Starting phenix.real_space_refine on Thu Jul 2 15:27:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibn_35344/07_2026/8ibn_35344.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 K 4 8.98 5 P 12 5.49 5 S 44 5.16 5 C 5520 2.51 5 N 1552 2.21 5 O 1808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "B" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "D" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8940 At special positions: 0 Unit cell: (65.1672, 58.9608, 202.742, 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) K 4 19.00 S 44 16.00 P 12 15.00 O 1808 8.00 N 1552 7.00 C 5520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 347.6 milliseconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 44.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 46 through 51 removed outlier: 4.414A pdb=" N LYS A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.525A pdb=" N LYS A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.368A pdb=" N GLY A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.765A pdb=" N ALA A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.549A pdb=" N GLY A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.669A pdb=" N PHE A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.592A pdb=" N LYS A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 3.756A pdb=" N ARG A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.639A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 271 through 283 removed outlier: 3.631A pdb=" N PHE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.723A pdb=" N MET B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.138A pdb=" N GLY B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 removed outlier: 3.562A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.918A pdb=" N ALA B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.928A pdb=" N PHE B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 4.151A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.561A pdb=" N THR B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.897A pdb=" N GLU B 219 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 220 " --> pdb=" O MET B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 220' Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.016A pdb=" N THR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.831A pdb=" N HIS C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 4.169A pdb=" N GLY C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.712A pdb=" N ALA C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.543A pdb=" N GLY C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.971A pdb=" N PHE C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.577A pdb=" N LYS C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 202 removed outlier: 3.500A pdb=" N ALA C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.610A pdb=" N THR C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.863A pdb=" N GLU C 219 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 220' Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 271 through 281 removed outlier: 3.885A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 removed outlier: 3.736A pdb=" N MET D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 73 through 83 removed outlier: 4.219A pdb=" N GLY D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.763A pdb=" N ALA D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.911A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 140 through 155 removed outlier: 3.531A pdb=" N ALA D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.560A pdb=" N LYS D 167 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 202 removed outlier: 4.026A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.541A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.851A pdb=" N GLU D 219 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 220 " --> pdb=" O MET D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 234 through 245 Processing helix chain 'D' and resid 271 through 284 removed outlier: 3.613A pdb=" N VAL D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 removed outlier: 8.036A pdb=" N ILE A 58 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 41 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 13 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 40 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 15 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 42 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 17 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 98 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 130 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 100 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 127 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE A 161 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA A 129 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 230 removed outlier: 6.140A pdb=" N VAL A 260 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 230 removed outlier: 7.775A pdb=" N SER A 297 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 264 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 59 removed outlier: 7.910A pdb=" N ILE B 58 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA B 41 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 13 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE B 40 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 15 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 42 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY B 17 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 130 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 100 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 159 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.540A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.540A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER B 297 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 264 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 59 removed outlier: 8.143A pdb=" N ILE C 58 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 41 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 13 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE C 40 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 15 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 42 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 17 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 98 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 130 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 100 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR C 127 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE C 161 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA C 129 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 225 through 230 removed outlier: 6.222A pdb=" N VAL C 260 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 225 through 230 removed outlier: 7.959A pdb=" N SER C 297 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 264 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 59 removed outlier: 8.090A pdb=" N ILE D 58 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 41 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 13 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE D 40 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 15 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 42 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY D 17 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 98 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 130 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 100 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 159 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLY D 226 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 260 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLY D 226 " --> pdb=" O VAL D 310 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.74 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: 3123 1.34 - 1.46: 1549 1.46 - 1.58: 4236 1.58 - 1.70: 20 1.70 - 1.81: 96 Bond restraints: 9024 Sorted by residual: bond pdb=" O3B G2P B 401 " pdb=" PG G2P B 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O3B G2P C 401 " pdb=" PG G2P C 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" O3B G2P D 401 " pdb=" PG G2P D 401 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3B G2P A 401 " pdb=" PG G2P A 401 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1B G2P A 401 " pdb=" PB G2P A 401 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11882 2.38 - 4.77: 249 4.77 - 7.15: 47 7.15 - 9.54: 37 9.54 - 11.92: 13 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C VAL D 30 " pdb=" N ARG D 31 " pdb=" CA ARG D 31 " ideal model delta sigma weight residual 123.91 131.28 -7.37 1.66e+00 3.63e-01 1.97e+01 angle pdb=" C3A G2P D 401 " pdb=" PA G2P D 401 " pdb=" O5' G2P D 401 " ideal model delta sigma weight residual 99.14 111.06 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C3A G2P C 401 " pdb=" PA G2P C 401 " pdb=" O5' G2P C 401 " ideal model delta sigma weight residual 99.14 110.99 -11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C VAL A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 125.66 132.92 -7.26 1.85e+00 2.92e-01 1.54e+01 angle pdb=" C3A G2P B 401 " pdb=" PA G2P B 401 " pdb=" O5' G2P B 401 " ideal model delta sigma weight residual 99.14 110.59 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4852 17.90 - 35.80: 409 35.80 - 53.70: 70 53.70 - 71.60: 6 71.60 - 89.49: 7 Dihedral angle restraints: 5344 sinusoidal: 2000 harmonic: 3344 Sorted by residual: dihedral pdb=" CA LEU B 205 " pdb=" C LEU B 205 " pdb=" N MET B 206 " pdb=" CA MET B 206 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 205 " pdb=" C LEU A 205 " pdb=" N MET A 206 " pdb=" CA MET A 206 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU C 205 " pdb=" C LEU C 205 " pdb=" N MET C 206 " pdb=" CA MET C 206 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1208 0.072 - 0.144: 238 0.144 - 0.215: 8 0.215 - 0.287: 0 0.287 - 0.359: 2 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1453 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 202 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 203 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 145 " 0.017 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE A 145 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 145 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 145 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 202 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ARG A 202 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG A 202 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 203 " 0.011 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 3157 2.86 - 3.43: 9494 3.43 - 4.00: 16264 4.00 - 4.57: 21988 4.57 - 5.14: 32286 Nonbonded interactions: 83189 Sorted by model distance: nonbonded pdb=" O1B G2P B 401 " pdb=" O2A G2P B 401 " model vdw 2.296 3.040 nonbonded pdb=" O1B G2P C 401 " pdb=" O2A G2P C 401 " model vdw 2.301 3.040 nonbonded pdb=" O ARG A 202 " pdb=" K K A 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG C 202 " pdb=" K K C 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG B 202 " pdb=" K K B 402 " model vdw 2.304 2.850 ... (remaining 83184 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 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 : 0.007 0.108 9024 Z= 0.324 Angle : 0.990 11.922 12228 Z= 0.458 Chirality : 0.055 0.359 1456 Planarity : 0.005 0.090 1604 Dihedral : 13.656 89.494 3224 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.21), residues: 1216 helix: -2.12 (0.18), residues: 432 sheet: 1.00 (0.36), residues: 248 loop : -1.68 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 283 TYR 0.006 0.001 TYR D 222 PHE 0.039 0.003 PHE A 145 HIS 0.003 0.001 HIS B 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.32 ( 9024) covalent geometry : angle 0.98979 / 0.46 (12228) hydrogen bonds : bond 0.25971 / 17.68 ( 374) hydrogen bonds : angle 8.35688 / 5.85 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.193 Fit side-chains REVERT: B 104 MET cc_start: 0.5212 (mtp) cc_final: 0.4643 (mmm) REVERT: B 209 ASP cc_start: 0.6687 (m-30) cc_final: 0.6462 (m-30) REVERT: D 29 MET cc_start: 0.3931 (mtt) cc_final: 0.3643 (mtt) REVERT: D 242 MET cc_start: 0.7492 (tpp) cc_final: 0.7243 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0617 time to fit residues: 12.6001 Evaluate side-chains 108 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.211668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.196613 restraints weight = 16397.372| |-----------------------------------------------------------------------------| r_work (start): 0.4951 rms_B_bonded: 2.98 r_work: 0.4842 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9024 Z= 0.122 Angle : 0.536 5.216 12228 Z= 0.288 Chirality : 0.047 0.176 1456 Planarity : 0.004 0.058 1604 Dihedral : 6.402 57.954 1300 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.67 % Allowed : 9.49 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1216 helix: -0.52 (0.24), residues: 424 sheet: 0.63 (0.31), residues: 288 loop : -1.67 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.002 0.000 TYR D 222 PHE 0.025 0.002 PHE A 145 HIS 0.002 0.001 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9024) covalent geometry : angle 0.53619 / 0.29 (12228) hydrogen bonds : bond 0.05217 / 3.52 ( 374) hydrogen bonds : angle 5.10586 / 3.62 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.200 Fit side-chains REVERT: A 186 ASN cc_start: 0.4973 (m-40) cc_final: 0.4616 (m-40) REVERT: B 104 MET cc_start: 0.5441 (mtp) cc_final: 0.5099 (mmm) REVERT: D 29 MET cc_start: 0.6327 (mtt) cc_final: 0.5576 (mtt) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.0597 time to fit residues: 9.7075 Evaluate side-chains 100 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN B 165 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN D 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.197553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.183413 restraints weight = 16724.259| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 2.73 r_work: 0.4751 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9024 Z= 0.274 Angle : 0.790 7.488 12228 Z= 0.414 Chirality : 0.055 0.192 1456 Planarity : 0.005 0.052 1604 Dihedral : 6.996 50.631 1300 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.12 % Allowed : 16.07 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1216 helix: -0.94 (0.23), residues: 444 sheet: -0.22 (0.29), residues: 300 loop : -1.75 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 142 TYR 0.013 0.003 TYR D 222 PHE 0.035 0.004 PHE D 145 HIS 0.004 0.002 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 ( 9024) covalent geometry : angle 0.78962 / 0.41 (12228) hydrogen bonds : bond 0.06305 / 4.30 ( 374) hydrogen bonds : angle 5.86150 / 4.15 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: B 104 MET cc_start: 0.5869 (mtp) cc_final: 0.5665 (mmm) outliers start: 19 outliers final: 5 residues processed: 113 average time/residue: 0.0560 time to fit residues: 9.8830 Evaluate side-chains 103 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.204421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.190276 restraints weight = 16754.308| |-----------------------------------------------------------------------------| r_work (start): 0.4942 rms_B_bonded: 2.78 r_work: 0.4840 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9024 Z= 0.112 Angle : 0.503 5.742 12228 Z= 0.274 Chirality : 0.047 0.173 1456 Planarity : 0.003 0.054 1604 Dihedral : 6.158 52.964 1300 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.00 % Allowed : 17.08 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1216 helix: -0.20 (0.24), residues: 444 sheet: 0.12 (0.29), residues: 288 loop : -1.67 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 142 TYR 0.004 0.001 TYR D 222 PHE 0.022 0.002 PHE B 145 HIS 0.001 0.000 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9024) covalent geometry : angle 0.50348 / 0.27 (12228) hydrogen bonds : bond 0.04405 / 3.02 ( 374) hydrogen bonds : angle 4.69592 / 3.34 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.5975 (tpp) cc_final: 0.5704 (tpp) REVERT: A 254 LEU cc_start: 0.5506 (tp) cc_final: 0.5148 (tp) REVERT: C 225 MET cc_start: 0.6466 (tmm) cc_final: 0.6200 (ptm) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.0557 time to fit residues: 10.1455 Evaluate side-chains 108 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain D residue 220 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.202989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.188702 restraints weight = 16822.578| |-----------------------------------------------------------------------------| r_work (start): 0.4918 rms_B_bonded: 2.79 r_work: 0.4812 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5681 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9024 Z= 0.129 Angle : 0.534 7.276 12228 Z= 0.282 Chirality : 0.047 0.167 1456 Planarity : 0.003 0.057 1604 Dihedral : 6.068 52.235 1300 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.90 % Allowed : 18.64 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1216 helix: 0.11 (0.25), residues: 440 sheet: 0.08 (0.29), residues: 292 loop : -1.61 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.006 0.001 TYR D 222 PHE 0.023 0.002 PHE A 145 HIS 0.001 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9024) covalent geometry : angle 0.53383 / 0.28 (12228) hydrogen bonds : bond 0.04464 / 3.06 ( 374) hydrogen bonds : angle 4.67267 / 3.33 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.5952 (tpp) cc_final: 0.5677 (tpp) REVERT: A 254 LEU cc_start: 0.5565 (tp) cc_final: 0.5207 (tp) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.0643 time to fit residues: 11.1779 Evaluate side-chains 112 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.199648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.185391 restraints weight = 16587.590| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 2.74 r_work: 0.4783 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9024 Z= 0.184 Angle : 0.625 7.240 12228 Z= 0.327 Chirality : 0.049 0.164 1456 Planarity : 0.004 0.073 1604 Dihedral : 6.367 50.709 1300 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.12 % Allowed : 18.19 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1216 helix: -0.14 (0.25), residues: 444 sheet: -0.10 (0.29), residues: 292 loop : -1.64 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.009 0.002 TYR D 222 PHE 0.027 0.003 PHE B 145 HIS 0.003 0.001 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9024) covalent geometry : angle 0.62492 / 0.33 (12228) hydrogen bonds : bond 0.05081 / 3.48 ( 374) hydrogen bonds : angle 5.03886 / 3.57 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.2182 (OUTLIER) cc_final: 0.1839 (mm-30) REVERT: B 276 GLU cc_start: 0.5744 (pm20) cc_final: 0.5225 (pm20) outliers start: 28 outliers final: 14 residues processed: 126 average time/residue: 0.0586 time to fit residues: 11.4182 Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 109 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.203755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.189298 restraints weight = 16742.474| |-----------------------------------------------------------------------------| r_work (start): 0.4926 rms_B_bonded: 2.80 r_work: 0.4820 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9024 Z= 0.117 Angle : 0.533 7.403 12228 Z= 0.280 Chirality : 0.047 0.169 1456 Planarity : 0.004 0.063 1604 Dihedral : 6.044 55.647 1300 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.01 % Allowed : 20.20 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1216 helix: 0.16 (0.25), residues: 444 sheet: 0.11 (0.29), residues: 292 loop : -1.58 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 142 TYR 0.004 0.001 TYR D 222 PHE 0.022 0.002 PHE B 145 HIS 0.001 0.000 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9024) covalent geometry : angle 0.53282 / 0.28 (12228) hydrogen bonds : bond 0.04263 / 2.92 ( 374) hydrogen bonds : angle 4.56222 / 3.24 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LEU cc_start: 0.5261 (tp) cc_final: 0.4839 (tp) REVERT: B 276 GLU cc_start: 0.5357 (pm20) cc_final: 0.4944 (pm20) REVERT: B 303 ASN cc_start: 0.4842 (p0) cc_final: 0.4641 (p0) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 0.0626 time to fit residues: 11.1248 Evaluate side-chains 115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.200439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.186076 restraints weight = 16590.285| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 2.76 r_work: 0.4797 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9024 Z= 0.169 Angle : 0.615 8.702 12228 Z= 0.319 Chirality : 0.049 0.165 1456 Planarity : 0.004 0.066 1604 Dihedral : 6.241 50.654 1300 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.34 % Allowed : 20.42 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1216 helix: -0.00 (0.25), residues: 444 sheet: 0.00 (0.29), residues: 292 loop : -1.65 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 142 TYR 0.009 0.002 TYR D 222 PHE 0.026 0.002 PHE B 145 HIS 0.002 0.001 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9024) covalent geometry : angle 0.61485 / 0.32 (12228) hydrogen bonds : bond 0.04815 / 3.31 ( 374) hydrogen bonds : angle 4.88349 / 3.47 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.2246 (OUTLIER) cc_final: 0.1935 (mm-30) REVERT: A 254 LEU cc_start: 0.5559 (tp) cc_final: 0.5172 (tp) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.0579 time to fit residues: 10.4075 Evaluate side-chains 119 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.202766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.188447 restraints weight = 16590.756| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 2.77 r_work: 0.4822 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9024 Z= 0.131 Angle : 0.566 8.149 12228 Z= 0.297 Chirality : 0.047 0.157 1456 Planarity : 0.004 0.067 1604 Dihedral : 6.100 53.436 1300 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 21.09 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.23), residues: 1216 helix: 0.13 (0.25), residues: 444 sheet: 0.15 (0.29), residues: 292 loop : -1.63 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.006 0.001 TYR D 222 PHE 0.023 0.002 PHE B 145 HIS 0.001 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9024) covalent geometry : angle 0.56553 / 0.30 (12228) hydrogen bonds : bond 0.04390 / 3.02 ( 374) hydrogen bonds : angle 4.67388 / 3.31 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.2223 (OUTLIER) cc_final: 0.1949 (mt-10) REVERT: A 254 LEU cc_start: 0.5650 (tp) cc_final: 0.5334 (tp) outliers start: 18 outliers final: 15 residues processed: 116 average time/residue: 0.0563 time to fit residues: 10.0324 Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.203287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.188980 restraints weight = 16432.376| |-----------------------------------------------------------------------------| r_work (start): 0.4942 rms_B_bonded: 2.74 r_work: 0.4830 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9024 Z= 0.124 Angle : 0.557 9.074 12228 Z= 0.291 Chirality : 0.047 0.159 1456 Planarity : 0.004 0.064 1604 Dihedral : 6.043 54.255 1300 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.34 % Allowed : 21.09 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1216 helix: 0.28 (0.26), residues: 440 sheet: 0.23 (0.29), residues: 292 loop : -1.63 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.006 0.001 TYR D 222 PHE 0.022 0.002 PHE B 145 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9024) covalent geometry : angle 0.55732 / 0.29 (12228) hydrogen bonds : bond 0.04253 / 2.94 ( 374) hydrogen bonds : angle 4.59174 / 3.26 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.5654 (mtt) cc_final: 0.5193 (mtt) REVERT: A 75 GLU cc_start: 0.2151 (OUTLIER) cc_final: 0.1864 (mt-10) REVERT: A 104 MET cc_start: 0.5083 (mmt) cc_final: 0.3422 (mtm) REVERT: A 254 LEU cc_start: 0.5459 (tp) cc_final: 0.5150 (tp) outliers start: 21 outliers final: 18 residues processed: 114 average time/residue: 0.0565 time to fit residues: 9.8608 Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.210741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.195275 restraints weight = 16428.456| |-----------------------------------------------------------------------------| r_work (start): 0.4953 rms_B_bonded: 2.93 r_work: 0.4840 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9024 Z= 0.115 Angle : 0.537 8.416 12228 Z= 0.281 Chirality : 0.047 0.169 1456 Planarity : 0.004 0.064 1604 Dihedral : 5.968 56.622 1300 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 21.32 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1216 helix: 0.40 (0.26), residues: 444 sheet: 0.29 (0.30), residues: 292 loop : -1.56 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 142 TYR 0.005 0.001 TYR D 222 PHE 0.021 0.001 PHE B 145 HIS 0.001 0.000 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9024) covalent geometry : angle 0.53657 / 0.28 (12228) hydrogen bonds : bond 0.04058 / 2.79 ( 374) hydrogen bonds : angle 4.43858 / 3.15 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1452.81 seconds wall clock time: 25 minutes 33.64 seconds (1533.64 seconds total)