Starting phenix.real_space_refine on Thu Mar 14 22:50:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g12_29659/03_2024/8g12_29659_neut_updated.pdb" } resolution = 2.17 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6296 2.51 5 N 1736 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 189": "OD1" <-> "OD2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "D ASP 189": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2495 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2495 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2495 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2495 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.53, per 1000 atoms: 0.55 Number of scatterers: 9980 At special positions: 0 Unit cell: (92.685, 98.53, 91.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1900 8.00 N 1736 7.00 C 6296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 16 sheets defined 29.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.940A pdb=" N ALA A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 153 through 168 removed outlier: 4.311A pdb=" N ALA A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 3.516A pdb=" N ILE A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 168 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.818A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 283 through 286 Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 105 through 111 removed outlier: 3.940A pdb=" N ALA B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 153 through 168 removed outlier: 4.312A pdb=" N ALA B 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 3.516A pdb=" N ILE B 164 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 168 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 3.818A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 283 through 286 Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 40 through 48 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.941A pdb=" N ALA C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 153 through 168 removed outlier: 4.311A pdb=" N ALA C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Proline residue: C 159 - end of helix removed outlier: 3.516A pdb=" N ILE C 164 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 168 " --> pdb=" O HIS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 220 removed outlier: 3.817A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 283 through 286 Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 105 through 111 removed outlier: 3.940A pdb=" N ALA D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 153 through 168 removed outlier: 4.311A pdb=" N ALA D 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) Proline residue: D 159 - end of helix removed outlier: 3.517A pdb=" N ILE D 164 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE D 168 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 removed outlier: 3.818A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 283 through 286 Processing helix chain 'D' and resid 320 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.686A pdb=" N VAL A 119 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 29 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 8 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL A 31 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 75 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 63 Processing sheet with id= C, first strand: chain 'A' and resid 208 through 210 removed outlier: 9.525A pdb=" N THR A 229 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY A 173 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET A 231 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET A 175 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE A 233 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 177 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG A 248 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY A 173 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR A 246 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET A 175 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP A 244 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 177 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 242 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 179 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 240 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS A 309 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA A 302 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 274 through 277 removed outlier: 6.630A pdb=" N SER A 293 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR A 277 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 295 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.685A pdb=" N VAL B 119 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 29 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL B 8 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL B 31 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR B 75 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= G, first strand: chain 'B' and resid 208 through 210 removed outlier: 9.525A pdb=" N THR B 229 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY B 173 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N MET B 231 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET B 175 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE B 233 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 177 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG B 248 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY B 173 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR B 246 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 175 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 244 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 177 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 242 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS B 179 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B 240 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS B 309 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 302 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 274 through 277 removed outlier: 6.629A pdb=" N SER B 293 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 277 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B 295 " --> pdb=" O THR B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.685A pdb=" N VAL C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 29 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL C 8 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL C 31 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR C 75 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 60 through 63 Processing sheet with id= K, first strand: chain 'C' and resid 208 through 210 removed outlier: 9.525A pdb=" N THR C 229 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY C 173 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET C 231 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET C 175 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE C 233 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR C 177 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG C 248 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY C 173 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR C 246 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET C 175 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP C 244 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR C 177 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL C 242 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS C 179 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 240 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 309 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA C 302 " --> pdb=" O LYS C 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 274 through 277 removed outlier: 6.630A pdb=" N SER C 293 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 277 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 295 " --> pdb=" O THR C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.685A pdb=" N VAL D 119 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP D 29 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL D 8 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL D 31 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR D 75 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 60 through 63 Processing sheet with id= O, first strand: chain 'D' and resid 208 through 210 removed outlier: 9.525A pdb=" N THR D 229 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY D 173 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET D 231 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET D 175 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N PHE D 233 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR D 177 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG D 248 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY D 173 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 246 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET D 175 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP D 244 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR D 177 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL D 242 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS D 179 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 240 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS D 309 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA D 302 " --> pdb=" O LYS D 309 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 274 through 277 removed outlier: 6.629A pdb=" N SER D 293 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR D 277 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE D 295 " --> pdb=" O THR D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 292 hydrogen bonds defined for protein. 732 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: 2.76 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2821 1.33 - 1.45: 1630 1.45 - 1.57: 5641 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 10180 Sorted by residual: bond pdb=" SG CSO B 152 " pdb=" OD CSO B 152 " ideal model delta sigma weight residual 1.668 1.735 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" SG CSO C 152 " pdb=" OD CSO C 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" SG CSO A 152 " pdb=" OD CSO A 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" SG CSO D 152 " pdb=" OD CSO D 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N ILE A 206 " pdb=" CA ILE A 206 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.28e-02 6.10e+03 8.95e+00 ... (remaining 10175 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.78: 275 106.78 - 113.64: 5671 113.64 - 120.50: 3938 120.50 - 127.36: 3841 127.36 - 134.22: 83 Bond angle restraints: 13808 Sorted by residual: angle pdb=" N ILE A 206 " pdb=" CA ILE A 206 " pdb=" C ILE A 206 " ideal model delta sigma weight residual 111.56 107.15 4.41 8.60e-01 1.35e+00 2.63e+01 angle pdb=" N ILE B 206 " pdb=" CA ILE B 206 " pdb=" C ILE B 206 " ideal model delta sigma weight residual 111.56 107.16 4.40 8.60e-01 1.35e+00 2.62e+01 angle pdb=" N ILE C 206 " pdb=" CA ILE C 206 " pdb=" C ILE C 206 " ideal model delta sigma weight residual 111.56 107.17 4.39 8.60e-01 1.35e+00 2.61e+01 angle pdb=" N ILE D 206 " pdb=" CA ILE D 206 " pdb=" C ILE D 206 " ideal model delta sigma weight residual 111.56 107.17 4.39 8.60e-01 1.35e+00 2.60e+01 angle pdb=" C ALA D 150 " pdb=" CA ALA D 150 " pdb=" CB ALA D 150 " ideal model delta sigma weight residual 116.34 110.47 5.87 1.40e+00 5.10e-01 1.76e+01 ... (remaining 13803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5440 17.75 - 35.49: 411 35.49 - 53.24: 101 53.24 - 70.99: 36 70.99 - 88.73: 16 Dihedral angle restraints: 6004 sinusoidal: 2228 harmonic: 3776 Sorted by residual: dihedral pdb=" CA VAL A 178 " pdb=" C VAL A 178 " pdb=" N HIS A 179 " pdb=" CA HIS A 179 " ideal model delta harmonic sigma weight residual -180.00 -164.53 -15.47 0 5.00e+00 4.00e-02 9.58e+00 dihedral pdb=" CA VAL B 178 " pdb=" C VAL B 178 " pdb=" N HIS B 179 " pdb=" CA HIS B 179 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA VAL D 178 " pdb=" C VAL D 178 " pdb=" N HIS D 179 " pdb=" CA HIS D 179 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 6001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 982 0.040 - 0.080: 343 0.080 - 0.119: 189 0.119 - 0.159: 50 0.159 - 0.199: 8 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA ILE C 206 " pdb=" N ILE C 206 " pdb=" C ILE C 206 " pdb=" CB ILE C 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1569 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 244 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" CG ASP A 244 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP A 244 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 244 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 244 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" CG ASP D 244 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP D 244 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP D 244 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 244 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" CG ASP B 244 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP B 244 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 244 " -0.016 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 3856 2.90 - 3.40: 9356 3.40 - 3.90: 16700 3.90 - 4.40: 19400 4.40 - 4.90: 32564 Nonbonded interactions: 81876 Sorted by model distance: nonbonded pdb=" O GLY C 201 " pdb=" ND2 ASN C 205 " model vdw 2.394 2.520 nonbonded pdb=" O GLY A 201 " pdb=" ND2 ASN A 205 " model vdw 2.394 2.520 nonbonded pdb=" O GLY D 201 " pdb=" ND2 ASN D 205 " model vdw 2.395 2.520 nonbonded pdb=" O GLY B 201 " pdb=" ND2 ASN B 205 " model vdw 2.395 2.520 nonbonded pdb=" OE2 GLU C 172 " pdb=" NH2 ARG C 248 " model vdw 2.435 2.520 ... (remaining 81871 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 3.410 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 29.210 Find NCS groups from input model: 0.630 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: 0.000 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 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 : 0.006 0.067 10180 Z= 0.380 Angle : 0.872 7.436 13808 Z= 0.569 Chirality : 0.055 0.199 1572 Planarity : 0.006 0.068 1796 Dihedral : 14.955 88.733 3596 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.38 % Allowed : 13.08 % Favored : 86.54 % 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: -1.26 (0.23), residues: 1316 helix: -1.32 (0.22), residues: 352 sheet: 0.24 (0.38), residues: 220 loop : -0.88 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 87 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE D 286 TYR 0.005 0.001 TYR A 276 ARG 0.003 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.086 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 1.6513 time to fit residues: 124.5606 Evaluate side-chains 50 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0770 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9317 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 10180 Z= 0.411 Angle : 0.591 8.429 13808 Z= 0.321 Chirality : 0.047 0.164 1572 Planarity : 0.006 0.059 1796 Dihedral : 4.263 18.511 1412 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.77 % Allowed : 12.40 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1316 helix: 0.11 (0.27), residues: 356 sheet: 0.33 (0.36), residues: 224 loop : -0.50 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 313 HIS 0.004 0.001 HIS D 53 PHE 0.014 0.001 PHE C 318 TYR 0.014 0.001 TYR B 314 ARG 0.009 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.237 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 62 average time/residue: 1.5603 time to fit residues: 103.7719 Evaluate side-chains 54 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10180 Z= 0.234 Angle : 0.509 7.179 13808 Z= 0.274 Chirality : 0.044 0.135 1572 Planarity : 0.005 0.054 1796 Dihedral : 3.969 18.025 1412 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.25 % Allowed : 12.31 % Favored : 86.44 % 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: -0.05 (0.24), residues: 1316 helix: 0.51 (0.27), residues: 356 sheet: 0.13 (0.36), residues: 232 loop : -0.27 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 313 HIS 0.003 0.001 HIS C 179 PHE 0.008 0.001 PHE B 318 TYR 0.010 0.001 TYR B 314 ARG 0.011 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.075 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 1.3784 time to fit residues: 97.7805 Evaluate side-chains 59 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9336 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 10180 Z= 0.456 Angle : 0.600 9.097 13808 Z= 0.323 Chirality : 0.048 0.171 1572 Planarity : 0.005 0.056 1796 Dihedral : 4.217 19.271 1412 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.83 % Allowed : 12.60 % Favored : 85.58 % 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: -0.03 (0.24), residues: 1316 helix: 0.57 (0.28), residues: 356 sheet: 0.19 (0.35), residues: 224 loop : -0.31 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 313 HIS 0.006 0.001 HIS D 179 PHE 0.011 0.001 PHE A 318 TYR 0.013 0.001 TYR B 314 ARG 0.012 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 1.215 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 73 average time/residue: 1.3701 time to fit residues: 107.5105 Evaluate side-chains 65 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9278 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10180 Z= 0.152 Angle : 0.474 6.041 13808 Z= 0.253 Chirality : 0.043 0.126 1572 Planarity : 0.005 0.060 1796 Dihedral : 3.825 20.550 1412 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.35 % Allowed : 13.08 % Favored : 85.58 % 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: 0.29 (0.25), residues: 1316 helix: 1.07 (0.28), residues: 352 sheet: 0.26 (0.36), residues: 232 loop : -0.20 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 313 HIS 0.002 0.000 HIS D 53 PHE 0.005 0.001 PHE D 286 TYR 0.008 0.001 TYR A 314 ARG 0.014 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.114 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 1.4416 time to fit residues: 103.4219 Evaluate side-chains 62 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10180 Z= 0.165 Angle : 0.478 6.540 13808 Z= 0.255 Chirality : 0.043 0.126 1572 Planarity : 0.005 0.066 1796 Dihedral : 3.747 20.771 1412 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.77 % Allowed : 14.04 % Favored : 85.19 % 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: 0.48 (0.25), residues: 1316 helix: 1.27 (0.28), residues: 352 sheet: 0.38 (0.37), residues: 232 loop : -0.10 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.002 0.000 HIS D 53 PHE 0.005 0.001 PHE D 286 TYR 0.009 0.001 TYR A 314 ARG 0.015 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 1.225 Fit side-chains REVERT: C 264 GLN cc_start: 0.9081 (tt0) cc_final: 0.8841 (tm-30) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 1.5233 time to fit residues: 102.6673 Evaluate side-chains 60 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0060 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 overall best weight: 2.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10180 Z= 0.233 Angle : 0.511 7.459 13808 Z= 0.274 Chirality : 0.044 0.126 1572 Planarity : 0.005 0.072 1796 Dihedral : 3.885 20.893 1412 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.63 % Allowed : 13.46 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1316 helix: 1.17 (0.28), residues: 356 sheet: 0.37 (0.37), residues: 232 loop : -0.05 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 313 HIS 0.003 0.001 HIS D 53 PHE 0.007 0.001 PHE A 286 TYR 0.010 0.001 TYR A 314 ARG 0.016 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.026 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 1.3738 time to fit residues: 100.5505 Evaluate side-chains 63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9320 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10180 Z= 0.317 Angle : 0.551 8.421 13808 Z= 0.294 Chirality : 0.046 0.142 1572 Planarity : 0.005 0.076 1796 Dihedral : 4.077 21.975 1412 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.35 % Allowed : 13.75 % Favored : 84.90 % 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: 0.44 (0.25), residues: 1316 helix: 1.09 (0.28), residues: 356 sheet: 0.57 (0.36), residues: 224 loop : -0.12 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 313 HIS 0.004 0.001 HIS A 179 PHE 0.009 0.001 PHE A 286 TYR 0.011 0.001 TYR B 314 ARG 0.017 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 1.222 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 1.3838 time to fit residues: 101.3867 Evaluate side-chains 63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 121 optimal weight: 0.0060 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10180 Z= 0.262 Angle : 0.527 7.782 13808 Z= 0.281 Chirality : 0.045 0.134 1572 Planarity : 0.005 0.079 1796 Dihedral : 4.031 22.379 1412 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.87 % Allowed : 14.42 % Favored : 84.71 % 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: 0.49 (0.25), residues: 1316 helix: 1.26 (0.28), residues: 352 sheet: 0.56 (0.36), residues: 224 loop : -0.14 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 313 HIS 0.003 0.001 HIS C 179 PHE 0.007 0.001 PHE A 286 TYR 0.010 0.001 TYR D 314 ARG 0.018 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.239 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 1.4189 time to fit residues: 96.2463 Evaluate side-chains 62 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 104 optimal weight: 0.0060 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9256 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10180 Z= 0.122 Angle : 0.463 6.751 13808 Z= 0.244 Chirality : 0.043 0.128 1572 Planarity : 0.005 0.083 1796 Dihedral : 3.707 21.552 1412 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.67 % Allowed : 14.71 % Favored : 84.62 % 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: 0.69 (0.25), residues: 1316 helix: 1.57 (0.28), residues: 352 sheet: 0.41 (0.37), residues: 232 loop : 0.00 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 313 HIS 0.002 0.000 HIS C 179 PHE 0.004 0.001 PHE B 11 TYR 0.005 0.001 TYR D 314 ARG 0.019 0.001 ARG A 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.964 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 1.3326 time to fit residues: 94.7396 Evaluate side-chains 59 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain D residue 177 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.0000 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.037906 restraints weight = 31287.426| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.84 r_work: 0.2518 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10180 Z= 0.135 Angle : 0.473 6.722 13808 Z= 0.250 Chirality : 0.043 0.127 1572 Planarity : 0.005 0.082 1796 Dihedral : 3.659 20.836 1412 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.48 % Allowed : 15.10 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1316 helix: 1.64 (0.28), residues: 352 sheet: 0.46 (0.37), residues: 232 loop : 0.01 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 313 HIS 0.002 0.000 HIS D 53 PHE 0.004 0.001 PHE A 286 TYR 0.007 0.001 TYR D 314 ARG 0.019 0.001 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.28 seconds wall clock time: 53 minutes 14.36 seconds (3194.36 seconds total)