Starting phenix.real_space_refine on Tue Jul 29 23:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_33007.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_33007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_33007.map" model { file = "/net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_33007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x54_33007/07_2025/7x54_33007.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.74, per 1000 atoms: 0.84 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: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.29 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: 3.11 Time building geometry restraints manager: 4.30 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 33.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.410 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP A 284 HIS 0.001 0.000 HIS A 265 PHE 0.004 0.001 PHE D 59 TYR 0.035 0.002 TYR B 253 ARG 0.002 0.000 ARG B 204 Details of bonding type rmsd hydrogen bonds : bond 0.14727 ( 450) hydrogen bonds : angle 6.48532 ( 1275) covalent geometry : bond 0.00260 (11750) covalent geometry : angle 0.61089 (15840) *********************** 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 : 1.296 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: 0.7121 (mt) REVERT: A 251 LYS cc_start: 0.7934 (ptmm) cc_final: 0.7545 (ttpp) REVERT: A 274 ASP cc_start: 0.8738 (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: 0.2913 time to fit residues: 129.1008 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 : 2.159 ------------------------------------------------------------------------------- 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 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN E 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100895 restraints weight = 23851.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103944 restraints weight = 14033.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106310 restraints weight = 9646.251| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11750 Z= 0.265 Angle : 0.774 6.679 15840 Z= 0.394 Chirality : 0.051 0.186 1795 Planarity : 0.004 0.050 1980 Dihedral : 13.676 169.956 1601 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.27 % Allowed : 10.51 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1415 helix: -0.11 (0.24), residues: 410 sheet: -0.88 (0.29), residues: 370 loop : -1.32 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 284 HIS 0.005 0.002 HIS C 265 PHE 0.028 0.002 PHE D 59 TYR 0.017 0.002 TYR D 253 ARG 0.008 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 450) hydrogen bonds : angle 5.85299 ( 1275) covalent geometry : bond 0.00608 (11750) covalent geometry : angle 0.77380 (15840) *********************** 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 244 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8602 (tp) cc_final: 0.8279 (tp) REVERT: A 65 ASP cc_start: 0.7973 (t0) cc_final: 0.7668 (t0) REVERT: A 169 ILE cc_start: 0.9070 (mp) cc_final: 0.8719 (tt) REVERT: A 202 ILE cc_start: 0.8387 (tt) cc_final: 0.7880 (mt) REVERT: A 220 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 224 ASP cc_start: 0.7352 (t70) cc_final: 0.6724 (m-30) REVERT: B 14 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8728 (mtmm) REVERT: B 64 ARG cc_start: 0.7492 (ptt90) cc_final: 0.7276 (ptt-90) REVERT: C 132 GLU cc_start: 0.7880 (tp30) cc_final: 0.7670 (tp30) REVERT: C 225 ILE cc_start: 0.9041 (pt) cc_final: 0.8819 (mt) REVERT: D 14 LYS cc_start: 0.9328 (mtmm) cc_final: 0.9050 (mtmm) REVERT: D 61 LYS cc_start: 0.8105 (pttt) cc_final: 0.7748 (pttp) REVERT: D 64 ARG cc_start: 0.7834 (ptt90) cc_final: 0.7633 (ptt-90) REVERT: D 96 MET cc_start: 0.8714 (mmm) cc_final: 0.8342 (tpp) REVERT: E 61 LYS cc_start: 0.7762 (pttt) cc_final: 0.7488 (ptpp) REVERT: E 96 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5773 (mmt) REVERT: E 202 ILE cc_start: 0.8753 (tt) cc_final: 0.8511 (mt) outliers start: 29 outliers final: 22 residues processed: 235 average time/residue: 0.2809 time to fit residues: 96.0030 Evaluate side-chains 184 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 5 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 5 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 234 ASN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 128 optimal weight: 50.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 69 GLN B 69 GLN D 69 GLN D 267 ASN E 60 ASN E 272 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104016 restraints weight = 23813.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107512 restraints weight = 13634.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109894 restraints weight = 9191.018| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11750 Z= 0.134 Angle : 0.646 9.099 15840 Z= 0.322 Chirality : 0.045 0.168 1795 Planarity : 0.004 0.044 1980 Dihedral : 12.750 175.340 1595 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.98 % Allowed : 14.12 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1415 helix: 0.69 (0.26), residues: 410 sheet: -0.75 (0.28), residues: 395 loop : -1.24 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 284 HIS 0.001 0.000 HIS D 265 PHE 0.008 0.001 PHE A 111 TYR 0.020 0.001 TYR A 72 ARG 0.004 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 450) hydrogen bonds : angle 5.12759 ( 1275) covalent geometry : bond 0.00301 (11750) covalent geometry : angle 0.64580 (15840) *********************** 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 268 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.330 Fit side-chains REVERT: A 65 ASP cc_start: 0.7846 (t0) cc_final: 0.7643 (t0) REVERT: A 169 ILE cc_start: 0.8961 (mp) cc_final: 0.8664 (tt) REVERT: A 220 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 224 ASP cc_start: 0.7295 (t70) cc_final: 0.6756 (m-30) REVERT: A 225 ILE cc_start: 0.9117 (pt) cc_final: 0.8778 (mt) REVERT: A 277 MET cc_start: 0.8026 (tmm) cc_final: 0.7688 (tpp) REVERT: B 14 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8827 (mtmm) REVERT: B 64 ARG cc_start: 0.7342 (ptt90) cc_final: 0.7120 (ptt-90) REVERT: C 2 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8135 (mmtt) REVERT: D 14 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9121 (mtmm) REVERT: D 96 MET cc_start: 0.8643 (mmm) cc_final: 0.8366 (tpp) REVERT: D 241 ILE cc_start: 0.9200 (mm) cc_final: 0.8965 (mm) REVERT: D 277 MET cc_start: 0.8081 (tpp) cc_final: 0.7776 (tpp) REVERT: E 201 ASP cc_start: 0.8089 (p0) cc_final: 0.7861 (p0) REVERT: E 202 ILE cc_start: 0.8670 (tt) cc_final: 0.8374 (mt) REVERT: E 248 LEU cc_start: 0.8543 (mm) cc_final: 0.8308 (tt) outliers start: 38 outliers final: 28 residues processed: 256 average time/residue: 0.2721 time to fit residues: 101.4420 Evaluate side-chains 206 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 156 SER 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 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 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 248 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 6 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 124 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN E 60 ASN E 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096597 restraints weight = 24377.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099846 restraints weight = 14446.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102050 restraints weight = 10004.016| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11750 Z= 0.267 Angle : 0.767 6.734 15840 Z= 0.386 Chirality : 0.048 0.157 1795 Planarity : 0.004 0.068 1980 Dihedral : 11.753 143.684 1595 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.92 % Allowed : 17.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1415 helix: 0.59 (0.25), residues: 410 sheet: -0.98 (0.27), residues: 405 loop : -1.25 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 284 HIS 0.003 0.001 HIS C 265 PHE 0.025 0.002 PHE D 59 TYR 0.019 0.002 TYR A 134 ARG 0.006 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 450) hydrogen bonds : angle 5.60064 ( 1275) covalent geometry : bond 0.00622 (11750) covalent geometry : angle 0.76711 (15840) *********************** 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 225 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8807 (tp) cc_final: 0.8607 (tp) REVERT: A 65 ASP cc_start: 0.7901 (t0) cc_final: 0.7622 (t0) REVERT: A 207 ASP cc_start: 0.8021 (m-30) cc_final: 0.7500 (t0) REVERT: A 224 ASP cc_start: 0.7564 (t70) cc_final: 0.6941 (m-30) REVERT: A 225 ILE cc_start: 0.9217 (pt) cc_final: 0.8912 (mt) REVERT: A 232 TYR cc_start: 0.8730 (m-80) cc_final: 0.8519 (m-80) REVERT: B 14 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8909 (mtmm) REVERT: B 64 ARG cc_start: 0.7582 (ptt90) cc_final: 0.7350 (ptt-90) REVERT: B 277 MET cc_start: 0.8207 (tpp) cc_final: 0.7754 (tpp) REVERT: C 2 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8134 (mmtt) REVERT: C 78 ASN cc_start: 0.8163 (p0) cc_final: 0.7937 (p0) REVERT: E 202 ILE cc_start: 0.8882 (tt) cc_final: 0.8566 (mt) REVERT: E 248 LEU cc_start: 0.8756 (mm) cc_final: 0.8427 (tt) outliers start: 50 outliers final: 34 residues processed: 212 average time/residue: 0.2459 time to fit residues: 77.6958 Evaluate side-chains 192 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE 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 140 LEU 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 124 ILE Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 163 VAL 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 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 248 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 6 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 158 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN C 86 ASN C 267 ASN E 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102766 restraints weight = 23600.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106158 restraints weight = 13627.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108449 restraints weight = 9210.373| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11750 Z= 0.122 Angle : 0.643 7.429 15840 Z= 0.321 Chirality : 0.045 0.167 1795 Planarity : 0.003 0.039 1980 Dihedral : 11.314 143.496 1595 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.59 % Allowed : 19.92 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1415 helix: 1.02 (0.26), residues: 410 sheet: -0.78 (0.27), residues: 405 loop : -1.13 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 284 HIS 0.002 0.001 HIS D 265 PHE 0.010 0.001 PHE A 23 TYR 0.012 0.001 TYR A 15 ARG 0.004 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 450) hydrogen bonds : angle 5.01936 ( 1275) covalent geometry : bond 0.00268 (11750) covalent geometry : angle 0.64252 (15840) *********************** 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 241 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8756 (tp) cc_final: 0.8150 (tp) REVERT: A 169 ILE cc_start: 0.8806 (mp) cc_final: 0.8450 (tt) REVERT: A 173 ASN cc_start: 0.8289 (t0) cc_final: 0.8009 (t0) REVERT: A 224 ASP cc_start: 0.7400 (t70) cc_final: 0.6809 (m-30) REVERT: A 225 ILE cc_start: 0.9121 (pt) cc_final: 0.8841 (mt) REVERT: A 232 TYR cc_start: 0.8548 (m-80) cc_final: 0.8177 (m-80) REVERT: B 277 MET cc_start: 0.8059 (tpp) cc_final: 0.7719 (tpp) REVERT: C 78 ASN cc_start: 0.8107 (p0) cc_final: 0.7866 (p0) REVERT: C 96 MET cc_start: 0.8745 (tpp) cc_final: 0.8513 (tpp) REVERT: D 241 ILE cc_start: 0.9214 (mm) cc_final: 0.8989 (mm) REVERT: E 202 ILE cc_start: 0.8748 (tt) cc_final: 0.8441 (mt) REVERT: E 248 LEU cc_start: 0.8663 (mm) cc_final: 0.8353 (tt) outliers start: 33 outliers final: 24 residues processed: 233 average time/residue: 0.2389 time to fit residues: 82.3406 Evaluate side-chains 201 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 B residue 5 VAL 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 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 248 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 40.0000 chunk 5 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 86 ASN B 267 ASN C 69 GLN C 144 ASN E 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098680 restraints weight = 24966.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101803 restraints weight = 14338.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104013 restraints weight = 9729.957| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11750 Z= 0.182 Angle : 0.688 8.562 15840 Z= 0.343 Chirality : 0.046 0.187 1795 Planarity : 0.004 0.039 1980 Dihedral : 11.187 143.457 1595 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.22 % Allowed : 20.08 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1415 helix: 0.96 (0.26), residues: 400 sheet: -0.80 (0.27), residues: 405 loop : -1.13 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 284 HIS 0.002 0.001 HIS D 265 PHE 0.014 0.002 PHE D 59 TYR 0.023 0.001 TYR A 72 ARG 0.009 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 450) hydrogen bonds : angle 5.19332 ( 1275) covalent geometry : bond 0.00426 (11750) covalent geometry : angle 0.68792 (15840) *********************** 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 218 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.8871 (mp) cc_final: 0.8523 (tt) REVERT: A 207 ASP cc_start: 0.8084 (m-30) cc_final: 0.7488 (t70) REVERT: A 224 ASP cc_start: 0.7499 (t70) cc_final: 0.6926 (m-30) REVERT: B 95 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: B 277 MET cc_start: 0.8110 (tpp) cc_final: 0.7817 (tpp) REVERT: C 95 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: D 95 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: D 169 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8138 (mt) REVERT: E 202 ILE cc_start: 0.8797 (tt) cc_final: 0.8497 (mt) REVERT: E 248 LEU cc_start: 0.8758 (mm) cc_final: 0.8441 (tt) outliers start: 41 outliers final: 30 residues processed: 210 average time/residue: 0.2088 time to fit residues: 65.9490 Evaluate side-chains 198 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 140 LEU 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 163 VAL 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 95 GLN Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 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 95 GLN 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 169 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 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 119 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN D 60 ASN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102120 restraints weight = 24698.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105348 restraints weight = 14108.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107576 restraints weight = 9461.290| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11750 Z= 0.126 Angle : 0.658 9.303 15840 Z= 0.324 Chirality : 0.045 0.177 1795 Planarity : 0.003 0.035 1980 Dihedral : 10.868 141.224 1595 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.14 % Allowed : 21.02 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1415 helix: 1.06 (0.27), residues: 405 sheet: -0.63 (0.28), residues: 395 loop : -1.13 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.001 HIS D 265 PHE 0.023 0.001 PHE D 59 TYR 0.017 0.001 TYR A 137 ARG 0.010 0.001 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 450) hydrogen bonds : angle 4.93120 ( 1275) covalent geometry : bond 0.00280 (11750) covalent geometry : angle 0.65769 (15840) *********************** 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 232 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 169 ILE cc_start: 0.8771 (mp) cc_final: 0.8491 (tt) REVERT: A 224 ASP cc_start: 0.7423 (t70) cc_final: 0.6879 (m-30) REVERT: A 241 ILE cc_start: 0.9324 (mm) cc_final: 0.9099 (mm) REVERT: B 14 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8882 (mtmm) REVERT: B 66 TYR cc_start: 0.6940 (p90) cc_final: 0.6502 (p90) REVERT: B 95 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: B 277 MET cc_start: 0.7982 (tpp) cc_final: 0.7754 (tpp) REVERT: D 95 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: E 96 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.6081 (mmp) REVERT: E 99 LYS cc_start: 0.8886 (tttt) cc_final: 0.8361 (tmtt) REVERT: E 202 ILE cc_start: 0.8774 (tt) cc_final: 0.8480 (mt) REVERT: E 248 LEU cc_start: 0.8681 (mm) cc_final: 0.8378 (tt) outliers start: 40 outliers final: 28 residues processed: 220 average time/residue: 0.2611 time to fit residues: 86.3423 Evaluate side-chains 207 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 170 VAL 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 240 THR 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 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 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 95 GLN 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 48 THR Chi-restraints excluded: chain E residue 60 ASN 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 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100186 restraints weight = 24749.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103414 restraints weight = 14160.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105586 restraints weight = 9529.401| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11750 Z= 0.157 Angle : 0.681 9.664 15840 Z= 0.336 Chirality : 0.046 0.176 1795 Planarity : 0.003 0.035 1980 Dihedral : 10.794 139.614 1595 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.45 % Allowed : 21.65 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1415 helix: 1.01 (0.27), residues: 405 sheet: -0.65 (0.27), residues: 395 loop : -1.09 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 284 HIS 0.003 0.001 HIS C 265 PHE 0.020 0.001 PHE A 262 TYR 0.016 0.001 TYR A 137 ARG 0.006 0.001 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 450) hydrogen bonds : angle 5.03179 ( 1275) covalent geometry : bond 0.00367 (11750) covalent geometry : angle 0.68128 (15840) *********************** 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 225 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ILE cc_start: 0.8790 (mp) cc_final: 0.8520 (tt) REVERT: A 224 ASP cc_start: 0.7394 (t70) cc_final: 0.6866 (m-30) REVERT: B 14 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8938 (mtmm) REVERT: B 95 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 277 MET cc_start: 0.8023 (tpp) cc_final: 0.7800 (tpp) REVERT: C 95 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: D 95 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: D 169 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8188 (mt) REVERT: E 96 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.5872 (mmp) REVERT: E 202 ILE cc_start: 0.8811 (tt) cc_final: 0.8525 (mt) REVERT: E 248 LEU cc_start: 0.8747 (mm) cc_final: 0.8425 (tt) REVERT: E 270 THR cc_start: 0.8203 (m) cc_final: 0.7983 (t) outliers start: 44 outliers final: 29 residues processed: 213 average time/residue: 0.2891 time to fit residues: 94.4322 Evaluate side-chains 204 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 240 THR 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 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 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 95 GLN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 169 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 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 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100170 restraints weight = 24770.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103402 restraints weight = 14189.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105581 restraints weight = 9561.631| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5263 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= 0.154 Angle : 0.698 9.184 15840 Z= 0.344 Chirality : 0.046 0.171 1795 Planarity : 0.003 0.037 1980 Dihedral : 10.655 141.194 1595 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.45 % Allowed : 21.88 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1415 helix: 0.99 (0.27), residues: 405 sheet: -0.64 (0.27), residues: 395 loop : -1.04 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 284 HIS 0.006 0.001 HIS C 265 PHE 0.010 0.001 PHE A 23 TYR 0.017 0.001 TYR A 137 ARG 0.004 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 450) hydrogen bonds : angle 5.02751 ( 1275) covalent geometry : bond 0.00360 (11750) covalent geometry : angle 0.69751 (15840) *********************** 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 228 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 3.737 Fit side-chains revert: symmetry clash REVERT: A 169 ILE cc_start: 0.8809 (mp) cc_final: 0.8510 (tt) REVERT: A 224 ASP cc_start: 0.7374 (t70) cc_final: 0.6854 (m-30) REVERT: B 14 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8914 (mtmm) REVERT: B 95 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: B 277 MET cc_start: 0.8023 (tpp) cc_final: 0.7808 (tpp) REVERT: C 95 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: D 95 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: D 169 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8203 (mt) REVERT: E 96 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6066 (mmp) REVERT: E 99 LYS cc_start: 0.8878 (tttt) cc_final: 0.8342 (tmtt) REVERT: E 202 ILE cc_start: 0.8817 (tt) cc_final: 0.8547 (mt) REVERT: E 248 LEU cc_start: 0.8754 (mm) cc_final: 0.8422 (tt) REVERT: E 270 THR cc_start: 0.8109 (m) cc_final: 0.7896 (t) outliers start: 44 outliers final: 35 residues processed: 214 average time/residue: 0.2522 time to fit residues: 84.6696 Evaluate side-chains 213 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 140 LEU 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 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 240 THR 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 140 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 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 95 GLN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 169 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 60 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 0.1980 chunk 135 optimal weight: 50.0000 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN C 265 HIS ** E 60 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 = 0.3650 r_free = 0.3650 target = 0.125066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100303 restraints weight = 24218.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103538 restraints weight = 13887.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105833 restraints weight = 9418.237| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11750 Z= 0.183 Angle : 0.915 59.200 15840 Z= 0.500 Chirality : 0.047 0.485 1795 Planarity : 0.004 0.076 1980 Dihedral : 10.658 141.140 1595 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.37 % Allowed : 22.27 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1415 helix: 0.98 (0.26), residues: 405 sheet: -0.63 (0.27), residues: 395 loop : -1.05 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 284 HIS 0.005 0.001 HIS C 265 PHE 0.012 0.001 PHE A 262 TYR 0.015 0.001 TYR A 137 ARG 0.004 0.000 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 450) hydrogen bonds : angle 5.01919 ( 1275) covalent geometry : bond 0.00391 (11750) covalent geometry : angle 0.91474 (15840) ********************** 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 217 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 169 ILE cc_start: 0.8784 (mp) cc_final: 0.8507 (tt) REVERT: A 224 ASP cc_start: 0.7342 (t70) cc_final: 0.6903 (m-30) REVERT: B 14 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8916 (mtmm) REVERT: B 95 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: B 277 MET cc_start: 0.8008 (tpp) cc_final: 0.7801 (tpp) REVERT: C 95 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: D 95 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: D 169 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8186 (mt) REVERT: E 99 LYS cc_start: 0.8886 (tttt) cc_final: 0.8345 (tmtt) REVERT: E 202 ILE cc_start: 0.8824 (tt) cc_final: 0.8553 (mt) REVERT: E 248 LEU cc_start: 0.8757 (mm) cc_final: 0.8427 (tt) REVERT: E 270 THR cc_start: 0.8102 (m) cc_final: 0.7884 (t) outliers start: 43 outliers final: 34 residues processed: 203 average time/residue: 0.2120 time to fit residues: 66.9904 Evaluate side-chains 208 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 140 LEU 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 163 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 240 THR 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 140 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 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 95 GLN Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 169 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 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 92 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099945 restraints weight = 24559.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103165 restraints weight = 14153.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105454 restraints weight = 9596.832| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 11750 Z= 0.219 Angle : 0.916 59.196 15840 Z= 0.501 Chirality : 0.047 0.485 1795 Planarity : 0.004 0.080 1980 Dihedral : 10.658 141.140 1595 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.06 % Allowed : 22.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1415 helix: 0.98 (0.26), residues: 405 sheet: -0.63 (0.27), residues: 395 loop : -1.05 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 284 HIS 0.005 0.001 HIS C 265 PHE 0.012 0.001 PHE A 262 TYR 0.015 0.001 TYR A 137 ARG 0.004 0.000 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 450) hydrogen bonds : angle 5.01919 ( 1275) covalent geometry : bond 0.00426 (11750) covalent geometry : angle 0.91554 (15840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4273.85 seconds wall clock time: 82 minutes 50.37 seconds (4970.37 seconds total)