Starting phenix.real_space_refine on Thu Aug 6 17:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6l_47572/08_2026/9e6l_47572.map" } resolution = 3.3 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= 0.003 sd= 0.017 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 36 5.49 5 Mg 12 5.21 5 S 108 5.16 5 C 10272 2.51 5 N 2944 2.21 5 O 3215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16587 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "H" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 31} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "J" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "K" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 283 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "X" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "E" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.46, per 1000 atoms: 0.21 Number of scatterers: 16587 At special positions: 0 Unit cell: (123.224, 121.536, 163.736, 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 108 16.00 P 36 15.00 Mg 12 11.99 O 3215 8.00 N 2944 7.00 C 10272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 529.1 milliseconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 52.1% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'G' and resid 109 through 115 removed outlier: 4.241A pdb=" N LEU G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'H' and resid 116 through 129 removed outlier: 3.672A pdb=" N LEU H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 115 removed outlier: 4.042A pdb=" N LEU I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 116 through 128 removed outlier: 3.524A pdb=" N LEU J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 115 removed outlier: 3.503A pdb=" N ALA K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 129 Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 92 through 102 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 120 removed outlier: 3.537A pdb=" N LEU C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.506A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.809A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 254 through 270 removed outlier: 4.063A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 4.183A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.652A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 354 " --> pdb=" O MET C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 92 through 102 Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.797A pdb=" N ILE F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 147 through 156 removed outlier: 3.781A pdb=" N GLU F 156 " --> pdb=" O MET F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.505A pdb=" N CYS F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 200 " --> pdb=" O HIS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.848A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 272 removed outlier: 4.028A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 295 through 318 Processing helix chain 'F' and resid 346 through 354 removed outlier: 3.836A pdb=" N MET F 350 " --> pdb=" O GLY F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.642A pdb=" N LYS B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.560A pdb=" N VAL B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.571A pdb=" N GLU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 203 through 204 No H-bonds generated for 'chain 'B' and resid 203 through 204' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.885A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 272 removed outlier: 4.138A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.721A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.544A pdb=" N MET B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 114 through 121 removed outlier: 3.544A pdb=" N ILE E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 190 through 202 Processing helix chain 'E' and resid 203 through 204 No H-bonds generated for 'chain 'E' and resid 203 through 204' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.803A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 272 removed outlier: 4.065A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.587A pdb=" N ARG E 287 " --> pdb=" O MET E 283 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.734A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.617A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.510A pdb=" N GLU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.597A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 254 through 272 removed outlier: 4.011A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.652A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.710A pdb=" N MET A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 164 through 171 removed outlier: 3.623A pdb=" N LEU D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 225 through 236 removed outlier: 3.893A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 254 through 270 removed outlier: 3.966A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.745A pdb=" N TYR D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 287 " --> pdb=" O MET D 283 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.486A pdb=" N CYS B 215 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA B 250 " --> pdb=" O CYS B 215 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR B 217 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS B 214 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 277 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 216 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 279 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 218 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER B 275 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL B 322 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 277 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR B 324 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 279 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 181 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASN B 325 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 183 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.650A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 181 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 325 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 183 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER C 275 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 322 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS C 214 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 277 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 216 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 279 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE C 218 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS C 215 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ALA C 250 " --> pdb=" O CYS C 215 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR C 217 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'F' and resid 145 through 146 removed outlier: 6.430A pdb=" N CYS E 215 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA E 250 " --> pdb=" O CYS E 215 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR E 217 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS E 214 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 277 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU E 216 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL E 279 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE E 218 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER E 275 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL E 322 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AA7, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.508A pdb=" N CYS F 215 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ALA F 250 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR F 217 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS F 214 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE F 277 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU F 216 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL F 279 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE F 218 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR F 181 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN F 325 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU F 183 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.423A pdb=" N CYS A 215 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA A 250 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 217 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS A 214 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 276 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 275 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL A 322 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 181 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ASN A 325 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 183 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB3, first strand: chain 'E' and resid 145 through 146 removed outlier: 6.455A pdb=" N CYS D 215 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA D 250 " --> pdb=" O CYS D 215 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR D 217 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS D 214 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N VAL D 278 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU D 216 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP D 280 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 218 " --> pdb=" O ASP D 280 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER D 275 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL D 322 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D 277 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL D 279 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR D 181 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASN D 325 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 183 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB6, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AB7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 327 through 329 776 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5438 1.34 - 1.46: 2051 1.46 - 1.58: 9139 1.58 - 1.69: 65 1.69 - 1.81: 168 Bond restraints: 16861 Sorted by residual: bond pdb=" C3' DT X 9 " pdb=" C2' DT X 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT X 15 " pdb=" C2' DT X 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 bond pdb=" N ARG H 129 " pdb=" CA ARG H 129 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.87e+00 bond pdb=" C3' DT X 17 " pdb=" C2' DT X 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.60e+00 bond pdb=" N LYS I 105 " pdb=" CA LYS I 105 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.33e-02 5.65e+03 5.67e+00 ... (remaining 16856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 22480 1.90 - 3.81: 326 3.81 - 5.71: 25 5.71 - 7.62: 16 7.62 - 9.52: 2 Bond angle restraints: 22849 Sorted by residual: angle pdb=" N SER H 130 " pdb=" CA SER H 130 " pdb=" C SER H 130 " ideal model delta sigma weight residual 110.24 119.76 -9.52 1.30e+00 5.92e-01 5.36e+01 angle pdb=" N ARG H 128 " pdb=" CA ARG H 128 " pdb=" C ARG H 128 " ideal model delta sigma weight residual 113.16 119.63 -6.47 1.24e+00 6.50e-01 2.73e+01 angle pdb=" N SER G 130 " pdb=" CA SER G 130 " pdb=" C SER G 130 " ideal model delta sigma weight residual 110.35 116.40 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N SER J 130 " pdb=" CA SER J 130 " pdb=" C SER J 130 " ideal model delta sigma weight residual 110.23 116.64 -6.41 1.45e+00 4.76e-01 1.96e+01 angle pdb=" N SER H 130 " pdb=" CA SER H 130 " pdb=" CB SER H 130 " ideal model delta sigma weight residual 109.92 103.02 6.90 1.60e+00 3.91e-01 1.86e+01 ... (remaining 22844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9433 18.00 - 35.99: 690 35.99 - 53.99: 183 53.99 - 71.98: 42 71.98 - 89.98: 13 Dihedral angle restraints: 10361 sinusoidal: 4397 harmonic: 5964 Sorted by residual: dihedral pdb=" CA ASP B 315 " pdb=" CB ASP B 315 " pdb=" CG ASP B 315 " pdb=" OD1 ASP B 315 " ideal model delta sinusoidal sigma weight residual -30.00 -88.83 58.83 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ARG A 293 " pdb=" CB ARG A 293 " pdb=" CG ARG A 293 " pdb=" CD ARG A 293 " ideal model delta sinusoidal sigma weight residual 60.00 111.02 -51.02 3 1.50e+01 4.44e-03 8.97e+00 dihedral pdb=" CB MET E 307 " pdb=" CG MET E 307 " pdb=" SD MET E 307 " pdb=" CE MET E 307 " ideal model delta sinusoidal sigma weight residual -60.00 -110.88 50.88 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 10358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2069 0.045 - 0.090: 359 0.090 - 0.135: 166 0.135 - 0.180: 4 0.180 - 0.225: 1 Chirality restraints: 2599 Sorted by residual: chirality pdb=" CA ARG H 119 " pdb=" N ARG H 119 " pdb=" C ARG H 119 " pdb=" CB ARG H 119 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG B 154 " pdb=" N ARG B 154 " pdb=" C ARG B 154 " pdb=" CB ARG B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ARG D 188 " pdb=" N ARG D 188 " pdb=" C ARG D 188 " pdb=" CB ARG D 188 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 2596 not shown) Planarity restraints: 2902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 187 " -0.008 2.00e-02 2.50e+03 9.40e-03 1.55e+00 pdb=" CG PHE A 187 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 187 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 187 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 187 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 187 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 187 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 204 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO C 205 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 204 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO E 205 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 205 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 205 " 0.015 5.00e-02 4.00e+02 ... (remaining 2899 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 50 2.38 - 3.01: 8933 3.01 - 3.64: 24645 3.64 - 4.27: 36054 4.27 - 4.90: 61720 Nonbonded interactions: 131402 Sorted by model distance: nonbonded pdb=" OG SER C 192 " pdb="MG MG C 503 " model vdw 1.753 2.170 nonbonded pdb=" OD2 ASP B 374 " pdb="MG MG B 502 " model vdw 1.991 2.170 nonbonded pdb=" O3B ATP B 501 " pdb="MG MG B 503 " model vdw 2.012 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 503 " model vdw 2.050 2.170 nonbonded pdb=" O3B ATP A 501 " pdb="MG MG A 502 " model vdw 2.056 2.170 ... (remaining 131397 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 81 through 502) selection = (chain 'B' and resid 81 through 502) selection = (chain 'C' and resid 81 through 502) selection = (chain 'D' and resid 81 through 502) selection = (chain 'E' and resid 81 through 502) selection = (chain 'F' and resid 81 through 502) } ncs_group { reference = (chain 'G' and (resid 103 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 5 or (resid 116 through 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 through 134 or (resid 135 and (name N or name CA or name C or \ name O or name CB )) or resid 136)) selection = chain 'H' selection = (chain 'I' and (resid 103 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 5 or (resid 116 through 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 through 134 or (resid 135 and (name N or name CA or name C or \ name O or name CB )) or resid 136)) selection = (chain 'J' and (resid 103 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 5 or (resid 116 through 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 through 134 or (resid 135 and (name N or name CA or name C or \ name O or name CB )) or resid 136)) selection = (chain 'K' and (resid 103 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 5 or (resid 116 through 117 and (name N or name CA or name C or name O or name C \ B )) or resid 118 through 134 or (resid 135 and (name N or name CA or name C or \ name O or name CB )) or resid 136)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.180 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 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 : 0.002 0.037 16861 Z= 0.150 Angle : 0.517 9.521 22849 Z= 0.335 Chirality : 0.041 0.225 2599 Planarity : 0.002 0.028 2902 Dihedral : 14.121 89.975 6521 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.30 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.86 (0.19), residues: 2072 helix: 1.79 (0.18), residues: 989 sheet: 2.85 (0.29), residues: 270 loop : 0.01 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 308 TYR 0.005 0.001 TYR D 217 PHE 0.022 0.001 PHE A 187 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.15 (16861) covalent geometry : angle 0.51682 / 0.34 (22849) hydrogen bonds : bond 0.14964 / 10.68 ( 776) hydrogen bonds : angle 4.70021 / 3.75 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.597 Fit side-chains REVERT: C 383 CYS cc_start: 0.7581 (m) cc_final: 0.7330 (m) REVERT: F 89 ASN cc_start: 0.8851 (t0) cc_final: 0.8583 (t0) REVERT: B 89 ASN cc_start: 0.9087 (m110) cc_final: 0.8715 (m110) REVERT: B 307 MET cc_start: 0.9461 (mmm) cc_final: 0.9237 (mmm) REVERT: E 89 ASN cc_start: 0.9002 (m110) cc_final: 0.8763 (m-40) REVERT: A 89 ASN cc_start: 0.8955 (t0) cc_final: 0.8641 (t0) REVERT: A 159 CYS cc_start: 0.7803 (p) cc_final: 0.7514 (p) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1062 time to fit residues: 18.2215 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 193 GLN E 87 GLN D 311 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.048051 restraints weight = 54536.101| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.70 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16861 Z= 0.155 Angle : 0.491 7.894 22849 Z= 0.262 Chirality : 0.040 0.139 2599 Planarity : 0.003 0.047 2902 Dihedral : 12.461 89.138 2661 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.99 % Rotamer: Outliers : 0.29 % Allowed : 4.39 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.19), residues: 2072 helix: 1.90 (0.18), residues: 993 sheet: 2.84 (0.29), residues: 272 loop : 0.10 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.006 0.001 TYR B 217 PHE 0.017 0.001 PHE A 187 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (16861) covalent geometry : angle 0.49083 / 0.26 (22849) hydrogen bonds : bond 0.03717 / 2.61 ( 776) hydrogen bonds : angle 3.89905 / 3.21 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.388 Fit side-chains REVERT: C 383 CYS cc_start: 0.7748 (m) cc_final: 0.7399 (m) REVERT: F 89 ASN cc_start: 0.8970 (t0) cc_final: 0.8619 (t0) REVERT: F 335 MET cc_start: 0.6419 (pmm) cc_final: 0.5749 (tpt) REVERT: B 89 ASN cc_start: 0.9096 (m110) cc_final: 0.8682 (m110) REVERT: E 89 ASN cc_start: 0.9127 (m110) cc_final: 0.8906 (m-40) REVERT: A 89 ASN cc_start: 0.9083 (t0) cc_final: 0.8720 (t0) REVERT: A 159 CYS cc_start: 0.8086 (p) cc_final: 0.7695 (p) REVERT: A 345 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8716 (tt) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1050 time to fit residues: 16.9042 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 86 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.046977 restraints weight = 55242.739| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.48 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16861 Z= 0.247 Angle : 0.546 6.710 22849 Z= 0.288 Chirality : 0.042 0.138 2599 Planarity : 0.003 0.045 2902 Dihedral : 11.967 89.378 2661 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Rotamer: Outliers : 0.70 % Allowed : 6.39 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.86 (0.20), residues: 2072 helix: 1.85 (0.18), residues: 995 sheet: 2.33 (0.30), residues: 294 loop : 0.02 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 154 TYR 0.009 0.001 TYR B 217 PHE 0.015 0.001 PHE A 187 HIS 0.002 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (16861) covalent geometry : angle 0.54616 / 0.29 (22849) hydrogen bonds : bond 0.04077 / 2.84 ( 776) hydrogen bonds : angle 3.97817 / 3.29 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.449 Fit side-chains REVERT: C 142 MET cc_start: 0.9334 (mmm) cc_final: 0.8585 (mmm) REVERT: C 383 CYS cc_start: 0.7771 (m) cc_final: 0.7375 (m) REVERT: F 89 ASN cc_start: 0.9010 (t0) cc_final: 0.8637 (t0) REVERT: F 335 MET cc_start: 0.6763 (pmm) cc_final: 0.6127 (tpt) REVERT: B 89 ASN cc_start: 0.9102 (m110) cc_final: 0.8689 (m110) REVERT: E 89 ASN cc_start: 0.9232 (m110) cc_final: 0.8953 (m-40) REVERT: A 89 ASN cc_start: 0.9026 (t0) cc_final: 0.8642 (t0) REVERT: A 345 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8823 (tt) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.0996 time to fit residues: 15.3326 Evaluate side-chains 85 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 155 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.047788 restraints weight = 54352.905| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.51 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16861 Z= 0.163 Angle : 0.480 8.263 22849 Z= 0.255 Chirality : 0.040 0.156 2599 Planarity : 0.003 0.040 2902 Dihedral : 11.800 89.701 2661 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % Rotamer: Outliers : 0.47 % Allowed : 7.85 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.91 (0.20), residues: 2072 helix: 1.89 (0.18), residues: 995 sheet: 2.46 (0.30), residues: 294 loop : 0.01 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 119 TYR 0.004 0.001 TYR C 217 PHE 0.014 0.001 PHE A 187 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (16861) covalent geometry : angle 0.48025 / 0.26 (22849) hydrogen bonds : bond 0.03293 / 2.30 ( 776) hydrogen bonds : angle 3.74352 / 3.12 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.425 Fit side-chains REVERT: C 142 MET cc_start: 0.9370 (mmm) cc_final: 0.8742 (mmm) REVERT: C 345 ILE cc_start: 0.9119 (mt) cc_final: 0.8916 (tt) REVERT: C 383 CYS cc_start: 0.7761 (m) cc_final: 0.7385 (m) REVERT: F 89 ASN cc_start: 0.8985 (t0) cc_final: 0.8603 (t0) REVERT: F 335 MET cc_start: 0.6847 (pmm) cc_final: 0.6282 (tpt) REVERT: B 89 ASN cc_start: 0.9066 (m110) cc_final: 0.8668 (m110) REVERT: E 89 ASN cc_start: 0.9255 (m110) cc_final: 0.8959 (m-40) REVERT: A 89 ASN cc_start: 0.9017 (t0) cc_final: 0.8626 (t0) REVERT: A 159 CYS cc_start: 0.8214 (p) cc_final: 0.7749 (p) REVERT: A 345 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8814 (tt) outliers start: 8 outliers final: 3 residues processed: 94 average time/residue: 0.1053 time to fit residues: 15.7444 Evaluate side-chains 87 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 138 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.0970 chunk 184 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.048284 restraints weight = 54024.576| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.54 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16861 Z= 0.120 Angle : 0.461 7.566 22849 Z= 0.245 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.047 2902 Dihedral : 11.727 89.100 2661 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.70 % Rotamer: Outliers : 0.82 % Allowed : 8.32 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.20), residues: 2072 helix: 1.92 (0.18), residues: 999 sheet: 2.84 (0.31), residues: 284 loop : 0.08 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 119 TYR 0.005 0.001 TYR B 286 PHE 0.011 0.001 PHE D 187 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16861) covalent geometry : angle 0.46066 / 0.24 (22849) hydrogen bonds : bond 0.02970 / 2.07 ( 776) hydrogen bonds : angle 3.59860 / 3.00 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.440 Fit side-chains REVERT: C 142 MET cc_start: 0.9347 (mmm) cc_final: 0.8780 (mmm) REVERT: C 383 CYS cc_start: 0.7771 (m) cc_final: 0.7363 (m) REVERT: F 89 ASN cc_start: 0.8975 (t0) cc_final: 0.8564 (t0) REVERT: B 89 ASN cc_start: 0.9053 (m110) cc_final: 0.8655 (m110) REVERT: B 345 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8783 (tt) REVERT: E 353 SER cc_start: 0.9471 (m) cc_final: 0.9185 (p) REVERT: A 89 ASN cc_start: 0.9001 (t0) cc_final: 0.8596 (t0) REVERT: A 159 CYS cc_start: 0.8155 (p) cc_final: 0.7682 (p) REVERT: A 345 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8781 (tt) REVERT: A 353 SER cc_start: 0.9269 (m) cc_final: 0.9017 (p) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 0.1018 time to fit residues: 17.2026 Evaluate side-chains 94 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.047283 restraints weight = 54802.470| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.48 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16861 Z= 0.208 Angle : 0.512 8.398 22849 Z= 0.269 Chirality : 0.041 0.145 2599 Planarity : 0.003 0.044 2902 Dihedral : 11.786 89.983 2661 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Rotamer: Outliers : 0.82 % Allowed : 8.90 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.90 (0.20), residues: 2072 helix: 1.87 (0.18), residues: 1003 sheet: 2.22 (0.31), residues: 306 loop : 0.07 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 119 TYR 0.007 0.001 TYR B 286 PHE 0.006 0.001 PHE A 184 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (16861) covalent geometry : angle 0.51172 / 0.27 (22849) hydrogen bonds : bond 0.03530 / 2.46 ( 776) hydrogen bonds : angle 3.78328 / 3.14 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.609 Fit side-chains REVERT: C 142 MET cc_start: 0.9327 (mmm) cc_final: 0.8798 (mmm) REVERT: C 383 CYS cc_start: 0.7807 (m) cc_final: 0.7453 (m) REVERT: F 89 ASN cc_start: 0.8997 (t0) cc_final: 0.8584 (t0) REVERT: F 335 MET cc_start: 0.6240 (pmm) cc_final: 0.5336 (tpt) REVERT: B 89 ASN cc_start: 0.9086 (m110) cc_final: 0.8723 (m110) REVERT: B 345 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8876 (tt) REVERT: A 89 ASN cc_start: 0.9010 (t0) cc_final: 0.8671 (t0) REVERT: A 345 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 353 SER cc_start: 0.9312 (m) cc_final: 0.9050 (p) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.1008 time to fit residues: 16.0797 Evaluate side-chains 94 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 91 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 4 optimal weight: 50.0000 chunk 61 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.047929 restraints weight = 54227.016| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.51 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16861 Z= 0.140 Angle : 0.472 7.726 22849 Z= 0.250 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.043 2902 Dihedral : 11.747 89.262 2661 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % Rotamer: Outliers : 0.70 % Allowed : 9.49 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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 (0.20), residues: 2072 helix: 1.87 (0.18), residues: 1007 sheet: 2.53 (0.31), residues: 298 loop : 0.11 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 119 TYR 0.005 0.001 TYR B 286 PHE 0.006 0.001 PHE F 317 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16861) covalent geometry : angle 0.47191 / 0.25 (22849) hydrogen bonds : bond 0.03085 / 2.15 ( 776) hydrogen bonds : angle 3.60486 / 3.02 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.521 Fit side-chains REVERT: C 142 MET cc_start: 0.9332 (mmm) cc_final: 0.8812 (mmm) REVERT: C 383 CYS cc_start: 0.7790 (m) cc_final: 0.7383 (m) REVERT: F 89 ASN cc_start: 0.8966 (t0) cc_final: 0.8543 (t0) REVERT: F 335 MET cc_start: 0.6392 (pmm) cc_final: 0.5543 (tpt) REVERT: B 89 ASN cc_start: 0.9138 (m110) cc_final: 0.8767 (m110) REVERT: B 345 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8800 (tt) REVERT: E 315 ASP cc_start: 0.8363 (p0) cc_final: 0.8153 (p0) REVERT: A 89 ASN cc_start: 0.9055 (t0) cc_final: 0.8656 (t0) REVERT: A 159 CYS cc_start: 0.8237 (p) cc_final: 0.7787 (p) REVERT: A 345 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 350 MET cc_start: 0.9368 (mmm) cc_final: 0.9153 (tpt) REVERT: A 353 SER cc_start: 0.9295 (m) cc_final: 0.9025 (p) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.1053 time to fit residues: 16.7265 Evaluate side-chains 93 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 136 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.048103 restraints weight = 54550.341| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.50 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16861 Z= 0.130 Angle : 0.461 7.712 22849 Z= 0.244 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.041 2902 Dihedral : 11.725 89.184 2661 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Rotamer: Outliers : 0.64 % Allowed : 10.31 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 2072 helix: 1.89 (0.18), residues: 1007 sheet: 2.58 (0.31), residues: 298 loop : 0.10 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.005 0.001 TYR B 286 PHE 0.006 0.001 PHE B 337 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16861) covalent geometry : angle 0.46117 / 0.24 (22849) hydrogen bonds : bond 0.02918 / 2.04 ( 776) hydrogen bonds : angle 3.53934 / 2.97 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.575 Fit side-chains REVERT: C 142 MET cc_start: 0.9348 (mmm) cc_final: 0.8854 (mmm) REVERT: C 383 CYS cc_start: 0.7812 (m) cc_final: 0.7383 (m) REVERT: F 89 ASN cc_start: 0.8939 (t0) cc_final: 0.8498 (t0) REVERT: F 335 MET cc_start: 0.6528 (pmm) cc_final: 0.5753 (tpt) REVERT: B 89 ASN cc_start: 0.9107 (m110) cc_final: 0.8728 (m110) REVERT: B 345 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8792 (tt) REVERT: E 350 MET cc_start: 0.9156 (mmm) cc_final: 0.8900 (mmm) REVERT: A 89 ASN cc_start: 0.9056 (t0) cc_final: 0.8672 (t0) REVERT: A 159 CYS cc_start: 0.8189 (p) cc_final: 0.7755 (p) REVERT: A 345 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8697 (tt) REVERT: A 353 SER cc_start: 0.9280 (m) cc_final: 0.9017 (p) outliers start: 11 outliers final: 8 residues processed: 93 average time/residue: 0.1149 time to fit residues: 17.6683 Evaluate side-chains 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.0980 chunk 84 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.048761 restraints weight = 54207.405| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.54 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16861 Z= 0.101 Angle : 0.464 9.592 22849 Z= 0.243 Chirality : 0.039 0.139 2599 Planarity : 0.003 0.039 2902 Dihedral : 11.696 88.867 2661 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.01 % Favored : 98.94 % Rotamer: Outliers : 0.47 % Allowed : 10.66 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.20), residues: 2072 helix: 1.95 (0.18), residues: 1001 sheet: 2.73 (0.31), residues: 298 loop : 0.14 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 119 TYR 0.005 0.001 TYR B 286 PHE 0.015 0.001 PHE E 274 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (16861) covalent geometry : angle 0.46408 / 0.24 (22849) hydrogen bonds : bond 0.02639 / 1.83 ( 776) hydrogen bonds : angle 3.45273 / 2.89 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.629 Fit side-chains REVERT: C 142 MET cc_start: 0.9347 (mmm) cc_final: 0.8869 (mmm) REVERT: C 383 CYS cc_start: 0.7820 (m) cc_final: 0.7371 (m) REVERT: F 89 ASN cc_start: 0.8882 (t0) cc_final: 0.8405 (t0) REVERT: F 335 MET cc_start: 0.6676 (pmm) cc_final: 0.5946 (tpt) REVERT: B 89 ASN cc_start: 0.9081 (m110) cc_final: 0.8702 (m110) REVERT: B 345 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8754 (tt) REVERT: E 350 MET cc_start: 0.9136 (mmm) cc_final: 0.8916 (mmm) REVERT: A 89 ASN cc_start: 0.9048 (t0) cc_final: 0.8666 (t0) REVERT: A 159 CYS cc_start: 0.8127 (p) cc_final: 0.7699 (p) REVERT: A 345 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8699 (tt) REVERT: A 350 MET cc_start: 0.9339 (mmm) cc_final: 0.9117 (tpt) REVERT: A 353 SER cc_start: 0.9256 (m) cc_final: 0.8878 (p) REVERT: D 277 ILE cc_start: 0.9038 (mt) cc_final: 0.8825 (tt) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.1146 time to fit residues: 16.6370 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 172 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.048073 restraints weight = 54432.965| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.53 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16861 Z= 0.154 Angle : 0.504 10.459 22849 Z= 0.259 Chirality : 0.040 0.176 2599 Planarity : 0.003 0.036 2902 Dihedral : 11.716 89.545 2661 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Rotamer: Outliers : 0.47 % Allowed : 10.84 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 2072 helix: 1.96 (0.18), residues: 1001 sheet: 2.60 (0.31), residues: 302 loop : 0.12 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.005 0.001 TYR B 286 PHE 0.013 0.001 PHE E 274 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16861) covalent geometry : angle 0.50372 / 0.26 (22849) hydrogen bonds : bond 0.02994 / 2.10 ( 776) hydrogen bonds : angle 3.56341 / 2.98 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.559 Fit side-chains REVERT: C 142 MET cc_start: 0.9345 (mmm) cc_final: 0.8840 (mmm) REVERT: C 383 CYS cc_start: 0.7829 (m) cc_final: 0.7398 (m) REVERT: F 89 ASN cc_start: 0.8820 (t0) cc_final: 0.8345 (t0) REVERT: F 335 MET cc_start: 0.6685 (pmm) cc_final: 0.5936 (tpt) REVERT: B 89 ASN cc_start: 0.9078 (m110) cc_final: 0.8696 (m110) REVERT: B 345 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8811 (tt) REVERT: E 315 ASP cc_start: 0.8333 (p0) cc_final: 0.8099 (p0) REVERT: A 89 ASN cc_start: 0.9044 (t0) cc_final: 0.8675 (t0) REVERT: A 159 CYS cc_start: 0.8216 (p) cc_final: 0.7773 (p) REVERT: A 307 MET cc_start: 0.9543 (mmm) cc_final: 0.9330 (mmt) REVERT: A 345 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8735 (tt) REVERT: A 353 SER cc_start: 0.9328 (m) cc_final: 0.9053 (p) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.1010 time to fit residues: 14.4484 Evaluate side-chains 87 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 177 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 148 optimal weight: 0.0470 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048375 restraints weight = 54330.137| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.53 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16861 Z= 0.126 Angle : 0.491 9.508 22849 Z= 0.253 Chirality : 0.040 0.207 2599 Planarity : 0.003 0.035 2902 Dihedral : 11.715 89.335 2661 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Rotamer: Outliers : 0.47 % Allowed : 10.78 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.20), residues: 2072 helix: 1.92 (0.18), residues: 1001 sheet: 2.65 (0.31), residues: 302 loop : 0.13 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.005 0.001 TYR B 286 PHE 0.013 0.001 PHE E 274 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16861) covalent geometry : angle 0.49086 / 0.25 (22849) hydrogen bonds : bond 0.02858 / 2.00 ( 776) hydrogen bonds : angle 3.50425 / 2.93 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.53 seconds wall clock time: 41 minutes 29.19 seconds (2489.19 seconds total)