Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 22:22:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/04_2023/7u5m_26355_updated.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.108 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 8 5.49 5 S 52 5.16 5 C 6448 2.51 5 N 1772 2.21 5 O 2347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10627 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2513 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2513 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "C" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2513 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "D" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2513 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Time building chain proxies: 6.16, per 1000 atoms: 0.58 Number of scatterers: 10627 At special positions: 0 Unit cell: (99.51, 93.09, 82.39, 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 52 16.00 P 8 15.00 O 2347 8.00 N 1772 7.00 C 6448 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: 4.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 12 sheets defined 31.3% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.817A pdb=" N ALA A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 150 through 165 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.923A pdb=" N GLY A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 85 through 88 No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.816A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 150 through 165 Proline residue: B 157 - end of helix Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.923A pdb=" N GLY B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 316 through 331 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 85 through 88 No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.817A pdb=" N ALA C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 150 through 165 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 211 through 218 removed outlier: 3.923A pdb=" N GLY C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 85 through 88 No H-bonds generated for 'chain 'D' and resid 85 through 88' Processing helix chain 'D' and resid 103 through 111 removed outlier: 3.817A pdb=" N ALA D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 150 through 165 Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.923A pdb=" N GLY D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 281 through 284 Processing helix chain 'D' and resid 316 through 331 Processing sheet with id= A, first strand: chain 'A' and resid 144 through 146 removed outlier: 6.465A pdb=" N VAL A 117 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A 27 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 6 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL A 29 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA A 71 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE A 31 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 73 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR A 227 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 171 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET A 229 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET A 173 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE A 231 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR A 175 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A 246 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 171 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 244 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET A 173 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP A 242 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR A 175 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 240 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS A 177 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 238 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 302 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 307 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA A 300 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 272 through 275 removed outlier: 6.497A pdb=" N SER A 291 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 275 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 293 " --> pdb=" O THR A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 144 through 146 removed outlier: 6.464A pdb=" N VAL B 117 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 27 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL B 6 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL B 29 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 71 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE B 31 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR B 73 " --> pdb=" O ILE B 31 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR B 227 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY B 171 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET B 229 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET B 173 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 231 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 175 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 246 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 171 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR B 244 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 173 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP B 242 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR B 175 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 240 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS B 177 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 238 " --> pdb=" O HIS B 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 305 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 302 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 307 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA B 300 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 272 through 275 removed outlier: 6.497A pdb=" N SER B 291 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR B 275 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 293 " --> pdb=" O THR B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.465A pdb=" N VAL C 117 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP C 27 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL C 6 " --> pdb=" O ASP C 27 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL C 29 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA C 71 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE C 31 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 73 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR C 227 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY C 171 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET C 229 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET C 173 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 231 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 175 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG C 246 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY C 171 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR C 244 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET C 173 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP C 242 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C 175 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 240 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS C 177 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL C 238 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 305 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 302 " --> pdb=" O PHE C 305 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS C 307 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA C 300 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 272 through 275 removed outlier: 6.497A pdb=" N SER C 291 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR C 275 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE C 293 " --> pdb=" O THR C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.465A pdb=" N VAL D 117 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP D 27 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL D 6 " --> pdb=" O ASP D 27 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL D 29 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA D 71 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE D 31 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR D 73 " --> pdb=" O ILE D 31 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR D 227 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY D 171 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET D 229 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET D 173 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE D 231 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR D 175 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG D 246 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY D 171 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR D 244 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET D 173 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP D 242 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR D 175 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 240 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS D 177 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL D 238 " --> pdb=" O HIS D 177 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 305 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN D 302 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS D 307 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA D 300 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 272 through 275 removed outlier: 6.497A pdb=" N SER D 291 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 275 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE D 293 " --> pdb=" O THR D 275 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 304 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1708 1.30 - 1.43: 2633 1.43 - 1.56: 5971 1.56 - 1.69: 36 1.69 - 1.82: 96 Bond restraints: 10444 Sorted by residual: bond pdb=" O5D NAD B 401 " pdb=" PN NAD B 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD A 401 " pdb=" PN NAD A 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD C 401 " pdb=" PN NAD C 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD D 401 " pdb=" PN NAD D 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5B NAD C 401 " pdb=" PA NAD C 401 " ideal model delta sigma weight residual 1.638 1.766 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 10439 not shown) Histogram of bond angle deviations from ideal: 98.72 - 107.42: 469 107.42 - 116.12: 6661 116.12 - 124.82: 6849 124.82 - 133.52: 181 133.52 - 142.22: 16 Bond angle restraints: 14176 Sorted by residual: angle pdb=" N ASN A 203 " pdb=" CA ASN A 203 " pdb=" C ASN A 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN C 203 " pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN D 203 " pdb=" CA ASN D 203 " pdb=" C ASN D 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" C ASN B 203 " ideal model delta sigma weight residual 109.50 127.28 -17.78 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N GLN B 202 " pdb=" CA GLN B 202 " pdb=" C GLN B 202 " ideal model delta sigma weight residual 111.82 119.98 -8.16 1.16e+00 7.43e-01 4.94e+01 ... (remaining 14171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5772 17.44 - 34.89: 244 34.89 - 52.33: 64 52.33 - 69.77: 16 69.77 - 87.21: 12 Dihedral angle restraints: 6108 sinusoidal: 2348 harmonic: 3760 Sorted by residual: dihedral pdb=" CA ASN A 237 " pdb=" C ASN A 237 " pdb=" N VAL A 238 " pdb=" CA VAL A 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN D 237 " pdb=" C ASN D 237 " pdb=" N VAL D 238 " pdb=" CA VAL D 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN C 237 " pdb=" C ASN C 237 " pdb=" N VAL C 238 " pdb=" CA VAL C 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1392 0.082 - 0.164: 176 0.164 - 0.246: 16 0.246 - 0.328: 20 0.328 - 0.410: 8 Chirality restraints: 1612 Sorted by residual: chirality pdb=" C2D NAD B 401 " pdb=" C1D NAD B 401 " pdb=" C3D NAD B 401 " pdb=" O2D NAD B 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2D NAD D 401 " pdb=" C1D NAD D 401 " pdb=" C3D NAD D 401 " pdb=" O2D NAD D 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2D NAD C 401 " pdb=" C1D NAD C 401 " pdb=" C3D NAD C 401 " pdb=" O2D NAD C 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 1609 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 196 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASP C 196 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP C 196 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY C 197 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 196 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ASP B 196 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP B 196 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 197 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 196 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ASP D 196 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP D 196 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY D 197 " -0.017 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3231 2.82 - 3.34: 10532 3.34 - 3.86: 21913 3.86 - 4.38: 24977 4.38 - 4.90: 39444 Nonbonded interactions: 100097 Sorted by model distance: nonbonded pdb=" O TRP D 194 " pdb=" O HOH D 501 " model vdw 2.296 2.440 nonbonded pdb=" O1N NAD D 401 " pdb=" O HOH D 502 " model vdw 2.297 2.440 nonbonded pdb=" O TRP C 194 " pdb=" O HOH C 501 " model vdw 2.301 2.440 nonbonded pdb=" O TRP A 194 " pdb=" O HOH A 501 " model vdw 2.301 2.440 nonbonded pdb=" O ASP B 294 " pdb=" O HOH B 501 " model vdw 2.310 2.440 ... (remaining 100092 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: 1.180 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: 0.000 Extract box with map and model: 4.380 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.240 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.008 0.136 10444 Z= 0.519 Angle : 0.961 17.802 14176 Z= 0.511 Chirality : 0.068 0.410 1612 Planarity : 0.005 0.039 1804 Dihedral : 12.190 87.213 3708 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.87 % 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: -0.13 (0.23), residues: 1320 helix: 0.98 (0.26), residues: 392 sheet: -0.92 (0.31), residues: 264 loop : -0.27 (0.25), residues: 664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.262 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 1.3896 time to fit residues: 332.4494 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6737 ------------------------------------------------------------------------------- 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: 0.0070 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 237 ASN A 289 HIS A 328 HIS B 22 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 237 ASN B 289 HIS B 328 HIS C 22 ASN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 237 ASN C 289 HIS C 328 HIS D 22 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN D 237 ASN D 289 HIS D 328 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10444 Z= 0.169 Angle : 0.502 5.087 14176 Z= 0.273 Chirality : 0.047 0.172 1612 Planarity : 0.004 0.027 1804 Dihedral : 7.758 85.645 1424 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.87 % 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: -0.17 (0.23), residues: 1320 helix: 1.05 (0.27), residues: 368 sheet: -0.98 (0.32), residues: 272 loop : -0.29 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 195 time to evaluate : 1.237 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 207 average time/residue: 1.3905 time to fit residues: 308.0066 Evaluate side-chains 206 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.1538 time to fit residues: 2.8437 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 68 ASN B 55 ASN B 68 ASN C 55 ASN C 68 ASN D 55 ASN D 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 10444 Z= 0.408 Angle : 0.683 5.599 14176 Z= 0.376 Chirality : 0.055 0.223 1612 Planarity : 0.005 0.033 1804 Dihedral : 8.174 80.649 1424 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.50 (0.23), residues: 1320 helix: 0.60 (0.26), residues: 364 sheet: -1.03 (0.31), residues: 256 loop : -0.47 (0.24), residues: 700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.238 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 196 average time/residue: 1.4546 time to fit residues: 305.0387 Evaluate side-chains 190 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1017 time to fit residues: 2.1386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10444 Z= 0.224 Angle : 0.541 5.111 14176 Z= 0.297 Chirality : 0.048 0.170 1612 Planarity : 0.004 0.032 1804 Dihedral : 7.840 81.039 1424 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.34 (0.23), residues: 1320 helix: 0.83 (0.26), residues: 364 sheet: -0.89 (0.32), residues: 264 loop : -0.44 (0.24), residues: 692 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.263 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 199 average time/residue: 1.4293 time to fit residues: 303.6885 Evaluate side-chains 201 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1072 time to fit residues: 2.2215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 10444 Z= 0.268 Angle : 0.578 5.211 14176 Z= 0.315 Chirality : 0.050 0.173 1612 Planarity : 0.004 0.029 1804 Dihedral : 7.944 81.092 1424 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.41 (0.23), residues: 1320 helix: 0.81 (0.27), residues: 364 sheet: -0.98 (0.32), residues: 264 loop : -0.48 (0.24), residues: 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.240 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 207 average time/residue: 1.4789 time to fit residues: 326.4500 Evaluate side-chains 205 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1047 time to fit residues: 2.3089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10444 Z= 0.242 Angle : 0.557 5.233 14176 Z= 0.304 Chirality : 0.049 0.168 1612 Planarity : 0.004 0.031 1804 Dihedral : 7.893 81.194 1424 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 1320 helix: 1.10 (0.27), residues: 348 sheet: -0.95 (0.32), residues: 264 loop : -0.53 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.309 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 212 average time/residue: 1.3717 time to fit residues: 311.4871 Evaluate side-chains 214 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.4760 time to fit residues: 3.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0470 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10444 Z= 0.202 Angle : 0.528 4.912 14176 Z= 0.287 Chirality : 0.048 0.166 1612 Planarity : 0.004 0.029 1804 Dihedral : 7.755 80.702 1424 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.26 (0.23), residues: 1320 helix: 1.24 (0.28), residues: 348 sheet: -0.86 (0.33), residues: 264 loop : -0.56 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.279 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 209 average time/residue: 1.3537 time to fit residues: 303.3305 Evaluate side-chains 200 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.5784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN B 278 GLN C 68 ASN D 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 10444 Z= 0.374 Angle : 0.673 5.835 14176 Z= 0.366 Chirality : 0.054 0.213 1612 Planarity : 0.005 0.031 1804 Dihedral : 8.178 81.609 1424 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.58 (0.22), residues: 1320 helix: 0.68 (0.26), residues: 364 sheet: -1.17 (0.31), residues: 256 loop : -0.57 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 204 average time/residue: 1.4328 time to fit residues: 312.4736 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.4725 time to fit residues: 3.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10444 Z= 0.192 Angle : 0.540 6.030 14176 Z= 0.290 Chirality : 0.047 0.165 1612 Planarity : 0.004 0.028 1804 Dihedral : 7.779 81.116 1424 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.27 (0.23), residues: 1320 helix: 1.25 (0.28), residues: 348 sheet: -0.94 (0.32), residues: 264 loop : -0.54 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 202 average time/residue: 1.5521 time to fit residues: 334.1747 Evaluate side-chains 202 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 111 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10444 Z= 0.210 Angle : 0.560 6.726 14176 Z= 0.299 Chirality : 0.048 0.166 1612 Planarity : 0.004 0.028 1804 Dihedral : 7.804 80.763 1424 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.34 (0.23), residues: 1320 helix: 1.21 (0.28), residues: 348 sheet: -1.11 (0.31), residues: 272 loop : -0.53 (0.23), residues: 700 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 201 average time/residue: 1.4224 time to fit residues: 305.5659 Evaluate side-chains 198 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 75 optimal weight: 0.0980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.177837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160294 restraints weight = 8732.052| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 0.74 r_work: 0.3636 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10444 Z= 0.162 Angle : 0.526 7.715 14176 Z= 0.278 Chirality : 0.046 0.163 1612 Planarity : 0.004 0.028 1804 Dihedral : 7.558 79.507 1424 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.31 % 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: -0.23 (0.23), residues: 1320 helix: 1.41 (0.28), residues: 348 sheet: -1.07 (0.32), residues: 272 loop : -0.51 (0.24), residues: 700 =============================================================================== Job complete usr+sys time: 4922.55 seconds wall clock time: 88 minutes 3.72 seconds (5283.72 seconds total)