Starting phenix.real_space_refine on Thu Aug 6 17:48:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxk_71972/08_2026/9pxk_71972.map" } resolution = 2.52 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 32 5.16 5 C 10220 2.51 5 N 2668 2.21 5 O 3148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16084 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "E" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 931 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "D" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2958 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'MQ8': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'MQ8:plan-2': 1, 'MQ8:plan-3': 1, 'MQ8:plan-4': 1, 'MQ8:plan-5': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'MQ8': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'MQ8:plan-2': 1, 'MQ8:plan-3': 1, 'MQ8:plan-4': 1, 'MQ8:plan-5': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'MQ8': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'MQ8:plan-2': 1, 'MQ8:plan-3': 1, 'MQ8:plan-4': 1, 'MQ8:plan-5': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'MQ8': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'MQ8:plan-2': 1, 'MQ8:plan-3': 1, 'MQ8:plan-4': 1, 'MQ8:plan-5': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.35, per 1000 atoms: 0.21 Number of scatterers: 16084 At special positions: 0 Unit cell: (139.784, 139.784, 116.352, 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 32 16.00 P 16 15.00 O 3148 8.00 N 2668 7.00 C 10220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 32 sheets defined 50.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 11 through 22 removed outlier: 4.097A pdb=" N LEU C 16 " --> pdb=" O TYR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 128 through 150 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 163 through 184 Proline residue: C 178 - end of helix removed outlier: 3.653A pdb=" N TYR C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 207 through 221 removed outlier: 3.525A pdb=" N ARG C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 267 Processing helix chain 'C' and resid 310 through 330 removed outlier: 3.638A pdb=" N TYR C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'E' and resid 27 through 38 Processing helix chain 'E' and resid 38 through 61 Processing helix chain 'E' and resid 62 through 101 Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 116 through 139 Processing helix chain 'F' and resid 27 through 61 Proline residue: F 40 - end of helix Processing helix chain 'F' and resid 62 through 100 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 116 through 139 Processing helix chain 'G' and resid 27 through 61 Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 62 through 101 Proline residue: G 79 - end of helix Processing helix chain 'G' and resid 106 through 115 Processing helix chain 'G' and resid 116 through 139 Processing helix chain 'H' and resid 27 through 61 Proline residue: H 40 - end of helix Processing helix chain 'H' and resid 62 through 100 Proline residue: H 79 - end of helix Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 116 through 139 Processing helix chain 'A' and resid 11 through 22 removed outlier: 4.097A pdb=" N LEU A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 163 through 184 Proline residue: A 178 - end of helix removed outlier: 3.653A pdb=" N TYR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.525A pdb=" N ARG A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 310 through 330 removed outlier: 3.637A pdb=" N TYR A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.097A pdb=" N LEU B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 128 through 150 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 163 through 184 Proline residue: B 178 - end of helix removed outlier: 3.653A pdb=" N TYR B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.525A pdb=" N ARG B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 Processing helix chain 'B' and resid 310 through 330 removed outlier: 3.638A pdb=" N TYR B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'D' and resid 11 through 22 removed outlier: 4.097A pdb=" N LEU D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 128 through 150 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 163 through 184 Proline residue: D 178 - end of helix removed outlier: 3.653A pdb=" N TYR D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 207 through 221 removed outlier: 3.525A pdb=" N ARG D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 267 Processing helix chain 'D' and resid 310 through 330 removed outlier: 3.637A pdb=" N TYR D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 384 Processing helix chain 'D' and resid 386 through 392 Processing sheet with id=AA1, first strand: chain 'C' and resid 73 through 77 removed outlier: 8.827A pdb=" N ASP C 74 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 32 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS C 76 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 34 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS C 3 " --> pdb=" O ARG C 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR C 33 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE C 5 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL C 35 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 7 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C 103 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY C 257 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 223 through 227 removed outlier: 6.769A pdb=" N LEU C 193 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU C 226 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 195 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 251 " --> pdb=" O THR C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.629A pdb=" N ASN C 233 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.331A pdb=" N ALA C 276 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AA9, first strand: chain 'A' and resid 73 through 77 removed outlier: 8.826A pdb=" N ASP A 74 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 32 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS A 76 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 34 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS A 3 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR A 33 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 5 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 35 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 7 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 103 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AB3, first strand: chain 'A' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY A 257 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.769A pdb=" N LEU A 193 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 226 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 195 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 251 " --> pdb=" O THR A 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.629A pdb=" N ASN A 233 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.330A pdb=" N ALA A 276 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'B' and resid 73 through 77 removed outlier: 8.827A pdb=" N ASP B 74 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 32 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS B 76 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 34 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS B 3 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR B 33 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 5 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL B 35 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 7 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 103 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 40 through 42 Processing sheet with id=AC1, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 112 removed outlier: 4.156A pdb=" N GLY B 257 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.769A pdb=" N LEU B 193 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU B 226 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 195 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 251 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.629A pdb=" N ASN B 233 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.331A pdb=" N ALA B 276 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC7, first strand: chain 'D' and resid 73 through 77 removed outlier: 8.827A pdb=" N ASP D 74 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 32 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS D 76 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 34 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS D 3 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR D 33 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 5 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL D 35 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 7 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU D 103 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 84 Processing sheet with id=AD1, first strand: chain 'D' and resid 109 through 112 removed outlier: 4.157A pdb=" N GLY D 257 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 223 through 227 removed outlier: 6.769A pdb=" N LEU D 193 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU D 226 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D 195 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 251 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.629A pdb=" N ASN D 233 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.331A pdb=" N ALA D 276 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 343 through 346 870 hydrogen bonds defined for protein. 2454 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: 3.40 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4096 1.33 - 1.45: 2717 1.45 - 1.57: 9459 1.57 - 1.69: 32 1.69 - 1.81: 64 Bond restraints: 16368 Sorted by residual: bond pdb=" O3P FAD B 401 " pdb=" P FAD B 401 " ideal model delta sigma weight residual 1.660 1.583 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O3P FAD D 401 " pdb=" P FAD D 401 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O3P FAD C 401 " pdb=" P FAD C 401 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O3P FAD A 401 " pdb=" P FAD A 401 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O5B FAD D 401 " pdb=" PA FAD D 401 " ideal model delta sigma weight residual 1.634 1.570 0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 16363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 21647 1.45 - 2.90: 399 2.90 - 4.35: 146 4.35 - 5.79: 36 5.79 - 7.24: 16 Bond angle restraints: 22244 Sorted by residual: angle pdb=" CA THR E 33 " pdb=" CB THR E 33 " pdb=" OG1 THR E 33 " ideal model delta sigma weight residual 109.60 105.39 4.21 1.50e+00 4.44e-01 7.87e+00 angle pdb=" O VAL E 28 " pdb=" C VAL E 28 " pdb=" N GLN E 29 " ideal model delta sigma weight residual 121.90 124.37 -2.47 1.01e+00 9.80e-01 6.00e+00 angle pdb=" O1P FAD A 401 " pdb=" P FAD A 401 " pdb=" O2P FAD A 401 " ideal model delta sigma weight residual 122.50 115.26 7.24 3.00e+00 1.11e-01 5.83e+00 angle pdb=" O1P FAD C 401 " pdb=" P FAD C 401 " pdb=" O2P FAD C 401 " ideal model delta sigma weight residual 122.50 115.26 7.24 3.00e+00 1.11e-01 5.83e+00 angle pdb=" O1P FAD D 401 " pdb=" P FAD D 401 " pdb=" O2P FAD D 401 " ideal model delta sigma weight residual 122.50 115.26 7.24 3.00e+00 1.11e-01 5.83e+00 ... (remaining 22239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 9096 17.60 - 35.20: 751 35.20 - 52.80: 139 52.80 - 70.40: 51 70.40 - 88.00: 35 Dihedral angle restraints: 10072 sinusoidal: 4232 harmonic: 5840 Sorted by residual: dihedral pdb=" CA TYR C 100 " pdb=" C TYR C 100 " pdb=" N ASP C 101 " pdb=" CA ASP C 101 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR D 100 " pdb=" C TYR D 100 " pdb=" N ASP D 101 " pdb=" CA ASP D 101 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 100 " pdb=" C TYR B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 10069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2168 0.052 - 0.104: 293 0.104 - 0.156: 130 0.156 - 0.208: 1 0.208 - 0.260: 4 Chirality restraints: 2596 Sorted by residual: chirality pdb=" C1D NAI B 403 " pdb=" C2D NAI B 403 " pdb=" N1N NAI B 403 " pdb=" O4D NAI B 403 " both_signs ideal model delta sigma weight residual False 2.29 2.55 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1D NAI C 403 " pdb=" C2D NAI C 403 " pdb=" N1N NAI C 403 " pdb=" O4D NAI C 403 " both_signs ideal model delta sigma weight residual False 2.29 2.55 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1D NAI D 403 " pdb=" C2D NAI D 403 " pdb=" N1N NAI D 403 " pdb=" O4D NAI D 403 " both_signs ideal model delta sigma weight residual False 2.29 2.55 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2593 not shown) Planarity restraints: 2792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 116 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO E 117 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 117 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 116 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO F 117 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 117 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 116 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO H 117 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " -0.028 5.00e-02 4.00e+02 ... (remaining 2789 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1428 2.74 - 3.28: 16391 3.28 - 3.82: 27290 3.82 - 4.36: 33535 4.36 - 4.90: 57247 Nonbonded interactions: 135891 Sorted by model distance: nonbonded pdb=" OG1 THR E 90 " pdb=" NH1 ARG F 136 " model vdw 2.196 3.120 nonbonded pdb=" ND2 ASN C 233 " pdb=" OE1 GLU C 235 " model vdw 2.239 3.120 nonbonded pdb=" ND2 ASN A 233 " pdb=" OE1 GLU A 235 " model vdw 2.239 3.120 nonbonded pdb=" ND2 ASN B 233 " pdb=" OE1 GLU B 235 " model vdw 2.239 3.120 nonbonded pdb=" ND2 ASN D 233 " pdb=" OE1 GLU D 235 " model vdw 2.240 3.120 ... (remaining 135886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 6.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.540 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 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 : 0.004 0.077 16368 Z= 0.206 Angle : 0.580 7.243 22244 Z= 0.261 Chirality : 0.043 0.260 2596 Planarity : 0.004 0.050 2792 Dihedral : 14.578 88.005 6328 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.20), residues: 2028 helix: 2.10 (0.18), residues: 988 sheet: 1.91 (0.38), residues: 216 loop : -0.29 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 31 TYR 0.009 0.001 TYR F 53 PHE 0.004 0.000 PHE D 83 TRP 0.009 0.001 TRP C 315 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (16368) covalent geometry : angle 0.57962 / 0.26 (22244) hydrogen bonds : bond 0.12713 / 8.39 ( 870) hydrogen bonds : angle 5.83593 / 4.09 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: H 51 LYS cc_start: 0.7195 (tmtt) cc_final: 0.6968 (mtpt) REVERT: H 95 LYS cc_start: 0.8357 (tttm) cc_final: 0.8070 (ttpp) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.7519 time to fit residues: 210.7235 Evaluate side-chains 206 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 HIS C 283 GLN F 127 ASN G 127 ASN H 127 ASN A 283 GLN B 48 HIS B 283 GLN D 283 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067854 restraints weight = 34470.287| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.44 r_work: 0.2893 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16368 Z= 0.112 Angle : 0.551 7.328 22244 Z= 0.268 Chirality : 0.042 0.165 2596 Planarity : 0.004 0.061 2792 Dihedral : 11.134 89.043 2648 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.19 % Allowed : 6.73 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.20), residues: 2028 helix: 2.67 (0.17), residues: 976 sheet: 1.74 (0.37), residues: 216 loop : -0.08 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.011 0.001 TYR B 380 PHE 0.018 0.001 PHE E 108 TRP 0.014 0.002 TRP C 315 HIS 0.001 0.000 HIS D 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (16368) covalent geometry : angle 0.55103 / 0.27 (22244) hydrogen bonds : bond 0.04007 / 2.63 ( 870) hydrogen bonds : angle 4.23404 / 2.94 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ASN cc_start: 0.9159 (m-40) cc_final: 0.8898 (m110) REVERT: F 95 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8022 (tttm) REVERT: A 54 ASN cc_start: 0.9170 (m-40) cc_final: 0.8912 (m110) REVERT: B 54 ASN cc_start: 0.9166 (m-40) cc_final: 0.8912 (m110) REVERT: D 54 ASN cc_start: 0.9177 (m-40) cc_final: 0.8926 (m110) outliers start: 20 outliers final: 7 residues processed: 231 average time/residue: 0.6782 time to fit residues: 172.0894 Evaluate side-chains 223 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 0.0060 chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 ASN E 138 ASN F 127 ASN G 127 ASN G 138 ASN H 127 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.065718 restraints weight = 34749.101| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.56 r_work: 0.2824 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16368 Z= 0.115 Angle : 0.515 6.586 22244 Z= 0.249 Chirality : 0.041 0.128 2596 Planarity : 0.004 0.062 2792 Dihedral : 9.806 79.758 2648 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.43 % Allowed : 9.17 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.20), residues: 2028 helix: 2.87 (0.17), residues: 976 sheet: 1.81 (0.37), residues: 216 loop : -0.08 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 124 TYR 0.011 0.001 TYR A 380 PHE 0.007 0.001 PHE D 83 TRP 0.014 0.002 TRP C 315 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (16368) covalent geometry : angle 0.51502 / 0.25 (22244) hydrogen bonds : bond 0.03745 / 2.46 ( 870) hydrogen bonds : angle 3.98895 / 2.79 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ASN cc_start: 0.9128 (m-40) cc_final: 0.8870 (m110) REVERT: C 374 GLU cc_start: 0.8025 (tp30) cc_final: 0.7652 (tt0) REVERT: F 95 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7991 (tttm) REVERT: A 54 ASN cc_start: 0.9132 (m-40) cc_final: 0.8869 (m110) REVERT: A 374 GLU cc_start: 0.8030 (tp30) cc_final: 0.7665 (tt0) REVERT: B 54 ASN cc_start: 0.9131 (m-40) cc_final: 0.8873 (m110) REVERT: B 235 GLU cc_start: 0.7902 (pm20) cc_final: 0.7692 (pm20) REVERT: B 374 GLU cc_start: 0.8029 (tp30) cc_final: 0.7672 (tt0) REVERT: D 54 ASN cc_start: 0.9133 (m-40) cc_final: 0.8877 (m110) REVERT: D 235 GLU cc_start: 0.7919 (pm20) cc_final: 0.7718 (pm20) outliers start: 24 outliers final: 6 residues processed: 228 average time/residue: 0.6826 time to fit residues: 170.2699 Evaluate side-chains 221 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 17 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 283 GLN E 127 ASN F 127 ASN G 127 ASN H 127 ASN A 48 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065498 restraints weight = 34424.952| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.54 r_work: 0.2829 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16368 Z= 0.115 Angle : 0.512 6.873 22244 Z= 0.248 Chirality : 0.041 0.128 2596 Planarity : 0.004 0.065 2792 Dihedral : 9.309 78.234 2648 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.43 % Allowed : 10.30 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.20), residues: 2028 helix: 2.84 (0.17), residues: 976 sheet: 1.84 (0.37), residues: 216 loop : -0.12 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 305 TYR 0.011 0.001 TYR B 380 PHE 0.008 0.001 PHE B 83 TRP 0.015 0.002 TRP C 315 HIS 0.002 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16368) covalent geometry : angle 0.51243 / 0.25 (22244) hydrogen bonds : bond 0.03535 / 2.33 ( 870) hydrogen bonds : angle 3.93096 / 2.75 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ASN cc_start: 0.9131 (m-40) cc_final: 0.8858 (m110) REVERT: C 374 GLU cc_start: 0.8044 (tp30) cc_final: 0.7639 (tt0) REVERT: F 57 GLN cc_start: 0.8279 (tp40) cc_final: 0.8074 (tp40) REVERT: F 95 LYS cc_start: 0.8426 (ttpp) cc_final: 0.7974 (tttm) REVERT: G 95 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8078 (tttm) REVERT: H 66 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8657 (mtmm) REVERT: A 54 ASN cc_start: 0.9134 (m-40) cc_final: 0.8835 (m110) REVERT: A 374 GLU cc_start: 0.8049 (tp30) cc_final: 0.7645 (tt0) REVERT: B 54 ASN cc_start: 0.9127 (m-40) cc_final: 0.8855 (m110) REVERT: B 235 GLU cc_start: 0.7930 (pm20) cc_final: 0.7698 (pm20) REVERT: B 374 GLU cc_start: 0.8022 (tp30) cc_final: 0.7628 (tt0) REVERT: B 383 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8172 (t-90) REVERT: D 54 ASN cc_start: 0.9128 (m-40) cc_final: 0.8843 (m110) REVERT: D 235 GLU cc_start: 0.7936 (pm20) cc_final: 0.7704 (pm20) REVERT: D 374 GLU cc_start: 0.8047 (tp30) cc_final: 0.7651 (tt0) outliers start: 24 outliers final: 11 residues processed: 229 average time/residue: 0.6783 time to fit residues: 170.0594 Evaluate side-chains 225 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain B residue 383 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 54 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN F 127 ASN G 127 ASN H 127 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064923 restraints weight = 34443.329| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.53 r_work: 0.2841 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16368 Z= 0.120 Angle : 0.510 7.250 22244 Z= 0.248 Chirality : 0.041 0.142 2596 Planarity : 0.004 0.066 2792 Dihedral : 9.117 75.964 2648 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.37 % Allowed : 11.55 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.20), residues: 2028 helix: 2.85 (0.17), residues: 976 sheet: 1.89 (0.36), residues: 216 loop : -0.12 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 273 TYR 0.012 0.001 TYR B 380 PHE 0.022 0.001 PHE E 108 TRP 0.015 0.002 TRP C 315 HIS 0.001 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16368) covalent geometry : angle 0.51001 / 0.25 (22244) hydrogen bonds : bond 0.03581 / 2.35 ( 870) hydrogen bonds : angle 3.91277 / 2.74 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ASN cc_start: 0.9133 (m-40) cc_final: 0.8871 (m110) REVERT: C 374 GLU cc_start: 0.8081 (tp30) cc_final: 0.7648 (tt0) REVERT: F 57 GLN cc_start: 0.8296 (tp40) cc_final: 0.8085 (tp40) REVERT: F 95 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7996 (tttm) REVERT: G 95 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8118 (tttm) REVERT: H 66 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8672 (mtmm) REVERT: H 75 GLU cc_start: 0.8641 (tt0) cc_final: 0.8229 (tp30) REVERT: A 374 GLU cc_start: 0.8105 (tp30) cc_final: 0.7665 (tt0) REVERT: B 54 ASN cc_start: 0.9133 (m-40) cc_final: 0.8871 (m110) REVERT: B 235 GLU cc_start: 0.7961 (pm20) cc_final: 0.7727 (pm20) REVERT: B 374 GLU cc_start: 0.8107 (tp30) cc_final: 0.7692 (tt0) REVERT: D 54 ASN cc_start: 0.9129 (m-40) cc_final: 0.8854 (m110) REVERT: D 235 GLU cc_start: 0.7973 (pm20) cc_final: 0.7740 (pm20) REVERT: D 374 GLU cc_start: 0.8088 (tp30) cc_final: 0.7661 (tt0) outliers start: 23 outliers final: 12 residues processed: 230 average time/residue: 0.6650 time to fit residues: 167.3179 Evaluate side-chains 227 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 ASN F 127 ASN G 127 ASN H 127 ASN A 283 GLN B 283 GLN D 283 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062795 restraints weight = 34385.635| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.48 r_work: 0.2804 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 16368 Z= 0.201 Angle : 0.556 7.236 22244 Z= 0.270 Chirality : 0.044 0.148 2596 Planarity : 0.004 0.068 2792 Dihedral : 9.362 74.342 2648 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.95 % Allowed : 12.02 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.19), residues: 2028 helix: 2.84 (0.17), residues: 964 sheet: 1.84 (0.36), residues: 216 loop : -0.13 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.012 0.001 TYR A 380 PHE 0.008 0.001 PHE D 83 TRP 0.014 0.002 TRP C 315 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (16368) covalent geometry : angle 0.55573 / 0.27 (22244) hydrogen bonds : bond 0.04434 / 2.90 ( 870) hydrogen bonds : angle 4.10841 / 2.89 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8265 (tp30) cc_final: 0.7786 (tt0) REVERT: E 75 GLU cc_start: 0.8842 (tt0) cc_final: 0.8376 (tp30) REVERT: E 116 ASP cc_start: 0.8980 (t0) cc_final: 0.8638 (t0) REVERT: F 75 GLU cc_start: 0.8836 (tt0) cc_final: 0.8405 (tp30) REVERT: F 95 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8114 (tttm) REVERT: F 116 ASP cc_start: 0.9009 (t0) cc_final: 0.8750 (t0) REVERT: G 75 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8518 (tp30) REVERT: G 116 ASP cc_start: 0.9010 (t0) cc_final: 0.8733 (t0) REVERT: H 66 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8717 (mtmm) REVERT: H 75 GLU cc_start: 0.8891 (tt0) cc_final: 0.8392 (tp30) REVERT: H 116 ASP cc_start: 0.8997 (t0) cc_final: 0.8762 (t0) REVERT: A 374 GLU cc_start: 0.8257 (tp30) cc_final: 0.7782 (tt0) REVERT: B 235 GLU cc_start: 0.8178 (pm20) cc_final: 0.7910 (pm20) REVERT: B 374 GLU cc_start: 0.8289 (tp30) cc_final: 0.7802 (tt0) REVERT: D 235 GLU cc_start: 0.8176 (pm20) cc_final: 0.7910 (pm20) REVERT: D 374 GLU cc_start: 0.8280 (tp30) cc_final: 0.7798 (tt0) outliers start: 16 outliers final: 11 residues processed: 222 average time/residue: 0.6441 time to fit residues: 156.1717 Evaluate side-chains 225 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 154 optimal weight: 0.9990 chunk 25 optimal weight: 0.0010 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064008 restraints weight = 33952.522| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.49 r_work: 0.2837 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16368 Z= 0.113 Angle : 0.515 7.700 22244 Z= 0.249 Chirality : 0.041 0.153 2596 Planarity : 0.004 0.070 2792 Dihedral : 9.077 75.671 2648 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.71 % Allowed : 12.02 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.20), residues: 2028 helix: 2.88 (0.17), residues: 968 sheet: 1.87 (0.36), residues: 216 loop : -0.11 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.010 0.001 TYR C 380 PHE 0.009 0.001 PHE D 83 TRP 0.017 0.002 TRP B 315 HIS 0.002 0.000 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16368) covalent geometry : angle 0.51464 / 0.25 (22244) hydrogen bonds : bond 0.03595 / 2.36 ( 870) hydrogen bonds : angle 3.94475 / 2.77 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8091 (tp30) cc_final: 0.7662 (tt0) REVERT: E 75 GLU cc_start: 0.8652 (tt0) cc_final: 0.8222 (tp30) REVERT: E 116 ASP cc_start: 0.8830 (t0) cc_final: 0.8474 (t0) REVERT: F 57 GLN cc_start: 0.8318 (tp40) cc_final: 0.8105 (tp40) REVERT: F 75 GLU cc_start: 0.8653 (tt0) cc_final: 0.8252 (tp30) REVERT: F 95 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8014 (tttm) REVERT: F 116 ASP cc_start: 0.8860 (t0) cc_final: 0.8587 (t0) REVERT: G 75 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: G 116 ASP cc_start: 0.8885 (t0) cc_final: 0.8609 (t0) REVERT: H 66 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8664 (mtmm) REVERT: H 75 GLU cc_start: 0.8705 (tt0) cc_final: 0.8217 (tp30) REVERT: A 374 GLU cc_start: 0.8095 (tp30) cc_final: 0.7672 (tt0) REVERT: B 235 GLU cc_start: 0.8002 (pm20) cc_final: 0.7741 (pm20) REVERT: B 374 GLU cc_start: 0.8122 (tp30) cc_final: 0.7686 (tt0) REVERT: D 235 GLU cc_start: 0.8009 (pm20) cc_final: 0.7745 (pm20) REVERT: D 374 GLU cc_start: 0.8100 (tp30) cc_final: 0.7676 (tt0) outliers start: 12 outliers final: 11 residues processed: 226 average time/residue: 0.6830 time to fit residues: 168.9258 Evaluate side-chains 229 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain H residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 0.0170 chunk 196 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 ASN F 127 ASN G 127 ASN H 127 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064926 restraints weight = 34345.574| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.48 r_work: 0.2849 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16368 Z= 0.111 Angle : 0.507 7.891 22244 Z= 0.246 Chirality : 0.041 0.162 2596 Planarity : 0.004 0.068 2792 Dihedral : 8.905 73.913 2648 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.07 % Allowed : 11.96 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.20), residues: 2028 helix: 2.86 (0.17), residues: 976 sheet: 1.86 (0.36), residues: 216 loop : -0.11 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.011 0.001 TYR C 380 PHE 0.008 0.001 PHE C 83 TRP 0.016 0.002 TRP B 315 HIS 0.001 0.000 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16368) covalent geometry : angle 0.50707 / 0.25 (22244) hydrogen bonds : bond 0.03445 / 2.27 ( 870) hydrogen bonds : angle 3.89908 / 2.73 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8251 (tp30) cc_final: 0.7729 (tt0) REVERT: E 75 GLU cc_start: 0.8821 (tt0) cc_final: 0.8351 (tp30) REVERT: E 116 ASP cc_start: 0.8925 (t0) cc_final: 0.8599 (t0) REVERT: F 57 GLN cc_start: 0.8400 (tp40) cc_final: 0.8186 (tp40) REVERT: F 75 GLU cc_start: 0.8831 (tt0) cc_final: 0.8386 (tp30) REVERT: F 95 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8056 (tttt) REVERT: F 116 ASP cc_start: 0.8977 (t0) cc_final: 0.8714 (t0) REVERT: G 75 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: G 95 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8187 (tttm) REVERT: G 116 ASP cc_start: 0.8988 (t0) cc_final: 0.8711 (t0) REVERT: H 66 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8669 (mtmm) REVERT: H 75 GLU cc_start: 0.8876 (tt0) cc_final: 0.8361 (tp30) REVERT: H 116 ASP cc_start: 0.9007 (t0) cc_final: 0.8760 (t0) REVERT: A 374 GLU cc_start: 0.8252 (tp30) cc_final: 0.7733 (tt0) REVERT: B 235 GLU cc_start: 0.8151 (pm20) cc_final: 0.7871 (pm20) REVERT: B 374 GLU cc_start: 0.8252 (tp30) cc_final: 0.7726 (tt0) REVERT: D 235 GLU cc_start: 0.8155 (pm20) cc_final: 0.7875 (pm20) REVERT: D 374 GLU cc_start: 0.8247 (tp30) cc_final: 0.7729 (tt0) outliers start: 18 outliers final: 10 residues processed: 233 average time/residue: 0.7227 time to fit residues: 183.6927 Evaluate side-chains 225 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 136 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 127 ASN H 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.063131 restraints weight = 34242.235| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.53 r_work: 0.2811 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16368 Z= 0.164 Angle : 0.546 7.859 22244 Z= 0.266 Chirality : 0.042 0.166 2596 Planarity : 0.004 0.068 2792 Dihedral : 9.033 72.700 2648 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.77 % Allowed : 12.68 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.20), residues: 2028 helix: 2.91 (0.17), residues: 964 sheet: 1.81 (0.36), residues: 216 loop : -0.12 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.012 0.001 TYR C 380 PHE 0.008 0.001 PHE C 83 TRP 0.015 0.002 TRP B 315 HIS 0.001 0.001 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (16368) covalent geometry : angle 0.54602 / 0.27 (22244) hydrogen bonds : bond 0.03996 / 2.62 ( 870) hydrogen bonds : angle 3.99515 / 2.81 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8127 (tp30) cc_final: 0.7686 (tt0) REVERT: E 75 GLU cc_start: 0.8679 (tt0) cc_final: 0.8254 (tp30) REVERT: E 116 ASP cc_start: 0.8826 (t0) cc_final: 0.8500 (t0) REVERT: F 75 GLU cc_start: 0.8681 (tt0) cc_final: 0.8262 (tp30) REVERT: F 95 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8000 (tttt) REVERT: F 116 ASP cc_start: 0.8893 (t0) cc_final: 0.8586 (t0) REVERT: G 75 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: G 116 ASP cc_start: 0.8910 (t0) cc_final: 0.8637 (t0) REVERT: H 66 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8656 (mtmm) REVERT: H 116 ASP cc_start: 0.8931 (t0) cc_final: 0.8658 (t0) REVERT: A 374 GLU cc_start: 0.8129 (tp30) cc_final: 0.7689 (tt0) REVERT: B 235 GLU cc_start: 0.8039 (pm20) cc_final: 0.7778 (pm20) REVERT: B 374 GLU cc_start: 0.8133 (tp30) cc_final: 0.7661 (tt0) REVERT: B 383 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7917 (t-90) REVERT: D 235 GLU cc_start: 0.8046 (pm20) cc_final: 0.7785 (pm20) REVERT: D 374 GLU cc_start: 0.8133 (tp30) cc_final: 0.7678 (tt0) outliers start: 13 outliers final: 9 residues processed: 222 average time/residue: 0.7020 time to fit residues: 170.3466 Evaluate side-chains 227 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain B residue 383 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 102 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN G 127 ASN H 127 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064524 restraints weight = 34158.060| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.53 r_work: 0.2835 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16368 Z= 0.114 Angle : 0.522 8.174 22244 Z= 0.254 Chirality : 0.041 0.163 2596 Planarity : 0.004 0.069 2792 Dihedral : 8.844 73.252 2648 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.60 % Allowed : 12.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.20), residues: 2028 helix: 2.86 (0.17), residues: 976 sheet: 1.82 (0.36), residues: 216 loop : -0.08 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.012 0.001 TYR C 380 PHE 0.008 0.001 PHE D 83 TRP 0.017 0.002 TRP B 315 HIS 0.002 0.000 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (16368) covalent geometry : angle 0.52201 / 0.25 (22244) hydrogen bonds : bond 0.03486 / 2.30 ( 870) hydrogen bonds : angle 3.90273 / 2.74 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 214 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 374 GLU cc_start: 0.8090 (tp30) cc_final: 0.7627 (tt0) REVERT: E 75 GLU cc_start: 0.8690 (tt0) cc_final: 0.8247 (tp30) REVERT: E 116 ASP cc_start: 0.8808 (t0) cc_final: 0.8495 (t0) REVERT: F 57 GLN cc_start: 0.8318 (tp40) cc_final: 0.8083 (tp40) REVERT: F 75 GLU cc_start: 0.8691 (tt0) cc_final: 0.8245 (tp30) REVERT: F 95 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7985 (tttt) REVERT: F 116 ASP cc_start: 0.8877 (t0) cc_final: 0.8607 (t0) REVERT: G 75 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: G 95 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8138 (tttm) REVERT: G 116 ASP cc_start: 0.8902 (t0) cc_final: 0.8632 (t0) REVERT: H 66 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8652 (mtmm) REVERT: H 116 ASP cc_start: 0.8920 (t0) cc_final: 0.8654 (t0) REVERT: A 374 GLU cc_start: 0.8094 (tp30) cc_final: 0.7632 (tt0) REVERT: B 235 GLU cc_start: 0.8025 (pm20) cc_final: 0.7751 (pm20) REVERT: B 374 GLU cc_start: 0.8112 (tp30) cc_final: 0.7624 (tt0) REVERT: D 235 GLU cc_start: 0.8032 (pm20) cc_final: 0.7756 (pm20) REVERT: D 374 GLU cc_start: 0.8096 (tp30) cc_final: 0.7623 (tt0) outliers start: 10 outliers final: 9 residues processed: 218 average time/residue: 0.6967 time to fit residues: 165.8640 Evaluate side-chains 223 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 136 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.2980 chunk 142 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 130 optimal weight: 0.0020 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.065506 restraints weight = 34061.404| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.48 r_work: 0.2829 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16368 Z= 0.099 Angle : 0.511 8.401 22244 Z= 0.248 Chirality : 0.040 0.162 2596 Planarity : 0.004 0.069 2792 Dihedral : 8.676 72.492 2648 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.71 % Allowed : 12.56 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.20), residues: 2028 helix: 2.89 (0.17), residues: 976 sheet: 1.86 (0.36), residues: 216 loop : -0.06 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.010 0.001 TYR C 380 PHE 0.008 0.001 PHE D 83 TRP 0.017 0.002 TRP B 315 HIS 0.001 0.000 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (16368) covalent geometry : angle 0.51087 / 0.25 (22244) hydrogen bonds : bond 0.03165 / 2.09 ( 870) hydrogen bonds : angle 3.81688 / 2.67 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5656.11 seconds wall clock time: 97 minutes 14.00 seconds (5834.00 seconds total)