm) cc_final: 0.6967 (ptp) REVERT: 3 195 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6955 (mtp85) REVERT: 4 11 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6796 (ttp80) REVERT: 4 63 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7276 (tt) REVERT: 4 167 VAL cc_start: 0.6481 (t) cc_final: 0.6201 (t) REVERT: 4 212 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.5924 (t80) REVERT: 4 214 ASP cc_start: 0.6813 (m-30) cc_final: 0.6471 (m-30) REVERT: 5 101 MET cc_start: 0.6448 (tmm) cc_final: 0.5395 (tmm) REVERT: 5 136 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: 5 211 GLU cc_start: 0.6324 (tt0) cc_final: 0.5968 (tt0) REVERT: 5 271 PHE cc_start: 0.7270 (t80) cc_final: 0.6900 (t80) REVERT: 6 14 ARG cc_start: 0.7379 (mpp80) cc_final: 0.7013 (mtm180) REVERT: 6 16 PHE cc_start: 0.7950 (t80) cc_final: 0.7603 (t80) REVERT: 6 60 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7609 (ttmm) REVERT: 6 141 GLU cc_start: 0.5751 (mm-30) cc_final: 0.4179 (mp0) REVERT: 6 156 LYS cc_start: 0.6905 (ttpp) cc_final: 0.6657 (ttmt) REVERT: 6 253 SER cc_start: 0.7327 (t) cc_final: 0.7099 (p) REVERT: 7 60 LYS cc_start: 0.7685 (tptp) cc_final: 0.7196 (tppt) REVERT: 7 116 THR cc_start: 0.5863 (m) cc_final: 0.5614 (p) REVERT: 7 153 ASN cc_start: 0.7308 (m-40) cc_final: 0.6698 (m-40) REVERT: 7 166 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7587 (mp) outliers start: 64 outliers final: 28 residues processed: 462 average time/residue: 0.3522 time to fit residues: 229.5385 Evaluate side-chains 435 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 399 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 22 VAL Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 2 residue 248 LEU Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 63 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 192 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 18 SER Chi-restraints excluded: chain 5 residue 115 LEU Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 267 GLU Chi-restraints excluded: chain 5 residue 275 LEU Chi-restraints excluded: chain 6 residue 115 LEU 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 187 ARG Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.0980 chunk 188 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 209 optimal weight: 0.0570 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 231 GLN ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17808 Z= 0.196 Angle : 0.689 11.917 24129 Z= 0.341 Chirality : 0.043 0.345 2695 Planarity : 0.007 0.267 3080 Dihedral : 9.940 88.258 2611 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.93 % Favored : 92.46 % Rotamer: Outliers : 2.92 % Allowed : 18.75 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 2163 helix: 0.86 (0.16), residues: 1106 sheet: -3.22 (0.34), residues: 210 loop : -1.73 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 154 HIS 0.022 0.001 HIS 5 138 PHE 0.031 0.002 PHE 5 269 TYR 0.033 0.001 TYR 4 173 ARG 0.027 0.001 ARG 6 187 *********************** 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 472 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 417 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6804 (ptp90) REVERT: 1 36 SER cc_start: 0.7867 (m) cc_final: 0.7335 (p) REVERT: 1 100 GLU cc_start: 0.6432 (mp0) cc_final: 0.6223 (mt-10) REVERT: 1 101 MET cc_start: 0.6642 (tpp) cc_final: 0.6347 (tpp) REVERT: 1 132 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5466 (mt) REVERT: 1 157 MET cc_start: 0.5743 (mtt) cc_final: 0.5463 (mtt) REVERT: 1 239 GLN cc_start: 0.7195 (mp10) cc_final: 0.6701 (mp10) REVERT: 2 23 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7663 (ttp-170) REVERT: 2 41 GLU cc_start: 0.6234 (tp30) cc_final: 0.5969 (tp30) REVERT: 2 60 LYS cc_start: 0.7405 (tppt) cc_final: 0.7080 (mppt) REVERT: 2 61 LYS cc_start: 0.7718 (tptt) cc_final: 0.7518 (tppt) REVERT: 2 191 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: 2 212 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5122 (t80) REVERT: 2 298 MET cc_start: 0.2752 (ptm) cc_final: 0.2213 (ptp) REVERT: 3 40 SER cc_start: 0.6802 (OUTLIER) cc_final: 0.6483 (m) REVERT: 3 43 THR cc_start: 0.6718 (p) cc_final: 0.6402 (p) REVERT: 3 45 MET cc_start: 0.7279 (ptm) cc_final: 0.7048 (ptp) REVERT: 3 121 GLU cc_start: 0.7287 (pp20) cc_final: 0.6976 (mp0) REVERT: 3 136 PHE cc_start: 0.6857 (m-80) cc_final: 0.6613 (m-80) REVERT: 3 255 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6988 (mm-30) REVERT: 4 29 MET cc_start: 0.6917 (tpp) cc_final: 0.6360 (mmm) REVERT: 4 57 THR cc_start: 0.7949 (m) cc_final: 0.7727 (t) REVERT: 4 61 LYS cc_start: 0.8349 (tptm) cc_final: 0.8120 (tptp) REVERT: 4 132 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6612 (mp) REVERT: 4 212 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.5911 (t80) REVERT: 4 214 ASP cc_start: 0.6896 (m-30) cc_final: 0.6619 (m-30) REVERT: 5 101 MET cc_start: 0.6389 (tmm) cc_final: 0.5595 (tmm) REVERT: 5 136 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: 5 211 GLU cc_start: 0.6373 (tt0) cc_final: 0.6031 (tt0) REVERT: 5 271 PHE cc_start: 0.7764 (t80) cc_final: 0.7248 (t80) REVERT: 6 60 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7596 (ttmm) REVERT: 6 100 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6763 (mp0) REVERT: 6 134 ASP cc_start: 0.6579 (m-30) cc_final: 0.6131 (m-30) REVERT: 6 141 GLU cc_start: 0.5802 (mm-30) cc_final: 0.4276 (mp0) REVERT: 6 171 MET cc_start: 0.3630 (mmm) cc_final: 0.3257 (mtt) REVERT: 6 253 SER cc_start: 0.7311 (t) cc_final: 0.7072 (p) REVERT: 7 60 LYS cc_start: 0.7702 (tptp) cc_final: 0.7220 (tppt) REVERT: 7 116 THR cc_start: 0.5995 (m) cc_final: 0.5739 (p) REVERT: 7 153 ASN cc_start: 0.7348 (m-40) cc_final: 0.6987 (m-40) REVERT: 7 166 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7600 (mp) outliers start: 55 outliers final: 29 residues processed: 447 average time/residue: 0.3646 time to fit residues: 227.7272 Evaluate side-chains 439 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 402 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 217 LEU Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 133 ILE Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 212 TYR Chi-restraints excluded: chain 3 residue 17 VAL Chi-restraints excluded: chain 3 residue 19 THR Chi-restraints excluded: chain 3 residue 40 SER Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 148 LEU 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 190 ILE Chi-restraints excluded: chain 4 residue 212 TYR 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 136 PHE Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 117 optimal weight: 0.5980 chunk 209 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 231 GLN ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 65 GLN ** 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: 0.6119 moved from start: 0.9149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 17808 Z= 0.267 Angle : 0.749 17.921 24129 Z= 0.369 Chirality : 0.044 0.243 2695 Planarity : 0.008 0.249 3080 Dihedral : 9.897 89.753 2611 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.58 % Favored : 91.82 % Rotamer: Outliers : 3.35 % Allowed : 19.12 % Favored : 77.54 % 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: -1.03 (0.19), residues: 2163 helix: 0.72 (0.16), residues: 1106 sheet: -3.26 (0.35), residues: 210 loop : -1.86 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 2 154 HIS 0.022 0.001 HIS 5 138 PHE 0.021 0.002 PHE 4 269 TYR 0.020 0.002 TYR 3 173 ARG 0.026 0.001 ARG 6 187 *********************** 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 507 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 444 time to evaluate : 2.033 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 60 LYS cc_start: 0.7274 (tptt) cc_final: 0.7026 (tppp) REVERT: 1 101 MET cc_start: 0.6588 (tpp) cc_final: 0.6301 (tpp) REVERT: 1 239 GLN cc_start: 0.7445 (mp10) cc_final: 0.7013 (mp10) REVERT: 2 41 GLU cc_start: 0.6351 (tp30) cc_final: 0.6067 (tp30) REVERT: 2 60 LYS cc_start: 0.7679 (tppt) cc_final: 0.7354 (mmtm) REVERT: 2 130 LEU cc_start: 0.8028 (tt) cc_final: 0.7658 (mt) REVERT: 2 157 MET cc_start: 0.6338 (tpp) cc_final: 0.6031 (tpp) REVERT: 2 182 SER cc_start: 0.7798 (t) cc_final: 0.7264 (m) REVERT: 2 191 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: 2 212 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5555 (t80) REVERT: 2 239 GLN cc_start: 0.7230 (mt0) cc_final: 0.6945 (mt0) REVERT: 2 248 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6769 (tt) REVERT: 2 298 MET cc_start: 0.2511 (ptm) cc_final: 0.1933 (ptp) REVERT: 3 23 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7532 (ttm-80) REVERT: 3 43 THR cc_start: 0.6785 (p) cc_final: 0.6509 (p) REVERT: 3 45 MET cc_start: 0.7433 (ptm) cc_final: 0.7018 (ptp) REVERT: 3 58 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6377 (t) REVERT: 3 62 TYR cc_start: 0.8069 (t80) cc_final: 0.7801 (t80) REVERT: 3 136 PHE cc_start: 0.6730 (m-80) cc_final: 0.6366 (m-80) REVERT: 3 195 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7266 (mtp85) REVERT: 4 29 MET cc_start: 0.7207 (tpp) cc_final: 0.6822 (mmm) REVERT: 4 41 GLU cc_start: 0.6438 (tp30) cc_final: 0.6196 (tp30) REVERT: 4 212 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6123 (t80) REVERT: 4 214 ASP cc_start: 0.7174 (m-30) cc_final: 0.6916 (m-30) REVERT: 4 305 ASP cc_start: 0.7031 (p0) cc_final: 0.6616 (p0) REVERT: 5 23 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7226 (mtt180) REVERT: 5 86 ASP cc_start: 0.5255 (t70) cc_final: 0.5031 (t70) REVERT: 5 101 MET cc_start: 0.5915 (tmm) cc_final: 0.5213 (tmm) REVERT: 5 211 GLU cc_start: 0.6606 (tt0) cc_final: 0.6257 (tt0) REVERT: 5 227 ASN cc_start: 0.5923 (p0) cc_final: 0.5408 (m-40) REVERT: 5 271 PHE cc_start: 0.7862 (t80) cc_final: 0.7635 (t80) REVERT: 6 101 MET cc_start: 0.6356 (tpt) cc_final: 0.5668 (tmm) REVERT: 6 134 ASP cc_start: 0.6783 (m-30) cc_final: 0.6453 (m-30) REVERT: 6 171 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3954 (mtp) REVERT: 6 211 GLU cc_start: 0.6665 (tt0) cc_final: 0.6415 (mt-10) REVERT: 6 253 SER cc_start: 0.7381 (t) cc_final: 0.7151 (p) REVERT: 7 24 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7776 (ttmm) REVERT: 7 39 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6866 (mt-10) REVERT: 7 60 LYS cc_start: 0.7639 (tptp) cc_final: 0.7213 (ttmm) REVERT: 7 101 MET cc_start: 0.6247 (tpt) cc_final: 0.5917 (tpt) REVERT: 7 116 THR cc_start: 0.6367 (m) cc_final: 0.6104 (p) REVERT: 7 129 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7588 (mtmt) REVERT: 7 134 ASP cc_start: 0.6314 (m-30) cc_final: 0.5782 (m-30) REVERT: 7 166 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7634 (mp) REVERT: 7 255 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6529 (tp30) outliers start: 63 outliers final: 34 residues processed: 474 average time/residue: 0.3559 time to fit residues: 236.5122 Evaluate side-chains 458 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 417 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 225 LEU Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG 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 248 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 58 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 148 LEU Chi-restraints excluded: chain 3 residue 166 ILE Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 107 LEU Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 245 LEU Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 79 VAL Chi-restraints excluded: chain 5 residue 166 ILE Chi-restraints excluded: chain 5 residue 289 GLU 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 187 ARG Chi-restraints excluded: chain 6 residue 271 PHE Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 ** 1 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 259 ASN ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 HIS 4 282 ASN ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 81 HIS ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.9884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17808 Z= 0.235 Angle : 0.740 16.637 24129 Z= 0.366 Chirality : 0.042 0.184 2695 Planarity : 0.007 0.243 3080 Dihedral : 10.031 89.655 2611 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.35 % Favored : 92.05 % Rotamer: Outliers : 3.03 % Allowed : 21.14 % Favored : 75.84 % 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: -1.03 (0.19), residues: 2163 helix: 0.72 (0.16), residues: 1106 sheet: -3.21 (0.37), residues: 196 loop : -1.91 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 154 HIS 0.015 0.001 HIS 5 138 PHE 0.020 0.002 PHE 4 288 TYR 0.023 0.002 TYR 3 311 ARG 0.026 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 511 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 454 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: symmetry clash REVERT: 1 14 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7541 (ptp90) REVERT: 1 101 MET cc_start: 0.6737 (tpp) cc_final: 0.6447 (tpp) REVERT: 1 239 GLN cc_start: 0.7330 (mp10) cc_final: 0.6982 (mp10) REVERT: 1 279 ASP cc_start: 0.6878 (p0) cc_final: 0.6636 (p0) REVERT: 2 41 GLU cc_start: 0.6415 (tp30) cc_final: 0.6144 (tp30) REVERT: 2 60 LYS cc_start: 0.7812 (tppt) cc_final: 0.7504 (mmtm) REVERT: 2 62 TYR cc_start: 0.7570 (t80) cc_final: 0.7278 (t80) REVERT: 2 156 LYS cc_start: 0.6790 (tptp) cc_final: 0.6578 (tptp) REVERT: 2 157 MET cc_start: 0.6389 (tpp) cc_final: 0.6162 (tpp) REVERT: 2 182 SER cc_start: 0.7831 (t) cc_final: 0.7342 (m) REVERT: 2 191 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: 2 239 GLN cc_start: 0.7357 (mt0) cc_final: 0.7115 (mt0) REVERT: 2 266 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6783 (mm-30) REVERT: 2 298 MET cc_start: 0.2705 (ptm) cc_final: 0.2291 (ptp) REVERT: 3 5 ARG cc_start: 0.6479 (ttm170) cc_final: 0.6088 (ttm170) REVERT: 3 45 MET cc_start: 0.7452 (ptm) cc_final: 0.7083 (ptp) REVERT: 3 57 THR cc_start: 0.7681 (m) cc_final: 0.7477 (t) REVERT: 3 62 TYR cc_start: 0.7948 (t80) cc_final: 0.7737 (t80) REVERT: 3 129 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7796 (mtmm) REVERT: 3 134 ASP cc_start: 0.5440 (t0) cc_final: 0.5228 (t0) REVERT: 3 136 PHE cc_start: 0.6832 (m-80) cc_final: 0.6487 (m-80) REVERT: 3 167 VAL cc_start: 0.6037 (t) cc_final: 0.5253 (p) REVERT: 3 181 ASN cc_start: 0.8004 (t0) cc_final: 0.7758 (t0) REVERT: 3 195 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7551 (ttm-80) REVERT: 4 27 SER cc_start: 0.7955 (t) cc_final: 0.7647 (t) REVERT: 4 29 MET cc_start: 0.7353 (tpp) cc_final: 0.7027 (mmm) REVERT: 4 212 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6151 (t80) REVERT: 4 273 SER cc_start: 0.7982 (t) cc_final: 0.7366 (t) REVERT: 4 305 ASP cc_start: 0.7223 (p0) cc_final: 0.6721 (p0) REVERT: 5 86 ASP cc_start: 0.5410 (t70) cc_final: 0.5178 (t70) REVERT: 5 101 MET cc_start: 0.5994 (tmm) cc_final: 0.5205 (tmm) REVERT: 5 227 ASN cc_start: 0.5640 (p0) cc_final: 0.5222 (m-40) REVERT: 5 241 ASN cc_start: 0.7396 (t0) cc_final: 0.7154 (m-40) REVERT: 5 271 PHE cc_start: 0.7846 (t80) cc_final: 0.7579 (t80) REVERT: 6 101 MET cc_start: 0.6441 (tpt) cc_final: 0.5883 (tmm) REVERT: 6 253 SER cc_start: 0.7559 (t) cc_final: 0.7114 (p) REVERT: 7 24 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7785 (ttmm) REVERT: 7 60 LYS cc_start: 0.7707 (tptp) cc_final: 0.7337 (tppt) REVERT: 7 101 MET cc_start: 0.6301 (tpt) cc_final: 0.6003 (tpt) REVERT: 7 116 THR cc_start: 0.6592 (m) cc_final: 0.6318 (p) REVERT: 7 129 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7901 (mtmt) REVERT: 7 166 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7681 (mm) REVERT: 7 255 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6537 (tp30) outliers start: 57 outliers final: 37 residues processed: 480 average time/residue: 0.3655 time to fit residues: 244.8950 Evaluate side-chains 472 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 432 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 160 ASN Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN Chi-restraints excluded: chain 1 residue 265 THR Chi-restraints excluded: chain 2 residue 19 THR Chi-restraints excluded: chain 2 residue 45 MET Chi-restraints excluded: chain 2 residue 79 VAL Chi-restraints excluded: chain 2 residue 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN 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 4 residue 19 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 153 ASN Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 245 LEU 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 79 VAL Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 6 residue 45 MET Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 6 residue 271 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 0.0070 chunk 59 optimal weight: 0.3980 chunk 176 optimal weight: 0.0980 chunk 184 optimal weight: 0.0870 chunk 127 optimal weight: 3.9990 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 179 GLN 4 81 HIS ** 5 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 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: 0.6209 moved from start: 1.0180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17808 Z= 0.206 Angle : 0.742 17.630 24129 Z= 0.365 Chirality : 0.043 0.181 2695 Planarity : 0.007 0.231 3080 Dihedral : 9.855 87.964 2611 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.35 % Favored : 92.05 % Rotamer: Outliers : 2.34 % Allowed : 22.62 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 2163 helix: 0.85 (0.16), residues: 1099 sheet: -3.15 (0.37), residues: 196 loop : -1.93 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 154 HIS 0.015 0.001 HIS 5 138 PHE 0.023 0.002 PHE 4 288 TYR 0.028 0.001 TYR 3 173 ARG 0.025 0.001 ARG 6 187 *********************** 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 480 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 436 time to evaluate : 1.956 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: 1 101 MET cc_start: 0.6704 (tpp) cc_final: 0.6371 (tpp) REVERT: 1 279 ASP cc_start: 0.6967 (p0) cc_final: 0.6754 (p0) REVERT: 2 41 GLU cc_start: 0.6372 (tp30) cc_final: 0.6051 (tp30) REVERT: 2 60 LYS cc_start: 0.7799 (tppt) cc_final: 0.7275 (mppt) REVERT: 2 62 TYR cc_start: 0.7696 (t80) cc_final: 0.7436 (t80) REVERT: 2 157 MET cc_start: 0.6347 (tpp) cc_final: 0.6107 (tpp) REVERT: 2 182 SER cc_start: 0.7886 (t) cc_final: 0.7464 (m) REVERT: 2 191 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: 2 239 GLN cc_start: 0.7360 (mt0) cc_final: 0.7118 (mt0) REVERT: 2 266 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6913 (mm-30) REVERT: 2 298 MET cc_start: 0.2738 (ptm) cc_final: 0.2364 (ptp) REVERT: 3 45 MET cc_start: 0.7475 (ptm) cc_final: 0.7082 (ptp) REVERT: 3 136 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: 3 167 VAL cc_start: 0.6092 (t) cc_final: 0.5301 (p) REVERT: 3 173 TYR cc_start: 0.8099 (p90) cc_final: 0.7829 (p90) REVERT: 3 181 ASN cc_start: 0.8040 (t0) cc_final: 0.7777 (t0) REVERT: 3 195 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7632 (ttm-80) REVERT: 3 255 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6497 (tt0) REVERT: 4 27 SER cc_start: 0.7967 (t) cc_final: 0.7646 (t) REVERT: 4 29 MET cc_start: 0.7196 (tpp) cc_final: 0.6918 (mmm) REVERT: 4 41 GLU cc_start: 0.6457 (tp30) cc_final: 0.6222 (tp30) REVERT: 4 182 SER cc_start: 0.6789 (p) cc_final: 0.6557 (m) REVERT: 4 212 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6088 (t80) REVERT: 4 305 ASP cc_start: 0.7268 (p0) cc_final: 0.6722 (p0) REVERT: 5 101 MET cc_start: 0.5938 (tmm) cc_final: 0.5125 (tmm) REVERT: 5 150 GLN cc_start: 0.7649 (mp10) cc_final: 0.7363 (mp10) REVERT: 5 153 ASN cc_start: 0.6812 (m-40) cc_final: 0.6573 (m-40) REVERT: 5 271 PHE cc_start: 0.7966 (t80) cc_final: 0.7723 (t80) REVERT: 6 100 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7065 (mp0) REVERT: 6 101 MET cc_start: 0.6517 (tpt) cc_final: 0.6020 (tmm) REVERT: 6 134 ASP cc_start: 0.7110 (m-30) cc_final: 0.6888 (m-30) REVERT: 6 253 SER cc_start: 0.7559 (t) cc_final: 0.7122 (p) REVERT: 7 24 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7651 (ttmm) REVERT: 7 60 LYS cc_start: 0.7689 (tptp) cc_final: 0.7311 (tppt) REVERT: 7 116 THR cc_start: 0.6613 (m) cc_final: 0.6318 (p) REVERT: 7 129 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7819 (mtmt) REVERT: 7 166 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (mm) REVERT: 7 179 GLN cc_start: 0.7170 (mp10) cc_final: 0.6964 (mp10) outliers start: 44 outliers final: 26 residues processed: 456 average time/residue: 0.3329 time to fit residues: 215.3492 Evaluate side-chains 454 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 424 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 ARG Chi-restraints excluded: chain 1 residue 163 LYS Chi-restraints excluded: chain 1 residue 200 ASN 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 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN 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 136 PHE Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 245 LEU Chi-restraints excluded: chain 4 residue 261 HIS Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 6 residue 115 LEU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 166 ILE Chi-restraints excluded: chain 7 residue 263 THR 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: 0.6980 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 216 optimal weight: 0.0020 chunk 198 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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** ** 2 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 137 GLN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 241 ASN ** 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: 0.6310 moved from start: 1.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17808 Z= 0.230 Angle : 0.762 15.039 24129 Z= 0.377 Chirality : 0.043 0.181 2695 Planarity : 0.007 0.235 3080 Dihedral : 9.898 88.731 2611 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.44 % Favored : 91.96 % Rotamer: Outliers : 2.02 % Allowed : 23.63 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2163 helix: 0.81 (0.16), residues: 1099 sheet: -3.39 (0.58), residues: 70 loop : -1.92 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 154 HIS 0.016 0.001 HIS 5 138 PHE 0.022 0.002 PHE 4 288 TYR 0.020 0.002 TYR 7 173 ARG 0.025 0.001 ARG 6 187 ********************** 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 486 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 448 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 41 GLU cc_start: 0.7639 (tt0) cc_final: 0.7228 (tt0) REVERT: 1 101 MET cc_start: 0.6683 (tpp) cc_final: 0.6355 (tpp) REVERT: 1 187 ARG cc_start: 0.6042 (ttm110) cc_final: 0.5597 (ttm-80) REVERT: 1 195 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6943 (ttm110) REVERT: 1 211 GLU cc_start: 0.7040 (tp30) cc_final: 0.6730 (tm-30) REVERT: 2 41 GLU cc_start: 0.6388 (tp30) cc_final: 0.6075 (tp30) REVERT: 2 60 LYS cc_start: 0.7919 (tppt) cc_final: 0.7631 (mmtm) REVERT: 2 130 LEU cc_start: 0.8092 (mt) cc_final: 0.7623 (mt) REVERT: 2 166 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7010 (pt) REVERT: 2 182 SER cc_start: 0.8055 (t) cc_final: 0.7597 (m) REVERT: 2 191 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: 3 45 MET cc_start: 0.7652 (ptm) cc_final: 0.7308 (ptp) REVERT: 3 57 THR cc_start: 0.7778 (m) cc_final: 0.7541 (t) REVERT: 3 136 PHE cc_start: 0.7191 (m-80) cc_final: 0.6896 (m-80) REVERT: 3 167 VAL cc_start: 0.6502 (t) cc_final: 0.5666 (p) REVERT: 3 181 ASN cc_start: 0.8116 (t0) cc_final: 0.7851 (t0) REVERT: 3 255 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6659 (tt0) REVERT: 4 27 SER cc_start: 0.8049 (t) cc_final: 0.7733 (t) REVERT: 4 29 MET cc_start: 0.7334 (tpp) cc_final: 0.7068 (mmm) REVERT: 4 41 GLU cc_start: 0.6709 (tp30) cc_final: 0.6299 (tp30) REVERT: 4 135 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5766 (mt-10) REVERT: 4 161 LYS cc_start: 0.7620 (mptt) cc_final: 0.7127 (mptt) REVERT: 4 212 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6053 (t80) REVERT: 4 255 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7444 (mt-10) REVERT: 4 305 ASP cc_start: 0.7454 (p0) cc_final: 0.6897 (p0) REVERT: 5 101 MET cc_start: 0.6036 (tmm) cc_final: 0.5131 (tmm) REVERT: 5 166 ILE cc_start: 0.7853 (pt) cc_final: 0.7558 (mt) REVERT: 5 242 MET cc_start: 0.7310 (tpp) cc_final: 0.7019 (tpp) REVERT: 5 271 PHE cc_start: 0.7974 (t80) cc_final: 0.7720 (t80) REVERT: 5 277 SER cc_start: 0.7538 (p) cc_final: 0.7256 (m) REVERT: 5 309 GLU cc_start: 0.4876 (mm-30) cc_final: 0.4448 (mm-30) REVERT: 6 100 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7100 (mp0) REVERT: 6 101 MET cc_start: 0.6526 (tpt) cc_final: 0.6079 (tmm) REVERT: 6 134 ASP cc_start: 0.7250 (m-30) cc_final: 0.6941 (m-30) REVERT: 6 242 MET cc_start: 0.8078 (tpp) cc_final: 0.7853 (tpp) REVERT: 6 253 SER cc_start: 0.7619 (t) cc_final: 0.7194 (p) REVERT: 7 24 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7738 (ttmm) REVERT: 7 60 LYS cc_start: 0.7710 (tptp) cc_final: 0.7386 (tppt) REVERT: 7 116 THR cc_start: 0.7199 (m) cc_final: 0.6925 (p) REVERT: 7 129 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7736 (mtmt) REVERT: 7 179 GLN cc_start: 0.6960 (mp10) cc_final: 0.6722 (mp10) REVERT: 7 255 GLU cc_start: 0.7095 (tp30) cc_final: 0.6584 (tp30) outliers start: 38 outliers final: 27 residues processed: 464 average time/residue: 0.3637 time to fit residues: 235.7944 Evaluate side-chains 465 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 435 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 ILE Chi-restraints excluded: chain 2 residue 183 GLN Chi-restraints excluded: chain 2 residue 187 ARG Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 3 residue 55 LYS Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 4 residue 19 THR Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 4 residue 115 LEU Chi-restraints excluded: chain 4 residue 136 PHE Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 4 residue 245 LEU 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 79 VAL Chi-restraints excluded: chain 5 residue 136 PHE Chi-restraints excluded: chain 5 residue 289 GLU Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 187 ARG Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 ** 1 261 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** ** 4 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 GLN 4 227 ASN ** 5 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 179 GLN ** 6 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 65 GLN ** 7 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157661 restraints weight = 27012.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162137 restraints weight = 14682.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165307 restraints weight = 9454.950| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 1.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17808 Z= 0.250 Angle : 0.777 12.481 24129 Z= 0.386 Chirality : 0.044 0.184 2695 Planarity : 0.007 0.275 3080 Dihedral : 10.134 87.441 2611 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.72 % Favored : 91.72 % Rotamer: Outliers : 2.02 % Allowed : 23.90 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 2163 helix: 0.74 (0.16), residues: 1099 sheet: -3.22 (0.49), residues: 119 loop : -1.89 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 154 HIS 0.016 0.001 HIS 5 138 PHE 0.022 0.002 PHE 4 288 TYR 0.024 0.002 TYR 3 62 ARG 0.042 0.001 ARG 6 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.25 seconds wall clock time: 75 minutes 48.25 seconds (4548.25 seconds total)