Starting phenix.real_space_refine on Wed Mar 4 07:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x54_33007/03_2026/7x54_33007.map" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 7370 2.51 5 N 1900 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "B" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "C" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2287 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.53, per 1000 atoms: 0.22 Number of scatterers: 11575 At special positions: 0 Unit cell: (80.04, 97.44, 160.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 10 15.00 Mg 5 11.99 O 2250 8.00 N 1900 7.00 C 7370 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: 0.90 Conformation dependent library (CDL) restraints added in 505.8 milliseconds 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 37.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.625A pdb=" N ARG A 64 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.552A pdb=" N LEU A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 removed outlier: 4.179A pdb=" N ARG A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.575A pdb=" N TYR A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.799A pdb=" N LYS A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.637A pdb=" N PHE A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'A' and resid 214 through 227 removed outlier: 4.093A pdb=" N TYR A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.584A pdb=" N LEU A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR A 253 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 4.067A pdb=" N ASN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.625A pdb=" N ARG B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.553A pdb=" N LEU B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 removed outlier: 4.178A pdb=" N ARG B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.574A pdb=" N TYR B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.800A pdb=" N LYS B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.640A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 214 through 227 removed outlier: 4.093A pdb=" N TYR B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.584A pdb=" N LEU B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR B 253 " --> pdb=" O MET B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 284 removed outlier: 4.067A pdb=" N ASN B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 276 " --> pdb=" O ASN B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.625A pdb=" N ARG C 64 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.551A pdb=" N LEU C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 removed outlier: 4.178A pdb=" N ARG C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.574A pdb=" N TYR C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.799A pdb=" N LYS C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.640A pdb=" N PHE C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 209 Processing helix chain 'C' and resid 214 through 227 removed outlier: 4.093A pdb=" N TYR C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.583A pdb=" N LEU C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 4.067A pdb=" N ASN C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 276 " --> pdb=" O ASN C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.625A pdb=" N ARG D 64 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 78 removed outlier: 3.553A pdb=" N LEU D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 removed outlier: 4.179A pdb=" N ARG D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 104 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.574A pdb=" N TYR D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.800A pdb=" N LYS D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.640A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 209 Processing helix chain 'D' and resid 214 through 227 removed outlier: 4.093A pdb=" N TYR D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.584A pdb=" N LEU D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 284 removed outlier: 4.066A pdb=" N ASN D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 276 " --> pdb=" O ASN D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 removed outlier: 3.624A pdb=" N ARG E 64 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 78 removed outlier: 3.553A pdb=" N LEU E 71 " --> pdb=" O MET E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 107 removed outlier: 4.179A pdb=" N ARG E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 removed outlier: 3.576A pdb=" N TYR E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.800A pdb=" N LYS E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 removed outlier: 3.639A pdb=" N PHE E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 209 Processing helix chain 'E' and resid 214 through 227 removed outlier: 4.092A pdb=" N TYR E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.584A pdb=" N LEU E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 4.068A pdb=" N ASN E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 276 " --> pdb=" O ASN E 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.208A pdb=" N LYS A 2 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 6 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 90 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE A 85 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 127 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 87 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 129 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 89 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 91 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.633A pdb=" N GLN A 39 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.676A pdb=" N LYS A 171 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 24 removed outlier: 4.208A pdb=" N LYS B 2 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 6 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 90 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE B 85 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 127 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 87 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B 129 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 89 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 91 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28 removed outlier: 4.632A pdb=" N GLN B 39 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 176 removed outlier: 3.676A pdb=" N LYS B 171 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 24 removed outlier: 4.208A pdb=" N LYS C 2 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 6 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 90 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE C 85 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 127 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 87 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL C 129 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 89 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 91 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.633A pdb=" N GLN C 39 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 176 removed outlier: 3.675A pdb=" N LYS C 171 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.207A pdb=" N LYS D 2 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 6 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 90 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE D 85 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 127 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 87 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL D 129 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 89 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU D 91 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 28 removed outlier: 4.632A pdb=" N GLN D 39 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 169 through 176 removed outlier: 3.674A pdb=" N LYS D 171 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 21 through 24 removed outlier: 4.208A pdb=" N LYS E 2 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 6 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 90 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 85 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU E 127 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU E 87 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL E 129 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU E 89 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 91 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.633A pdb=" N GLN E 39 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 176 removed outlier: 3.676A pdb=" N LYS E 171 " --> pdb=" O VAL E 163 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1275 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: 1.79 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3665 1.34 - 1.46: 2469 1.46 - 1.58: 5531 1.58 - 1.69: 15 1.69 - 1.81: 70 Bond restraints: 11750 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 ... (remaining 11745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 15318 1.34 - 2.69: 383 2.69 - 4.03: 84 4.03 - 5.37: 35 5.37 - 6.72: 20 Bond angle restraints: 15840 Sorted by residual: angle pdb=" CA MET A 277 " pdb=" CB MET A 277 " pdb=" CG MET A 277 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.91e+00 angle pdb=" CA MET B 277 " pdb=" CB MET B 277 " pdb=" CG MET B 277 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" CA MET D 277 " pdb=" CB MET D 277 " pdb=" CG MET D 277 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" CA MET C 277 " pdb=" CB MET C 277 " pdb=" CG MET C 277 " ideal model delta sigma weight residual 114.10 119.32 -5.22 2.00e+00 2.50e-01 6.80e+00 angle pdb=" CA MET E 277 " pdb=" CB MET E 277 " pdb=" CG MET E 277 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 ... (remaining 15835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 6969 31.05 - 62.11: 156 62.11 - 93.16: 15 93.16 - 124.22: 5 124.22 - 155.27: 10 Dihedral angle restraints: 7155 sinusoidal: 2985 harmonic: 4170 Sorted by residual: dihedral pdb=" C5' ADP B 300 " pdb=" O5' ADP B 300 " pdb=" PA ADP B 300 " pdb=" O2A ADP B 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.27 -155.27 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP E 300 " pdb=" O5' ADP E 300 " pdb=" PA ADP E 300 " pdb=" O2A ADP E 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.27 -155.27 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' ADP C 300 " pdb=" O5' ADP C 300 " pdb=" PA ADP C 300 " pdb=" O2A ADP C 300 " ideal model delta sinusoidal sigma weight residual -60.00 95.26 -155.26 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 7152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1220 0.032 - 0.064: 374 0.064 - 0.097: 94 0.097 - 0.129: 88 0.129 - 0.161: 19 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CB VAL A 5 " pdb=" CA VAL A 5 " pdb=" CG1 VAL A 5 " pdb=" CG2 VAL A 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB VAL B 5 " pdb=" CA VAL B 5 " pdb=" CG1 VAL B 5 " pdb=" CG2 VAL B 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CB VAL C 5 " pdb=" CA VAL C 5 " pdb=" CG1 VAL C 5 " pdb=" CG2 VAL C 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1792 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 253 " -0.014 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR B 253 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 253 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 253 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 253 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 253 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 253 " 0.014 2.00e-02 2.50e+03 1.46e-02 4.29e+00 pdb=" CG TYR C 253 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 253 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 253 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 253 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 253 " -0.014 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR D 253 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 253 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 253 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 253 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 253 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 253 " -0.002 2.00e-02 2.50e+03 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 392 2.68 - 3.23: 12299 3.23 - 3.79: 16773 3.79 - 4.34: 24302 4.34 - 4.90: 40041 Nonbonded interactions: 93807 Sorted by model distance: nonbonded pdb=" O3B ADP E 300 " pdb="MG MG E 301 " model vdw 2.121 2.170 nonbonded pdb=" O3B ADP A 300 " pdb="MG MG A 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP C 300 " pdb="MG MG C 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP B 300 " pdb="MG MG B 301 " model vdw 2.122 2.170 nonbonded pdb=" O3B ADP D 300 " pdb="MG MG D 301 " model vdw 2.122 2.170 ... (remaining 93802 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.170 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 0.032 11750 Z= 0.127 Angle : 0.611 6.718 15840 Z= 0.309 Chirality : 0.042 0.161 1795 Planarity : 0.003 0.045 1980 Dihedral : 15.234 155.270 4485 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.39 % Allowed : 0.47 % Favored : 99.14 % 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 (0.22), residues: 1415 helix: -0.21 (0.26), residues: 365 sheet: -1.53 (0.29), residues: 295 loop : -1.31 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.035 0.002 TYR B 253 PHE 0.004 0.001 PHE D 59 TRP 0.003 0.001 TRP A 284 HIS 0.001 0.000 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00260 (11750) covalent geometry : angle 0.61089 (15840) hydrogen bonds : bond 0.14727 ( 450) hydrogen bonds : angle 6.48532 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 322 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7865 (mmm) cc_final: 0.7648 (mmp) REVERT: A 148 ASP cc_start: 0.7242 (p0) cc_final: 0.6901 (p0) REVERT: A 202 ILE cc_start: 0.7642 (tt) cc_final: 0.7122 (mt) REVERT: A 251 LYS cc_start: 0.7934 (ptmm) cc_final: 0.7545 (ttpp) REVERT: A 274 ASP cc_start: 0.8739 (m-30) cc_final: 0.8405 (m-30) REVERT: B 14 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8117 (mtmm) REVERT: B 39 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 196 ASP cc_start: 0.7318 (p0) cc_final: 0.7001 (p0) REVERT: C 2 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7813 (mmtt) REVERT: C 39 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7960 (mm-40) REVERT: C 255 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8302 (mm-30) REVERT: D 14 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8614 (mtmm) REVERT: D 39 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7962 (mm-40) REVERT: E 39 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8162 (mm-40) REVERT: E 196 ASP cc_start: 0.7604 (p0) cc_final: 0.7382 (p0) REVERT: E 202 ILE cc_start: 0.8570 (tt) cc_final: 0.8242 (mt) REVERT: E 270 THR cc_start: 0.8318 (p) cc_final: 0.7932 (m) outliers start: 5 outliers final: 2 residues processed: 322 average time/residue: 0.1187 time to fit residues: 53.2056 Evaluate side-chains 184 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain B residue 277 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 60 ASN A 69 GLN D 267 ASN E 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110119 restraints weight = 23223.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113585 restraints weight = 13057.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116036 restraints weight = 8620.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117602 restraints weight = 6367.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118659 restraints weight = 5151.847| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11750 Z= 0.154 Angle : 0.658 6.486 15840 Z= 0.334 Chirality : 0.048 0.207 1795 Planarity : 0.003 0.039 1980 Dihedral : 13.418 163.407 1601 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.04 % Allowed : 9.49 % Favored : 88.47 % 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: -1.09 (0.23), residues: 1415 helix: 0.40 (0.26), residues: 405 sheet: -0.94 (0.28), residues: 395 loop : -1.22 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.012 0.002 TYR A 15 PHE 0.017 0.001 PHE A 59 TRP 0.003 0.001 TRP C 284 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00347 (11750) covalent geometry : angle 0.65772 (15840) hydrogen bonds : bond 0.03357 ( 450) hydrogen bonds : angle 5.39548 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8289 (tp) cc_final: 0.8027 (tp) REVERT: A 65 ASP cc_start: 0.7728 (t0) cc_final: 0.7407 (t0) REVERT: A 202 ILE cc_start: 0.8170 (tt) cc_final: 0.7704 (mt) REVERT: A 220 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 224 ASP cc_start: 0.7127 (t70) cc_final: 0.6606 (m-30) REVERT: B 14 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8361 (mtmm) REVERT: B 65 ASP cc_start: 0.6704 (t0) cc_final: 0.6496 (t0) REVERT: D 14 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8845 (mtmm) REVERT: D 64 ARG cc_start: 0.7436 (ptt90) cc_final: 0.7132 (ptt-90) REVERT: D 191 ASN cc_start: 0.8452 (t0) cc_final: 0.8145 (t0) outliers start: 26 outliers final: 16 residues processed: 252 average time/residue: 0.0978 time to fit residues: 36.5264 Evaluate side-chains 185 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 267 ASN B 267 ASN D 285 ASN E 60 ASN E 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103386 restraints weight = 24074.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106785 restraints weight = 13937.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109108 restraints weight = 9448.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110660 restraints weight = 7096.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111659 restraints weight = 5802.844| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11750 Z= 0.182 Angle : 0.683 8.362 15840 Z= 0.345 Chirality : 0.047 0.175 1795 Planarity : 0.004 0.053 1980 Dihedral : 13.320 177.918 1595 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.51 % Allowed : 13.41 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1415 helix: 0.65 (0.25), residues: 410 sheet: -0.90 (0.27), residues: 405 loop : -1.27 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 40 TYR 0.019 0.002 TYR A 72 PHE 0.014 0.001 PHE B 59 TRP 0.004 0.001 TRP E 284 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00417 (11750) covalent geometry : angle 0.68265 (15840) hydrogen bonds : bond 0.03302 ( 450) hydrogen bonds : angle 5.20818 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8549 (tp) cc_final: 0.7694 (tp) REVERT: A 66 TYR cc_start: 0.7569 (p90) cc_final: 0.7349 (p90) REVERT: A 110 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 111 PHE cc_start: 0.7664 (m-10) cc_final: 0.6261 (m-10) REVERT: A 169 ILE cc_start: 0.8950 (mp) cc_final: 0.8675 (tt) REVERT: A 202 ILE cc_start: 0.8499 (tt) cc_final: 0.8275 (mt) REVERT: A 207 ASP cc_start: 0.7958 (m-30) cc_final: 0.7453 (t70) REVERT: A 220 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 224 ASP cc_start: 0.7190 (t70) cc_final: 0.6657 (m-30) REVERT: B 14 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8756 (mtmm) REVERT: C 2 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8029 (mmtt) REVERT: C 14 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8795 (mtmm) REVERT: D 14 LYS cc_start: 0.9296 (mtmm) cc_final: 0.9007 (mtmm) REVERT: D 96 MET cc_start: 0.8557 (mmm) cc_final: 0.8314 (tpp) REVERT: D 277 MET cc_start: 0.8065 (tpp) cc_final: 0.7767 (tpp) REVERT: E 96 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5225 (mmp) REVERT: E 248 LEU cc_start: 0.8551 (mm) cc_final: 0.8331 (tt) outliers start: 32 outliers final: 21 residues processed: 241 average time/residue: 0.1004 time to fit residues: 35.6677 Evaluate side-chains 196 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 0.0020 chunk 35 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 111 optimal weight: 0.7980 overall best weight: 0.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 86 ASN A 110 ASN B 69 GLN C 60 ASN C 86 ASN C 267 ASN E 272 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107700 restraints weight = 23446.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111195 restraints weight = 13380.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113595 restraints weight = 8911.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115183 restraints weight = 6633.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116302 restraints weight = 5376.632| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.122 Angle : 0.635 6.250 15840 Z= 0.321 Chirality : 0.045 0.157 1795 Planarity : 0.003 0.035 1980 Dihedral : 13.038 177.224 1595 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.27 % Allowed : 16.86 % Favored : 80.86 % 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: -0.71 (0.24), residues: 1415 helix: 1.02 (0.26), residues: 410 sheet: -0.78 (0.29), residues: 365 loop : -1.22 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 64 TYR 0.018 0.001 TYR A 134 PHE 0.008 0.001 PHE A 23 TRP 0.004 0.001 TRP C 284 HIS 0.004 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00260 (11750) covalent geometry : angle 0.63530 (15840) hydrogen bonds : bond 0.02819 ( 450) hydrogen bonds : angle 4.96664 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.6764 (ptt90) cc_final: 0.6546 (ptt90) REVERT: A 220 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 224 ASP cc_start: 0.7101 (t70) cc_final: 0.6612 (m-30) REVERT: A 232 TYR cc_start: 0.8444 (m-10) cc_final: 0.8113 (m-80) REVERT: A 277 MET cc_start: 0.8046 (tpp) cc_final: 0.7356 (tpp) REVERT: B 196 ASP cc_start: 0.7659 (p0) cc_final: 0.7454 (p0) REVERT: C 14 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8812 (mtmm) REVERT: C 78 ASN cc_start: 0.8016 (p0) cc_final: 0.7728 (p0) REVERT: D 14 LYS cc_start: 0.9293 (mtmm) cc_final: 0.9048 (mtmm) REVERT: D 132 GLU cc_start: 0.8185 (tp30) cc_final: 0.7889 (tp30) REVERT: D 191 ASN cc_start: 0.8672 (t0) cc_final: 0.8379 (t0) REVERT: D 241 ILE cc_start: 0.9115 (mm) cc_final: 0.8880 (mm) REVERT: E 40 ARG cc_start: 0.8502 (ptt-90) cc_final: 0.8087 (ptt-90) REVERT: E 248 LEU cc_start: 0.8454 (mm) cc_final: 0.8226 (tt) outliers start: 29 outliers final: 20 residues processed: 235 average time/residue: 0.1056 time to fit residues: 36.4328 Evaluate side-chains 201 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 122 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 10 ASN C 265 HIS D 60 ASN D 265 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.131272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107891 restraints weight = 23685.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111250 restraints weight = 13457.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113553 restraints weight = 8969.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115098 restraints weight = 6673.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116161 restraints weight = 5421.663| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11750 Z= 0.127 Angle : 0.642 6.436 15840 Z= 0.321 Chirality : 0.045 0.158 1795 Planarity : 0.003 0.027 1980 Dihedral : 12.711 171.843 1595 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.75 % Allowed : 18.98 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1415 helix: 1.21 (0.27), residues: 410 sheet: -0.68 (0.29), residues: 365 loop : -1.17 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.024 0.001 TYR A 72 PHE 0.019 0.001 PHE A 262 TRP 0.002 0.001 TRP A 284 HIS 0.002 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00284 (11750) covalent geometry : angle 0.64236 (15840) hydrogen bonds : bond 0.02730 ( 450) hydrogen bonds : angle 4.89026 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.8490 (m-10) cc_final: 0.8200 (m-10) REVERT: A 277 MET cc_start: 0.8108 (tpp) cc_final: 0.7902 (tpp) REVERT: C 241 ILE cc_start: 0.9238 (mm) cc_final: 0.8972 (mm) REVERT: D 14 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9086 (mtmm) REVERT: D 191 ASN cc_start: 0.8748 (t0) cc_final: 0.8460 (t0) REVERT: D 241 ILE cc_start: 0.9135 (mm) cc_final: 0.8900 (mm) REVERT: E 40 ARG cc_start: 0.8532 (ptt-90) cc_final: 0.8110 (ptt-90) REVERT: E 248 LEU cc_start: 0.8455 (mm) cc_final: 0.8215 (tt) outliers start: 35 outliers final: 26 residues processed: 230 average time/residue: 0.1015 time to fit residues: 34.5712 Evaluate side-chains 199 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN D 265 HIS D 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099840 restraints weight = 24413.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103114 restraints weight = 14198.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105398 restraints weight = 9668.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106935 restraints weight = 7359.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107968 restraints weight = 6046.925| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11750 Z= 0.185 Angle : 0.691 6.746 15840 Z= 0.346 Chirality : 0.046 0.164 1795 Planarity : 0.003 0.030 1980 Dihedral : 12.371 177.679 1595 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.82 % Allowed : 20.08 % Favored : 77.10 % 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: -0.64 (0.23), residues: 1415 helix: 0.95 (0.26), residues: 420 sheet: -0.75 (0.29), residues: 365 loop : -1.11 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 64 TYR 0.013 0.001 TYR A 134 PHE 0.014 0.001 PHE C 59 TRP 0.004 0.001 TRP D 284 HIS 0.006 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00434 (11750) covalent geometry : angle 0.69074 (15840) hydrogen bonds : bond 0.03085 ( 450) hydrogen bonds : angle 5.16974 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9353 (mm) cc_final: 0.9120 (mt) REVERT: A 277 MET cc_start: 0.8200 (tpp) cc_final: 0.7999 (tpp) REVERT: D 14 LYS cc_start: 0.9369 (mtmm) cc_final: 0.9143 (mtmm) REVERT: D 241 ILE cc_start: 0.9204 (mm) cc_final: 0.8985 (mm) REVERT: E 248 LEU cc_start: 0.8665 (mm) cc_final: 0.8359 (tt) outliers start: 36 outliers final: 29 residues processed: 197 average time/residue: 0.0920 time to fit residues: 27.5692 Evaluate side-chains 191 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 22 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 10 ASN E 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103209 restraints weight = 24632.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106447 restraints weight = 13926.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108710 restraints weight = 9306.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110210 restraints weight = 6969.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111236 restraints weight = 5695.724| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11750 Z= 0.131 Angle : 0.654 9.646 15840 Z= 0.322 Chirality : 0.045 0.166 1795 Planarity : 0.003 0.034 1980 Dihedral : 11.925 168.547 1595 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.59 % Allowed : 20.94 % Favored : 76.47 % 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: -0.42 (0.24), residues: 1415 helix: 1.08 (0.27), residues: 420 sheet: -0.55 (0.27), residues: 395 loop : -0.99 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.011 0.001 TYR A 134 PHE 0.020 0.001 PHE A 262 TRP 0.004 0.001 TRP A 284 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00298 (11750) covalent geometry : angle 0.65426 (15840) hydrogen bonds : bond 0.02702 ( 450) hydrogen bonds : angle 4.95652 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.7962 (m-30) cc_final: 0.7386 (t0) REVERT: A 232 TYR cc_start: 0.8265 (m-10) cc_final: 0.7903 (m-80) REVERT: A 241 ILE cc_start: 0.9360 (mm) cc_final: 0.9153 (mt) REVERT: A 277 MET cc_start: 0.8213 (tpp) cc_final: 0.7983 (tpp) REVERT: B 95 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: D 241 ILE cc_start: 0.9189 (mm) cc_final: 0.8979 (mm) REVERT: E 96 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5907 (mmp) REVERT: E 248 LEU cc_start: 0.8581 (mm) cc_final: 0.8268 (tt) outliers start: 33 outliers final: 24 residues processed: 213 average time/residue: 0.0868 time to fit residues: 28.6121 Evaluate side-chains 192 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN C 10 ASN D 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100013 restraints weight = 24572.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103286 restraints weight = 14207.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105525 restraints weight = 9558.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107058 restraints weight = 7186.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108085 restraints weight = 5884.526| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11750 Z= 0.184 Angle : 0.708 8.207 15840 Z= 0.351 Chirality : 0.046 0.182 1795 Planarity : 0.003 0.036 1980 Dihedral : 11.725 148.890 1595 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.14 % Allowed : 21.73 % Favored : 75.14 % 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: -0.52 (0.23), residues: 1415 helix: 0.93 (0.26), residues: 420 sheet: -0.71 (0.27), residues: 385 loop : -0.90 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 57 TYR 0.012 0.001 TYR A 134 PHE 0.013 0.001 PHE B 59 TRP 0.003 0.001 TRP C 284 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00436 (11750) covalent geometry : angle 0.70775 (15840) hydrogen bonds : bond 0.03118 ( 450) hydrogen bonds : angle 5.18945 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: C 169 ILE cc_start: 0.8571 (mt) cc_final: 0.8246 (tt) REVERT: E 64 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7492 (ptt-90) REVERT: E 96 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5908 (mmp) REVERT: E 248 LEU cc_start: 0.8694 (mm) cc_final: 0.8441 (tt) outliers start: 40 outliers final: 30 residues processed: 205 average time/residue: 0.0877 time to fit residues: 27.9399 Evaluate side-chains 194 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099599 restraints weight = 24485.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102824 restraints weight = 14290.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105044 restraints weight = 9751.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106565 restraints weight = 7416.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107594 restraints weight = 6129.543| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11750 Z= 0.161 Angle : 0.713 9.586 15840 Z= 0.349 Chirality : 0.046 0.200 1795 Planarity : 0.003 0.040 1980 Dihedral : 11.399 144.439 1595 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.14 % Allowed : 22.43 % Favored : 74.43 % 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: -0.56 (0.23), residues: 1415 helix: 0.92 (0.27), residues: 420 sheet: -0.66 (0.27), residues: 395 loop : -1.00 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 57 TYR 0.016 0.001 TYR A 134 PHE 0.021 0.001 PHE A 262 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00379 (11750) covalent geometry : angle 0.71330 (15840) hydrogen bonds : bond 0.03036 ( 450) hydrogen bonds : angle 5.16648 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8756 (tp) cc_final: 0.8533 (mp) REVERT: A 232 TYR cc_start: 0.8344 (m-10) cc_final: 0.8016 (m-80) REVERT: B 95 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: C 169 ILE cc_start: 0.8552 (mt) cc_final: 0.8256 (tt) REVERT: D 96 MET cc_start: 0.8541 (tpp) cc_final: 0.8134 (mmt) REVERT: E 64 ARG cc_start: 0.7710 (ptt-90) cc_final: 0.7437 (ptt-90) REVERT: E 248 LEU cc_start: 0.8788 (mm) cc_final: 0.8440 (tt) outliers start: 40 outliers final: 31 residues processed: 194 average time/residue: 0.0837 time to fit residues: 25.6255 Evaluate side-chains 193 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN C 10 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098962 restraints weight = 24673.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102050 restraints weight = 14567.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104328 restraints weight = 9981.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105868 restraints weight = 7609.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106961 restraints weight = 6288.335| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11750 Z= 0.163 Angle : 0.715 9.211 15840 Z= 0.351 Chirality : 0.046 0.181 1795 Planarity : 0.003 0.040 1980 Dihedral : 11.137 141.435 1595 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.98 % Allowed : 22.51 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.23), residues: 1415 helix: 0.90 (0.26), residues: 420 sheet: -0.68 (0.27), residues: 395 loop : -0.99 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.016 0.001 TYR A 134 PHE 0.010 0.001 PHE A 59 TRP 0.006 0.001 TRP A 284 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00385 (11750) covalent geometry : angle 0.71483 (15840) hydrogen bonds : bond 0.03059 ( 450) hydrogen bonds : angle 5.19333 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2830 Ramachandran restraints generated. 1415 Oldfield, 0 Emsley, 1415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8737 (tp) cc_final: 0.8509 (mp) REVERT: B 64 ARG cc_start: 0.6910 (ptt90) cc_final: 0.6437 (ptt180) REVERT: B 95 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: C 95 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: C 169 ILE cc_start: 0.8564 (mt) cc_final: 0.8264 (tt) REVERT: D 96 MET cc_start: 0.8571 (tpp) cc_final: 0.8167 (mmt) REVERT: E 64 ARG cc_start: 0.7697 (ptt-90) cc_final: 0.7431 (ptt-90) REVERT: E 248 LEU cc_start: 0.8809 (mm) cc_final: 0.8447 (tt) outliers start: 38 outliers final: 30 residues processed: 194 average time/residue: 0.0870 time to fit residues: 26.2131 Evaluate side-chains 186 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 191 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 36 optimal weight: 0.0170 chunk 119 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN C 10 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102140 restraints weight = 24377.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105387 restraints weight = 13988.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107650 restraints weight = 9456.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109165 restraints weight = 7151.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110174 restraints weight = 5879.163| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11750 Z= 0.133 Angle : 0.694 8.886 15840 Z= 0.339 Chirality : 0.046 0.178 1795 Planarity : 0.003 0.039 1980 Dihedral : 10.638 139.514 1595 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.43 % Allowed : 23.37 % Favored : 74.20 % 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: -0.49 (0.24), residues: 1415 helix: 1.00 (0.27), residues: 420 sheet: -0.64 (0.27), residues: 405 loop : -0.97 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.015 0.001 TYR A 15 PHE 0.021 0.001 PHE A 262 TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00311 (11750) covalent geometry : angle 0.69375 (15840) hydrogen bonds : bond 0.02874 ( 450) hydrogen bonds : angle 5.07873 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.22 seconds wall clock time: 35 minutes 32.26 seconds (2132.26 seconds total)