Starting phenix.real_space_refine on Fri Mar 15 05:08:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/03_2024/7u5m_26355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/03_2024/7u5m_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_26355/03_2024/7u5m_26355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/03_2024/7u5m_26355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/03_2024/7u5m_26355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5m_26355/03_2024/7u5m_26355_updated.pdb" } resolution = 2.28 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= 0.108 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-dev-5265/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: 5.80, per 1000 atoms: 0.55 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 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: 2.19 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: 3.33 Time building geometry restraints manager: 4.46 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: 5848 17.44 - 34.89: 308 34.89 - 52.33: 100 52.33 - 69.77: 28 69.77 - 87.21: 24 Dihedral angle restraints: 6308 sinusoidal: 2548 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 6305 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.200 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.810 ------------------------------------------------------------------------------- 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 : 14.032 87.213 3908 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 % Allowed : 5.60 % Favored : 92.54 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 194 HIS 0.004 0.001 HIS B 51 PHE 0.020 0.002 PHE D 231 TYR 0.014 0.002 TYR C 318 ARG 0.005 0.001 ARG D 232 *********************** 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 : 0.930 Fit side-chains REVERT: A 41 MET cc_start: 0.8276 (mtp) cc_final: 0.7962 (mtp) REVERT: A 103 MET cc_start: 0.7867 (mmm) cc_final: 0.7537 (mmm) REVERT: A 131 MET cc_start: 0.8693 (mmm) cc_final: 0.8409 (mmm) REVERT: A 170 GLU cc_start: 0.8668 (pt0) cc_final: 0.8182 (pt0) REVERT: B 41 MET cc_start: 0.8277 (mtp) cc_final: 0.7964 (mtp) REVERT: B 103 MET cc_start: 0.7877 (mmm) cc_final: 0.7559 (mmm) REVERT: B 131 MET cc_start: 0.8687 (mmm) cc_final: 0.8400 (mmm) REVERT: B 170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8166 (pt0) REVERT: C 41 MET cc_start: 0.8267 (mtp) cc_final: 0.7953 (mtp) REVERT: C 103 MET cc_start: 0.7858 (mmm) cc_final: 0.7522 (mmm) REVERT: C 131 MET cc_start: 0.8691 (mmm) cc_final: 0.8402 (mmm) REVERT: C 170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8176 (pt0) REVERT: D 41 MET cc_start: 0.8275 (mtp) cc_final: 0.7961 (mtp) REVERT: D 103 MET cc_start: 0.7872 (mmm) cc_final: 0.7528 (mmm) REVERT: D 131 MET cc_start: 0.8693 (mmm) cc_final: 0.8410 (mmm) REVERT: D 170 GLU cc_start: 0.8654 (pt0) cc_final: 0.8180 (pt0) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 1.3640 time to fit residues: 326.2541 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0970 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: 0.6980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10444 Z= 0.164 Angle : 0.490 5.000 14176 Z= 0.268 Chirality : 0.047 0.170 1612 Planarity : 0.004 0.027 1804 Dihedral : 12.439 89.328 1640 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.24 % Allowed : 10.45 % Favored : 87.31 % 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: -0.14 (0.24), residues: 1320 helix: 1.10 (0.27), residues: 368 sheet: -0.96 (0.32), residues: 272 loop : -0.27 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 85 HIS 0.003 0.001 HIS B 51 PHE 0.012 0.001 PHE A 231 TYR 0.011 0.002 TYR B 312 ARG 0.003 0.001 ARG A 116 *********************** 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 220 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.300 Fit side-chains REVERT: A 41 MET cc_start: 0.8294 (mtp) cc_final: 0.7913 (mtp) REVERT: A 75 PHE cc_start: 0.8265 (m-80) cc_final: 0.7962 (m-80) REVERT: A 103 MET cc_start: 0.7781 (mmm) cc_final: 0.7313 (mmm) REVERT: A 170 GLU cc_start: 0.8653 (pt0) cc_final: 0.8134 (pt0) REVERT: A 316 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 37 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6519 (p0) REVERT: B 41 MET cc_start: 0.8295 (mtp) cc_final: 0.7911 (mtp) REVERT: B 75 PHE cc_start: 0.8260 (m-80) cc_final: 0.7964 (m-80) REVERT: B 103 MET cc_start: 0.7776 (mmm) cc_final: 0.7272 (mmm) REVERT: B 170 GLU cc_start: 0.8641 (pt0) cc_final: 0.8121 (pt0) REVERT: B 316 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8077 (t80) REVERT: C 37 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6519 (p0) REVERT: C 41 MET cc_start: 0.8286 (mtp) cc_final: 0.7900 (mtp) REVERT: C 75 PHE cc_start: 0.8264 (m-80) cc_final: 0.7971 (m-80) REVERT: C 103 MET cc_start: 0.7745 (mmm) cc_final: 0.7433 (mmm) REVERT: C 170 GLU cc_start: 0.8644 (pt0) cc_final: 0.8125 (pt0) REVERT: C 316 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8080 (t80) REVERT: D 37 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6529 (p0) REVERT: D 41 MET cc_start: 0.8294 (mtp) cc_final: 0.7906 (mtp) REVERT: D 75 PHE cc_start: 0.8263 (m-80) cc_final: 0.7963 (m-80) REVERT: D 103 MET cc_start: 0.7762 (mmm) cc_final: 0.7445 (mmm) REVERT: D 170 GLU cc_start: 0.8641 (pt0) cc_final: 0.8132 (pt0) REVERT: D 316 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8073 (t80) outliers start: 24 outliers final: 9 residues processed: 208 average time/residue: 1.4003 time to fit residues: 310.8238 Evaluate side-chains 209 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE 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: 0.1980 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 55 ASN D 68 ASN D 278 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0919 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= 0.219 Angle : 0.531 4.978 14176 Z= 0.291 Chirality : 0.048 0.181 1612 Planarity : 0.004 0.026 1804 Dihedral : 12.250 87.000 1636 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.59 % Allowed : 12.50 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1320 helix: 0.99 (0.27), residues: 368 sheet: -1.02 (0.32), residues: 272 loop : -0.34 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 85 HIS 0.004 0.001 HIS C 51 PHE 0.009 0.002 PHE B 284 TYR 0.014 0.002 TYR A 318 ARG 0.002 0.001 ARG C 116 *********************** 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 212 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 37 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6532 (p0) REVERT: A 41 MET cc_start: 0.8310 (mtp) cc_final: 0.7984 (mtp) REVERT: A 75 PHE cc_start: 0.8358 (m-80) cc_final: 0.8053 (m-80) REVERT: A 103 MET cc_start: 0.7696 (mmm) cc_final: 0.7326 (mmm) REVERT: A 170 GLU cc_start: 0.8667 (pt0) cc_final: 0.8186 (pt0) REVERT: A 316 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8104 (t80) REVERT: B 37 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6537 (p0) REVERT: B 41 MET cc_start: 0.8310 (mtp) cc_final: 0.7984 (mtp) REVERT: B 75 PHE cc_start: 0.8360 (m-80) cc_final: 0.8052 (m-80) REVERT: B 103 MET cc_start: 0.7688 (mmm) cc_final: 0.7273 (mmm) REVERT: B 170 GLU cc_start: 0.8658 (pt0) cc_final: 0.8166 (pt0) REVERT: B 316 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 37 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6522 (p0) REVERT: C 41 MET cc_start: 0.8306 (mtp) cc_final: 0.7975 (mtp) REVERT: C 75 PHE cc_start: 0.8362 (m-80) cc_final: 0.8059 (m-80) REVERT: C 170 GLU cc_start: 0.8655 (pt0) cc_final: 0.8175 (pt0) REVERT: C 316 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8107 (t80) REVERT: D 37 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6531 (p0) REVERT: D 41 MET cc_start: 0.8307 (mtp) cc_final: 0.7984 (mtp) REVERT: D 75 PHE cc_start: 0.8360 (m-80) cc_final: 0.8058 (m-80) REVERT: D 103 MET cc_start: 0.7717 (mmm) cc_final: 0.7296 (mmm) REVERT: D 170 GLU cc_start: 0.8652 (pt0) cc_final: 0.8180 (pt0) REVERT: D 316 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8099 (t80) outliers start: 17 outliers final: 9 residues processed: 203 average time/residue: 1.3993 time to fit residues: 303.2542 Evaluate side-chains 208 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10444 Z= 0.319 Angle : 0.613 5.326 14176 Z= 0.337 Chirality : 0.052 0.193 1612 Planarity : 0.004 0.030 1804 Dihedral : 12.598 88.248 1636 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.24 % Allowed : 11.75 % Favored : 86.01 % 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: -0.43 (0.23), residues: 1320 helix: 0.74 (0.26), residues: 368 sheet: -1.00 (0.32), residues: 264 loop : -0.47 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 194 HIS 0.005 0.002 HIS C 39 PHE 0.010 0.002 PHE B 284 TYR 0.019 0.003 TYR A 318 ARG 0.004 0.001 ARG A 18 *********************** 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 209 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.242 Fit side-chains REVERT: A 37 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6544 (p0) REVERT: A 131 MET cc_start: 0.8680 (mmm) cc_final: 0.8232 (mmm) REVERT: A 170 GLU cc_start: 0.8665 (pt0) cc_final: 0.8270 (pt0) REVERT: A 316 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8080 (t80) REVERT: B 37 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6492 (p0) REVERT: B 103 MET cc_start: 0.7703 (mmm) cc_final: 0.7360 (mmm) REVERT: B 170 GLU cc_start: 0.8654 (pt0) cc_final: 0.8210 (pt0) REVERT: B 316 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8080 (t80) REVERT: C 37 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6486 (p0) REVERT: C 170 GLU cc_start: 0.8653 (pt0) cc_final: 0.8263 (pt0) REVERT: C 316 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8099 (t80) REVERT: D 37 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6494 (p0) REVERT: D 131 MET cc_start: 0.8662 (mmm) cc_final: 0.8211 (mmm) REVERT: D 170 GLU cc_start: 0.8651 (pt0) cc_final: 0.8269 (pt0) REVERT: D 316 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8077 (t80) outliers start: 24 outliers final: 11 residues processed: 197 average time/residue: 1.3978 time to fit residues: 293.9628 Evaluate side-chains 202 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10444 Z= 0.189 Angle : 0.507 4.971 14176 Z= 0.278 Chirality : 0.047 0.168 1612 Planarity : 0.004 0.027 1804 Dihedral : 11.955 85.411 1636 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.05 % Allowed : 12.41 % Favored : 85.54 % 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: -0.33 (0.23), residues: 1320 helix: 0.98 (0.27), residues: 368 sheet: -1.03 (0.32), residues: 272 loop : -0.44 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 85 HIS 0.004 0.001 HIS D 51 PHE 0.008 0.001 PHE A 231 TYR 0.013 0.002 TYR D 318 ARG 0.002 0.001 ARG A 198 *********************** 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 212 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8283 (m-80) cc_final: 0.8004 (m-80) REVERT: A 131 MET cc_start: 0.8631 (mmm) cc_final: 0.8263 (mmm) REVERT: A 170 GLU cc_start: 0.8664 (pt0) cc_final: 0.8141 (pt0) REVERT: A 217 LYS cc_start: 0.7934 (mttp) cc_final: 0.7725 (mttm) REVERT: A 316 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 103 MET cc_start: 0.7741 (mmm) cc_final: 0.7333 (mmm) REVERT: B 170 GLU cc_start: 0.8653 (pt0) cc_final: 0.8120 (pt0) REVERT: B 316 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 170 GLU cc_start: 0.8653 (pt0) cc_final: 0.8130 (pt0) REVERT: C 316 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8109 (t80) REVERT: D 75 PHE cc_start: 0.8282 (m-80) cc_final: 0.7997 (m-80) REVERT: D 103 MET cc_start: 0.7708 (mmm) cc_final: 0.7325 (mmm) REVERT: D 170 GLU cc_start: 0.8665 (pt0) cc_final: 0.8150 (pt0) REVERT: D 316 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8102 (t80) outliers start: 22 outliers final: 9 residues processed: 202 average time/residue: 1.4003 time to fit residues: 302.2670 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 0.0670 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 10444 Z= 0.449 Angle : 0.716 6.152 14176 Z= 0.393 Chirality : 0.057 0.238 1612 Planarity : 0.005 0.031 1804 Dihedral : 12.790 84.817 1636 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.52 % Allowed : 11.85 % Favored : 85.63 % 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: -0.69 (0.22), residues: 1320 helix: 0.43 (0.25), residues: 380 sheet: -1.16 (0.31), residues: 256 loop : -0.58 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 194 HIS 0.007 0.002 HIS D 39 PHE 0.012 0.003 PHE C 129 TYR 0.025 0.004 TYR D 318 ARG 0.006 0.001 ARG C 18 *********************** 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 213 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.7856 (mmm) cc_final: 0.7516 (mmm) REVERT: B 170 GLU cc_start: 0.8657 (pt0) cc_final: 0.8292 (pt0) REVERT: B 316 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8095 (t80) REVERT: C 170 GLU cc_start: 0.8657 (pt0) cc_final: 0.8301 (pt0) REVERT: C 316 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8105 (t80) REVERT: D 111 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6874 (mtpt) REVERT: D 170 GLU cc_start: 0.8654 (pt0) cc_final: 0.8266 (pt0) REVERT: D 316 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8091 (t80) outliers start: 27 outliers final: 14 residues processed: 202 average time/residue: 1.4382 time to fit residues: 309.7838 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10444 Z= 0.193 Angle : 0.524 4.980 14176 Z= 0.287 Chirality : 0.047 0.166 1612 Planarity : 0.004 0.031 1804 Dihedral : 11.944 85.328 1636 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.21 % Allowed : 13.25 % Favored : 85.54 % 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: -0.36 (0.23), residues: 1320 helix: 0.91 (0.27), residues: 368 sheet: -0.91 (0.32), residues: 264 loop : -0.51 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 85 HIS 0.004 0.001 HIS C 51 PHE 0.009 0.002 PHE B 231 TYR 0.013 0.002 TYR C 318 ARG 0.006 0.001 ARG D 78 *********************** 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 202 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.7742 (mmm) cc_final: 0.7370 (mmm) REVERT: A 131 MET cc_start: 0.8667 (mmm) cc_final: 0.8109 (mmm) REVERT: A 170 GLU cc_start: 0.8661 (pt0) cc_final: 0.8156 (pt0) REVERT: A 217 LYS cc_start: 0.7867 (mttp) cc_final: 0.7656 (mttm) REVERT: A 316 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 131 MET cc_start: 0.8640 (mmm) cc_final: 0.8106 (mmm) REVERT: B 170 GLU cc_start: 0.8643 (pt0) cc_final: 0.8134 (pt0) REVERT: B 316 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8164 (t80) REVERT: C 131 MET cc_start: 0.8640 (mmm) cc_final: 0.8106 (mmm) REVERT: C 170 GLU cc_start: 0.8652 (pt0) cc_final: 0.8154 (pt0) REVERT: C 316 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8167 (t80) REVERT: D 75 PHE cc_start: 0.8268 (m-80) cc_final: 0.7996 (m-80) REVERT: D 103 MET cc_start: 0.7600 (mmm) cc_final: 0.7353 (mmm) REVERT: D 170 GLU cc_start: 0.8650 (pt0) cc_final: 0.8160 (pt0) REVERT: D 316 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8154 (t80) outliers start: 13 outliers final: 9 residues processed: 197 average time/residue: 1.3847 time to fit residues: 291.5008 Evaluate side-chains 202 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10444 Z= 0.323 Angle : 0.630 5.102 14176 Z= 0.343 Chirality : 0.052 0.194 1612 Planarity : 0.004 0.029 1804 Dihedral : 12.269 85.032 1636 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.87 % Allowed : 12.97 % Favored : 85.17 % 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 (0.23), residues: 1320 helix: 0.54 (0.26), residues: 384 sheet: -1.10 (0.31), residues: 256 loop : -0.54 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 194 HIS 0.005 0.002 HIS D 328 PHE 0.010 0.002 PHE C 284 TYR 0.020 0.003 TYR A 318 ARG 0.005 0.001 ARG D 78 *********************** 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 210 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.7886 (mmm) cc_final: 0.7377 (mmm) REVERT: A 170 GLU cc_start: 0.8665 (pt0) cc_final: 0.8225 (pt0) REVERT: B 103 MET cc_start: 0.7743 (mmm) cc_final: 0.7275 (mmm) REVERT: B 170 GLU cc_start: 0.8640 (pt0) cc_final: 0.8192 (pt0) REVERT: B 316 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8076 (t80) REVERT: C 170 GLU cc_start: 0.8643 (pt0) cc_final: 0.8204 (pt0) REVERT: C 316 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8121 (t80) REVERT: D 75 PHE cc_start: 0.8357 (m-80) cc_final: 0.8009 (m-80) REVERT: D 170 GLU cc_start: 0.8646 (pt0) cc_final: 0.8214 (pt0) REVERT: D 316 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8111 (t80) outliers start: 20 outliers final: 10 residues processed: 198 average time/residue: 1.4097 time to fit residues: 297.8495 Evaluate side-chains 203 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE 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: 0.0070 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.1326 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= 0.156 Angle : 0.501 6.287 14176 Z= 0.271 Chirality : 0.046 0.162 1612 Planarity : 0.004 0.027 1804 Dihedral : 11.381 85.724 1636 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.40 % Allowed : 14.37 % Favored : 84.24 % 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: -0.34 (0.23), residues: 1320 helix: 1.07 (0.27), residues: 368 sheet: -1.07 (0.32), residues: 272 loop : -0.50 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 85 HIS 0.003 0.001 HIS B 51 PHE 0.011 0.001 PHE B 231 TYR 0.010 0.001 TYR A 318 ARG 0.006 0.001 ARG D 78 *********************** 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 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7765 (mmm) cc_final: 0.7332 (mmm) REVERT: A 170 GLU cc_start: 0.8639 (pt0) cc_final: 0.8108 (pt0) REVERT: A 316 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8135 (t80) REVERT: B 103 MET cc_start: 0.7665 (mmm) cc_final: 0.7370 (mmm) REVERT: B 131 MET cc_start: 0.8655 (mmm) cc_final: 0.7974 (mmm) REVERT: B 170 GLU cc_start: 0.8624 (pt0) cc_final: 0.8090 (pt0) REVERT: B 316 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 170 GLU cc_start: 0.8631 (pt0) cc_final: 0.8105 (pt0) REVERT: C 316 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (t80) REVERT: D 75 PHE cc_start: 0.8309 (m-80) cc_final: 0.7985 (m-80) REVERT: D 103 MET cc_start: 0.7728 (mmm) cc_final: 0.7384 (mmm) REVERT: D 170 GLU cc_start: 0.8632 (pt0) cc_final: 0.8115 (pt0) REVERT: D 316 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8137 (t80) outliers start: 15 outliers final: 8 residues processed: 197 average time/residue: 1.4029 time to fit residues: 295.0688 Evaluate side-chains 198 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10444 Z= 0.383 Angle : 0.685 6.705 14176 Z= 0.373 Chirality : 0.054 0.223 1612 Planarity : 0.005 0.029 1804 Dihedral : 12.241 85.479 1636 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 13.81 % Favored : 84.98 % 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: -0.64 (0.22), residues: 1320 helix: 0.54 (0.26), residues: 380 sheet: -1.13 (0.31), residues: 256 loop : -0.60 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 194 HIS 0.005 0.002 HIS C 39 PHE 0.011 0.003 PHE C 231 TYR 0.023 0.004 TYR A 318 ARG 0.005 0.001 ARG D 18 ********************** 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 199 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7964 (mmm) cc_final: 0.7438 (mmm) REVERT: A 170 GLU cc_start: 0.8674 (pt0) cc_final: 0.8258 (pt0) REVERT: A 316 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 103 MET cc_start: 0.7879 (mmm) cc_final: 0.7564 (mmm) REVERT: B 316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8117 (t80) REVERT: C 170 GLU cc_start: 0.8667 (pt0) cc_final: 0.8257 (pt0) REVERT: C 316 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8116 (t80) REVERT: D 75 PHE cc_start: 0.8397 (m-80) cc_final: 0.8027 (m-80) REVERT: D 111 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6833 (mtpt) REVERT: D 170 GLU cc_start: 0.8662 (pt0) cc_final: 0.8265 (pt0) REVERT: D 316 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8107 (t80) outliers start: 13 outliers final: 8 residues processed: 194 average time/residue: 1.3619 time to fit residues: 282.3522 Evaluate side-chains 194 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.176401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158938 restraints weight = 8736.253| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 0.74 r_work: 0.3621 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10444 Z= 0.177 Angle : 0.535 7.368 14176 Z= 0.288 Chirality : 0.047 0.165 1612 Planarity : 0.004 0.027 1804 Dihedral : 11.503 86.059 1636 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.31 % Allowed : 14.18 % Favored : 84.51 % 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: -0.38 (0.23), residues: 1320 helix: 1.01 (0.27), residues: 368 sheet: -1.07 (0.32), residues: 272 loop : -0.51 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 85 HIS 0.003 0.001 HIS B 51 PHE 0.010 0.001 PHE A 75 TYR 0.012 0.002 TYR D 318 ARG 0.005 0.001 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4857.23 seconds wall clock time: 86 minutes 26.74 seconds (5186.74 seconds total)