Starting phenix.real_space_refine on Fri Aug 7 04:02:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2s_51817/08_2026/9h2s_51817.map" } resolution = 2.7 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 11963 2.51 5 N 3073 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 18235 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "E" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "G" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.54, per 1000 atoms: 0.19 Number of scatterers: 18235 At special positions: 0 Unit cell: (122.034, 122.98, 148.522, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3143 8.00 N 3073 7.00 C 11963 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: 1.09 Conformation dependent library (CDL) restraints added in 511.9 milliseconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 59.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'D' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN D 9 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 24 " --> pdb=" O CYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 294 through 314 Processing helix chain 'B' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 24 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 removed outlier: 3.691A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 294 through 314 Processing helix chain 'C' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 24 " --> pdb=" O CYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 294 through 314 Processing helix chain 'E' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN E 9 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU E 11 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 24 " --> pdb=" O CYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 246 through 260 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU F 11 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 24 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 246 through 260 Processing helix chain 'F' and resid 294 through 314 Processing helix chain 'G' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN G 12 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 24 " --> pdb=" O CYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 53 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 216 through 221 Processing helix chain 'G' and resid 246 through 260 Processing helix chain 'G' and resid 294 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.566A pdb=" N VAL A 185 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 203 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 197 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 185 " --> pdb=" O GLY G 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR G 203 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 197 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLY F 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 203 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL F 197 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER F 201 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 185 " --> pdb=" O GLY E 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR E 203 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL E 197 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR D 203 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL D 197 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 185 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR C 203 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 197 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 185 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR B 203 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 197 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN A 283 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 327 removed outlier: 8.374A pdb=" N MET B 322 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 323 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 324 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN A 325 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 326 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS A 327 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N MET C 322 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 323 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 324 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 325 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 326 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS B 327 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET E 322 " --> pdb=" O GLN D 321 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP D 323 " --> pdb=" O MET E 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL E 324 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASN D 325 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE E 326 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS D 327 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N MET F 322 " --> pdb=" O GLN E 321 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP E 323 " --> pdb=" O MET F 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL F 324 " --> pdb=" O ASP E 323 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN E 325 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE F 326 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS E 327 " --> pdb=" O PHE F 326 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET G 322 " --> pdb=" O GLN F 321 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP F 323 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL G 324 " --> pdb=" O ASP F 323 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN F 325 " --> pdb=" O VAL G 324 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE G 326 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS F 327 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN D 283 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN B 283 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN C 283 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 232 through 241 removed outlier: 6.627A pdb=" N ASN E 283 " --> pdb=" O ASN E 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN F 283 " --> pdb=" O ASN F 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN G 283 " --> pdb=" O ASN G 275 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.46 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: 4440 1.33 - 1.45: 3241 1.45 - 1.57: 10729 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18508 Sorted by residual: bond pdb=" C ILE B 60 " pdb=" O ILE B 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.09e+00 bond pdb=" C ILE G 60 " pdb=" O ILE G 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.07e+00 bond pdb=" C ILE C 60 " pdb=" O ILE C 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.02e+00 bond pdb=" C ILE A 60 " pdb=" O ILE A 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.02e+00 bond pdb=" C ILE D 60 " pdb=" O ILE D 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.01e+00 ... (remaining 18503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 24381 1.53 - 3.05: 460 3.05 - 4.58: 65 4.58 - 6.10: 14 6.10 - 7.63: 14 Bond angle restraints: 24934 Sorted by residual: angle pdb=" N GLY B 58 " pdb=" CA GLY B 58 " pdb=" C GLY B 58 " ideal model delta sigma weight residual 112.49 104.86 7.63 1.21e+00 6.83e-01 3.97e+01 angle pdb=" N GLY E 58 " pdb=" CA GLY E 58 " pdb=" C GLY E 58 " ideal model delta sigma weight residual 112.49 104.90 7.59 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 112.49 104.91 7.58 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N GLY C 58 " pdb=" CA GLY C 58 " pdb=" C GLY C 58 " ideal model delta sigma weight residual 112.49 104.92 7.57 1.21e+00 6.83e-01 3.92e+01 angle pdb=" N GLY D 58 " pdb=" CA GLY D 58 " pdb=" C GLY D 58 " ideal model delta sigma weight residual 112.49 104.92 7.57 1.21e+00 6.83e-01 3.92e+01 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 9660 17.57 - 35.14: 1057 35.14 - 52.71: 336 52.71 - 70.28: 7 70.28 - 87.86: 28 Dihedral angle restraints: 11088 sinusoidal: 4508 harmonic: 6580 Sorted by residual: dihedral pdb=" CG LYS B 327 " pdb=" CD LYS B 327 " pdb=" CE LYS B 327 " pdb=" NZ LYS B 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.83 53.83 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CG LYS C 327 " pdb=" CD LYS C 327 " pdb=" CE LYS C 327 " pdb=" NZ LYS C 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.81 53.81 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CG LYS F 327 " pdb=" CD LYS F 327 " pdb=" CE LYS F 327 " pdb=" NZ LYS F 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.79 53.79 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 11085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1917 0.025 - 0.050: 508 0.050 - 0.075: 291 0.075 - 0.099: 153 0.099 - 0.124: 99 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA VAL E 64 " pdb=" N VAL E 64 " pdb=" C VAL E 64 " pdb=" CB VAL E 64 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL C 64 " pdb=" N VAL C 64 " pdb=" C VAL C 64 " pdb=" CB VAL C 64 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2965 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 56 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ALA D 56 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA D 56 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 56 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ALA G 56 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA G 56 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL G 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 56 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C ALA B 56 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA B 56 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 57 " -0.008 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 98 2.57 - 3.15: 15876 3.15 - 3.74: 27583 3.74 - 4.32: 37856 4.32 - 4.90: 64884 Nonbonded interactions: 146297 Sorted by model distance: nonbonded pdb=" N GLU G 136 " pdb=" OE1 GLU G 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU C 136 " pdb=" OE1 GLU C 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU E 136 " pdb=" OE1 GLU E 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU D 136 " pdb=" OE1 GLU D 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU A 136 " pdb=" OE1 GLU A 136 " model vdw 1.990 3.120 ... (remaining 146292 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.024 18508 Z= 0.159 Angle : 0.521 7.626 24934 Z= 0.370 Chirality : 0.038 0.124 2968 Planarity : 0.002 0.014 3087 Dihedral : 15.781 87.856 6846 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.84 % Allowed : 28.62 % Favored : 69.53 % 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: 1.64 (0.19), residues: 2275 helix: 2.72 (0.15), residues: 1344 sheet: 0.02 (0.31), residues: 245 loop : -2.01 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 234 TYR 0.005 0.001 TYR E 299 PHE 0.017 0.001 PHE F 101 TRP 0.002 0.000 TRP E 289 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 (18508) covalent geometry : angle 0.52116 / 0.37 (24934) hydrogen bonds : bond 0.20933 / 13.84 ( 1256) hydrogen bonds : angle 7.26447 / 5.25 ( 3684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.530 Fit side-chains REVERT: A 60 ILE cc_start: 0.5136 (OUTLIER) cc_final: 0.4851 (tt) REVERT: D 60 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5174 (tt) REVERT: D 80 PHE cc_start: 0.6917 (t80) cc_final: 0.6715 (t80) REVERT: D 116 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.7252 (ttm110) REVERT: D 183 GLU cc_start: 0.8396 (tt0) cc_final: 0.7940 (tt0) REVERT: B 60 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4735 (tt) REVERT: B 183 GLU cc_start: 0.8333 (tt0) cc_final: 0.7908 (tt0) REVERT: C 60 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5304 (tt) REVERT: C 328 ARG cc_start: 0.6693 (mmm160) cc_final: 0.6464 (ttm-80) REVERT: E 60 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5268 (tt) REVERT: E 116 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7272 (ttm110) REVERT: E 183 GLU cc_start: 0.8490 (tt0) cc_final: 0.7982 (tt0) REVERT: E 276 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: F 60 ILE cc_start: 0.5649 (OUTLIER) cc_final: 0.5439 (tt) REVERT: F 183 GLU cc_start: 0.8650 (tt0) cc_final: 0.8263 (tt0) REVERT: G 60 ILE cc_start: 0.5142 (OUTLIER) cc_final: 0.4871 (tt) outliers start: 36 outliers final: 7 residues processed: 242 average time/residue: 0.4876 time to fit residues: 134.4265 Evaluate side-chains 210 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 122 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS A 141 GLN D 137 HIS D 283 ASN B 137 HIS B 235 ASN C 137 HIS E 137 HIS E 141 GLN E 235 ASN E 283 ASN F 137 HIS F 141 GLN F 283 ASN G 137 HIS G 141 GLN G 283 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.185314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103198 restraints weight = 25403.978| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.26 r_work: 0.3426 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 18508 Z= 0.288 Angle : 0.598 7.717 24934 Z= 0.323 Chirality : 0.045 0.200 2968 Planarity : 0.004 0.024 3087 Dihedral : 5.430 57.997 2698 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 6.76 % Allowed : 23.35 % Favored : 69.89 % 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: 1.28 (0.17), residues: 2275 helix: 1.92 (0.14), residues: 1372 sheet: 1.07 (0.31), residues: 238 loop : -1.61 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 180 TYR 0.011 0.001 TYR A 134 PHE 0.014 0.001 PHE E 237 TRP 0.009 0.001 TRP D 29 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.29 (18508) covalent geometry : angle 0.59787 / 0.32 (24934) hydrogen bonds : bond 0.05738 / 3.87 ( 1256) hydrogen bonds : angle 4.65118 / 3.35 ( 3684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 230 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4903 (OUTLIER) cc_final: 0.4493 (t0) REVERT: A 96 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7383 (tm) REVERT: A 204 MET cc_start: 0.8961 (ptm) cc_final: 0.8689 (ptp) REVERT: D 12 ASN cc_start: 0.5252 (OUTLIER) cc_final: 0.4930 (t0) REVERT: D 80 PHE cc_start: 0.6914 (t80) cc_final: 0.6692 (t80) REVERT: B 12 ASN cc_start: 0.4840 (OUTLIER) cc_final: 0.4393 (t0) REVERT: B 183 GLU cc_start: 0.8755 (tt0) cc_final: 0.8522 (tt0) REVERT: C 12 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4783 (t0) REVERT: C 137 HIS cc_start: 0.5362 (m90) cc_final: 0.5135 (m-70) REVERT: C 273 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: E 96 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7657 (tm) REVERT: E 190 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (m) REVERT: F 12 ASN cc_start: 0.4783 (OUTLIER) cc_final: 0.4547 (t0) REVERT: F 96 LEU cc_start: 0.7810 (mm) cc_final: 0.7530 (tp) REVERT: F 190 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (m) REVERT: G 12 ASN cc_start: 0.4482 (OUTLIER) cc_final: 0.4099 (t0) REVERT: G 96 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7347 (tp) REVERT: G 183 GLU cc_start: 0.8910 (tt0) cc_final: 0.8629 (tt0) REVERT: G 190 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (m) outliers start: 132 outliers final: 48 residues processed: 339 average time/residue: 0.5081 time to fit residues: 197.0901 Evaluate side-chains 280 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 200 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS A 235 ASN D 137 HIS D 235 ASN B 137 HIS C 235 ASN E 137 HIS F 137 HIS G 235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.206168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124531 restraints weight = 25382.569| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.15 r_work: 0.3508 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18508 Z= 0.143 Angle : 0.503 7.986 24934 Z= 0.262 Chirality : 0.041 0.138 2968 Planarity : 0.003 0.025 3087 Dihedral : 5.003 59.919 2681 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 7.22 % Allowed : 22.17 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.17), residues: 2275 helix: 1.86 (0.14), residues: 1372 sheet: 1.21 (0.30), residues: 238 loop : -1.11 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 116 TYR 0.009 0.001 TYR C 134 PHE 0.009 0.001 PHE G 326 TRP 0.005 0.001 TRP C 29 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (18508) covalent geometry : angle 0.50331 / 0.26 (24934) hydrogen bonds : bond 0.04333 / 2.94 ( 1256) hydrogen bonds : angle 4.01924 / 2.90 ( 3684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 227 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4679 (OUTLIER) cc_final: 0.4362 (t0) REVERT: A 96 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7482 (tm) REVERT: A 273 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6992 (ptm160) REVERT: D 12 ASN cc_start: 0.5065 (OUTLIER) cc_final: 0.4829 (t0) REVERT: D 116 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7294 (ttm170) REVERT: D 273 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7719 (ptm160) REVERT: D 326 PHE cc_start: 0.7362 (m-10) cc_final: 0.7060 (m-80) REVERT: B 12 ASN cc_start: 0.4931 (OUTLIER) cc_final: 0.4542 (t0) REVERT: B 183 GLU cc_start: 0.8653 (tt0) cc_final: 0.8414 (tt0) REVERT: C 12 ASN cc_start: 0.4961 (OUTLIER) cc_final: 0.4575 (t0) REVERT: C 116 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7308 (ttm170) REVERT: C 273 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7616 (ptm160) REVERT: E 26 MET cc_start: 0.1677 (mmp) cc_final: 0.1255 (mmm) REVERT: E 190 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8163 (m) REVERT: E 309 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 12 ASN cc_start: 0.4808 (OUTLIER) cc_final: 0.4381 (t0) REVERT: F 96 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (tm) REVERT: F 137 HIS cc_start: 0.5180 (m90) cc_final: 0.4843 (m-70) REVERT: F 190 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8095 (m) REVERT: G 12 ASN cc_start: 0.4583 (OUTLIER) cc_final: 0.4196 (t0) REVERT: G 96 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7407 (tm) REVERT: G 116 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7286 (ttm170) REVERT: G 183 GLU cc_start: 0.8646 (tt0) cc_final: 0.8291 (tt0) REVERT: G 190 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (m) REVERT: G 273 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6849 (ptm160) outliers start: 141 outliers final: 47 residues processed: 339 average time/residue: 0.5021 time to fit residues: 193.5494 Evaluate side-chains 279 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 173 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 71 optimal weight: 0.0030 chunk 73 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS D 43 HIS D 137 HIS B 137 HIS B 283 ASN C 137 HIS C 141 GLN E 43 HIS E 137 HIS F 141 GLN G 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101376 restraints weight = 24973.477| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.28 r_work: 0.3221 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 18508 Z= 0.302 Angle : 0.608 8.713 24934 Z= 0.315 Chirality : 0.044 0.176 2968 Planarity : 0.004 0.028 3087 Dihedral : 5.263 59.716 2677 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 7.07 % Allowed : 22.02 % Favored : 70.92 % 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: 1.29 (0.17), residues: 2275 helix: 1.76 (0.14), residues: 1372 sheet: 0.52 (0.28), residues: 280 loop : -1.01 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.009 0.001 TYR F 299 PHE 0.017 0.001 PHE G 237 TRP 0.006 0.001 TRP G 289 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.30 (18508) covalent geometry : angle 0.60831 / 0.32 (24934) hydrogen bonds : bond 0.04958 / 3.36 ( 1256) hydrogen bonds : angle 4.08029 / 2.95 ( 3684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 219 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4328 (OUTLIER) cc_final: 0.3982 (t0) REVERT: A 96 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7452 (tm) REVERT: D 269 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: B 12 ASN cc_start: 0.4538 (OUTLIER) cc_final: 0.4207 (t0) REVERT: C 12 ASN cc_start: 0.4727 (OUTLIER) cc_final: 0.4316 (t0) REVERT: C 269 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: C 273 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (ptm160) REVERT: E 26 MET cc_start: 0.1418 (mmp) cc_final: 0.1058 (mmm) REVERT: E 190 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (m) REVERT: F 12 ASN cc_start: 0.4282 (OUTLIER) cc_final: 0.3980 (t0) REVERT: F 96 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7483 (tm) REVERT: F 190 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (m) REVERT: G 12 ASN cc_start: 0.4108 (OUTLIER) cc_final: 0.3820 (t0) REVERT: G 96 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7431 (tm) REVERT: G 183 GLU cc_start: 0.8736 (tt0) cc_final: 0.8263 (tt0) REVERT: G 190 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (m) outliers start: 138 outliers final: 66 residues processed: 327 average time/residue: 0.4996 time to fit residues: 186.0277 Evaluate side-chains 287 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 39 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.1227 > 50:) chunk 78 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 137 HIS D 137 HIS B 137 HIS C 137 HIS C 141 GLN F 141 GLN G 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.180315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104968 restraints weight = 24454.297| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.19 r_work: 0.3266 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18508 Z= 0.197 Angle : 0.553 7.688 24934 Z= 0.283 Chirality : 0.042 0.138 2968 Planarity : 0.003 0.041 3087 Dihedral : 4.941 59.455 2675 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 6.20 % Allowed : 22.68 % Favored : 71.12 % 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: 1.50 (0.17), residues: 2275 helix: 1.93 (0.14), residues: 1372 sheet: 0.70 (0.27), residues: 273 loop : -0.96 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 116 TYR 0.006 0.001 TYR A 299 PHE 0.015 0.001 PHE D 326 TRP 0.004 0.001 TRP G 289 HIS 0.002 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (18508) covalent geometry : angle 0.55289 / 0.28 (24934) hydrogen bonds : bond 0.04229 / 2.88 ( 1256) hydrogen bonds : angle 3.82844 / 2.77 ( 3684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 216 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4224 (OUTLIER) cc_final: 0.3925 (t0) REVERT: D 183 GLU cc_start: 0.8939 (tt0) cc_final: 0.8519 (tt0) REVERT: D 326 PHE cc_start: 0.7394 (m-10) cc_final: 0.7145 (m-80) REVERT: C 12 ASN cc_start: 0.4716 (OUTLIER) cc_final: 0.4329 (t0) REVERT: C 116 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7261 (ttm170) REVERT: C 273 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: E 26 MET cc_start: 0.1680 (mmp) cc_final: 0.1357 (mmm) REVERT: E 190 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (m) REVERT: F 190 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8046 (m) REVERT: G 183 GLU cc_start: 0.8689 (tt0) cc_final: 0.8256 (tt0) REVERT: G 190 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (m) REVERT: G 269 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7882 (pp20) REVERT: G 273 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6837 (ptm160) outliers start: 121 outliers final: 57 residues processed: 315 average time/residue: 0.4413 time to fit residues: 158.0865 Evaluate side-chains 274 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 22 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS D 137 HIS B 43 HIS B 137 HIS C 137 HIS C 141 GLN F 141 GLN G 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.182995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.108715 restraints weight = 24440.326| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.20 r_work: 0.3316 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18508 Z= 0.111 Angle : 0.511 8.867 24934 Z= 0.255 Chirality : 0.041 0.191 2968 Planarity : 0.003 0.044 3087 Dihedral : 4.314 58.309 2673 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.27 % Allowed : 24.12 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.17), residues: 2275 helix: 2.17 (0.14), residues: 1372 sheet: 0.76 (0.26), residues: 273 loop : -0.85 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 116 TYR 0.004 0.001 TYR C 134 PHE 0.014 0.001 PHE C 326 TRP 0.004 0.000 TRP E 300 HIS 0.002 0.000 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (18508) covalent geometry : angle 0.51088 / 0.25 (24934) hydrogen bonds : bond 0.03504 / 2.39 ( 1256) hydrogen bonds : angle 3.54883 / 2.57 ( 3684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 206 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4141 (OUTLIER) cc_final: 0.3867 (t0) REVERT: A 273 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6867 (ptm160) REVERT: D 12 ASN cc_start: 0.4598 (OUTLIER) cc_final: 0.4374 (t0) REVERT: D 116 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7183 (ttm170) REVERT: D 326 PHE cc_start: 0.7186 (m-10) cc_final: 0.6899 (m-80) REVERT: B 12 ASN cc_start: 0.4461 (OUTLIER) cc_final: 0.4101 (t0) REVERT: B 60 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5496 (mm) REVERT: C 116 ARG cc_start: 0.7446 (ttm110) cc_final: 0.7223 (ttm170) REVERT: C 183 GLU cc_start: 0.8807 (tt0) cc_final: 0.8540 (tt0) REVERT: E 26 MET cc_start: 0.1665 (mmp) cc_final: 0.1325 (mmm) REVERT: E 190 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8133 (m) REVERT: E 309 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7864 (mm-30) REVERT: F 137 HIS cc_start: 0.5488 (m90) cc_final: 0.5284 (m-70) REVERT: F 190 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8000 (m) REVERT: G 183 GLU cc_start: 0.8633 (tt0) cc_final: 0.8305 (tt0) REVERT: G 190 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7963 (m) REVERT: G 273 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6686 (ptm160) outliers start: 103 outliers final: 45 residues processed: 294 average time/residue: 0.4933 time to fit residues: 163.8810 Evaluate side-chains 257 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 114 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 147 optimal weight: 0.0470 chunk 107 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS B 137 HIS F 141 GLN G 43 HIS G 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.184896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111419 restraints weight = 24313.687| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.20 r_work: 0.3300 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18508 Z= 0.127 Angle : 0.517 8.311 24934 Z= 0.260 Chirality : 0.040 0.125 2968 Planarity : 0.003 0.038 3087 Dihedral : 3.991 51.638 2669 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.15 % Allowed : 25.60 % Favored : 70.25 % 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: 1.93 (0.17), residues: 2275 helix: 2.28 (0.14), residues: 1372 sheet: 0.79 (0.26), residues: 273 loop : -0.78 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 116 TYR 0.004 0.001 TYR F 134 PHE 0.013 0.001 PHE D 326 TRP 0.003 0.001 TRP E 300 HIS 0.001 0.000 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (18508) covalent geometry : angle 0.51682 / 0.26 (24934) hydrogen bonds : bond 0.03579 / 2.44 ( 1256) hydrogen bonds : angle 3.46854 / 2.52 ( 3684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 273 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7019 (ptm160) REVERT: D 116 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7255 (ttm170) REVERT: D 269 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: D 326 PHE cc_start: 0.7138 (m-10) cc_final: 0.6876 (m-80) REVERT: B 12 ASN cc_start: 0.4475 (OUTLIER) cc_final: 0.4120 (t0) REVERT: B 60 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5466 (mm) REVERT: C 326 PHE cc_start: 0.8021 (m-10) cc_final: 0.7783 (m-10) REVERT: E 26 MET cc_start: 0.1929 (mmp) cc_final: 0.1600 (mmm) REVERT: E 183 GLU cc_start: 0.8863 (tt0) cc_final: 0.8419 (tt0) REVERT: E 190 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8108 (m) REVERT: F 137 HIS cc_start: 0.5353 (m90) cc_final: 0.5142 (m-70) REVERT: F 183 GLU cc_start: 0.8742 (tt0) cc_final: 0.8282 (tt0) REVERT: F 190 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8016 (m) REVERT: G 183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8361 (tt0) REVERT: G 190 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (m) REVERT: G 273 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6870 (ptm160) outliers start: 81 outliers final: 49 residues processed: 273 average time/residue: 0.5705 time to fit residues: 175.0467 Evaluate side-chains 251 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 65 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 161 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 50.0000 chunk 125 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS B 137 HIS C 283 ASN F 43 HIS G 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.184741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.111149 restraints weight = 24246.866| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.20 r_work: 0.3294 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18508 Z= 0.137 Angle : 0.540 8.346 24934 Z= 0.266 Chirality : 0.041 0.131 2968 Planarity : 0.003 0.056 3087 Dihedral : 3.985 48.988 2669 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.99 % Allowed : 26.47 % Favored : 69.53 % 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: 1.96 (0.17), residues: 2275 helix: 2.31 (0.14), residues: 1372 sheet: 0.78 (0.26), residues: 273 loop : -0.78 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 116 TYR 0.006 0.001 TYR F 134 PHE 0.013 0.001 PHE E 326 TRP 0.004 0.001 TRP D 300 HIS 0.003 0.000 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18508) covalent geometry : angle 0.54031 / 0.27 (24934) hydrogen bonds : bond 0.03585 / 2.44 ( 1256) hydrogen bonds : angle 3.45532 / 2.51 ( 3684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 204 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 273 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6957 (ptm160) REVERT: D 116 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7264 (ttm170) REVERT: D 183 GLU cc_start: 0.8906 (tt0) cc_final: 0.8696 (tt0) REVERT: D 269 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7294 (pp20) REVERT: D 326 PHE cc_start: 0.7132 (m-10) cc_final: 0.6865 (m-80) REVERT: B 12 ASN cc_start: 0.4466 (OUTLIER) cc_final: 0.4100 (t0) REVERT: B 60 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5443 (mm) REVERT: B 230 GLU cc_start: 0.8064 (tp30) cc_final: 0.7723 (tp30) REVERT: C 116 ARG cc_start: 0.7347 (ttm110) cc_final: 0.7131 (ttm170) REVERT: C 183 GLU cc_start: 0.8820 (tt0) cc_final: 0.8515 (tt0) REVERT: E 26 MET cc_start: 0.1916 (mmp) cc_final: 0.1593 (mmm) REVERT: E 183 GLU cc_start: 0.8893 (tt0) cc_final: 0.8452 (tt0) REVERT: E 190 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8094 (m) REVERT: F 137 HIS cc_start: 0.5295 (m90) cc_final: 0.5090 (m-70) REVERT: F 183 GLU cc_start: 0.8722 (tt0) cc_final: 0.8257 (tt0) REVERT: F 190 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7997 (m) REVERT: G 183 GLU cc_start: 0.8638 (tt0) cc_final: 0.8302 (tt0) REVERT: G 190 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7947 (m) REVERT: G 273 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6855 (ptm160) outliers start: 78 outliers final: 48 residues processed: 269 average time/residue: 0.5459 time to fit residues: 165.1062 Evaluate side-chains 266 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 102 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS B 137 HIS G 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102311 restraints weight = 24839.092| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.27 r_work: 0.3230 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 18508 Z= 0.273 Angle : 0.613 8.079 24934 Z= 0.311 Chirality : 0.044 0.170 2968 Planarity : 0.003 0.053 3087 Dihedral : 4.431 43.941 2669 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.30 % Allowed : 26.27 % Favored : 69.43 % 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: 1.75 (0.17), residues: 2275 helix: 2.15 (0.14), residues: 1372 sheet: 0.53 (0.28), residues: 280 loop : -0.81 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 116 TYR 0.009 0.001 TYR F 134 PHE 0.018 0.001 PHE E 326 TRP 0.006 0.001 TRP G 289 HIS 0.002 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.27 (18508) covalent geometry : angle 0.61330 / 0.31 (24934) hydrogen bonds : bond 0.04434 / 3.02 ( 1256) hydrogen bonds : angle 3.70111 / 2.69 ( 3684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 208 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: D 116 ARG cc_start: 0.7536 (ttm110) cc_final: 0.7304 (ttm170) REVERT: D 269 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: B 12 ASN cc_start: 0.4458 (OUTLIER) cc_final: 0.4104 (t0) REVERT: B 60 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5359 (mm) REVERT: B 230 GLU cc_start: 0.8129 (tp30) cc_final: 0.7741 (tp30) REVERT: C 116 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7271 (ttm170) REVERT: C 230 GLU cc_start: 0.8007 (tp30) cc_final: 0.7369 (mp0) REVERT: E 26 MET cc_start: 0.1926 (mmp) cc_final: 0.1602 (mmm) REVERT: E 190 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8156 (m) REVERT: F 190 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8085 (m) REVERT: G 183 GLU cc_start: 0.8705 (tt0) cc_final: 0.8231 (tt0) REVERT: G 190 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (m) REVERT: G 269 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7808 (pp20) outliers start: 84 outliers final: 53 residues processed: 279 average time/residue: 0.6039 time to fit residues: 188.9125 Evaluate side-chains 258 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 178 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS B 137 HIS C 9 ASN F 137 HIS G 9 ASN G 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.182931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103962 restraints weight = 24936.256| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.29 r_work: 0.3250 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18508 Z= 0.191 Angle : 0.575 8.066 24934 Z= 0.288 Chirality : 0.042 0.136 2968 Planarity : 0.003 0.056 3087 Dihedral : 4.323 40.150 2669 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.28 % Allowed : 27.44 % Favored : 69.28 % 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: 1.82 (0.17), residues: 2275 helix: 2.22 (0.14), residues: 1372 sheet: 0.71 (0.27), residues: 273 loop : -0.89 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 116 TYR 0.006 0.001 TYR F 299 PHE 0.021 0.001 PHE E 326 TRP 0.004 0.001 TRP G 289 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (18508) covalent geometry : angle 0.57541 / 0.29 (24934) hydrogen bonds : bond 0.03962 / 2.71 ( 1256) hydrogen bonds : angle 3.60831 / 2.62 ( 3684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.9059 (tt0) cc_final: 0.8858 (tt0) REVERT: A 273 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6565 (ptm160) REVERT: D 116 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7308 (ttm170) REVERT: D 269 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7367 (pp20) REVERT: B 12 ASN cc_start: 0.4449 (OUTLIER) cc_final: 0.4092 (t0) REVERT: B 60 ILE cc_start: 0.5870 (OUTLIER) cc_final: 0.5433 (mm) REVERT: B 230 GLU cc_start: 0.8122 (tp30) cc_final: 0.7752 (tp30) REVERT: C 116 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7267 (ttm170) REVERT: C 183 GLU cc_start: 0.8870 (tt0) cc_final: 0.8383 (tt0) REVERT: C 230 GLU cc_start: 0.8022 (tp30) cc_final: 0.7387 (mp0) REVERT: E 26 MET cc_start: 0.1955 (mmp) cc_final: 0.1647 (mmm) REVERT: E 183 GLU cc_start: 0.8993 (tt0) cc_final: 0.8724 (tt0) REVERT: E 190 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8180 (m) REVERT: F 141 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: F 183 GLU cc_start: 0.8861 (tt0) cc_final: 0.8442 (tt0) REVERT: F 190 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8069 (m) REVERT: G 183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8221 (tt0) REVERT: G 190 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (m) REVERT: G 269 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: G 273 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6843 (ptm160) outliers start: 64 outliers final: 44 residues processed: 259 average time/residue: 0.6083 time to fit residues: 176.5737 Evaluate side-chains 254 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain E residue 72 PHE Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 100 GLN Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.0170 chunk 104 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS D 9 ASN B 137 HIS F 9 ASN G 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108102 restraints weight = 25075.084| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.31 r_work: 0.3302 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18508 Z= 0.108 Angle : 0.533 8.421 24934 Z= 0.261 Chirality : 0.040 0.127 2968 Planarity : 0.003 0.046 3087 Dihedral : 3.949 36.056 2669 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.76 % Allowed : 27.91 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.17), residues: 2275 helix: 2.38 (0.14), residues: 1372 sheet: 1.07 (0.27), residues: 238 loop : -0.85 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 116 TYR 0.003 0.000 TYR D 184 PHE 0.019 0.001 PHE C 326 TRP 0.003 0.000 TRP D 300 HIS 0.003 0.000 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18508) covalent geometry : angle 0.53266 / 0.26 (24934) hydrogen bonds : bond 0.03311 / 2.27 ( 1256) hydrogen bonds : angle 3.43297 / 2.49 ( 3684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7983.22 seconds wall clock time: 136 minutes 3.85 seconds (8163.85 seconds total)