Starting phenix.real_space_refine on Fri Jul 3 22:01:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6l_47572/07_2026/9e6l_47572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6l_47572/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6l_47572/07_2026/9e6l_47572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6l_47572/07_2026/9e6l_47572.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6l_47572/07_2026/9e6l_47572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6l_47572/07_2026/9e6l_47572.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.51, 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: 1.01 Conformation dependent library (CDL) restraints added in 535.1 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: 0.52 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: 2.54 Time building geometry restraints manager: 1.36 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- 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 0.51662 / 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 : 0.396 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: 0.1164 time to fit residues: 19.8056 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 : 0.544 ------------------------------------------------------------------------------- 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 ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.048930 restraints weight = 54026.864| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.52 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16861 Z= 0.154 Angle : 0.489 7.444 22849 Z= 0.260 Chirality : 0.040 0.139 2599 Planarity : 0.003 0.045 2902 Dihedral : 12.421 88.857 2661 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.92 % Favored : 99.03 % 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: 2.83 (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 0.00343 / 0.15 (16861) covalent geometry : angle 0.48933 / 0.26 (22849) hydrogen bonds : bond 0.03541 / 2.48 ( 776) hydrogen bonds : angle 3.85563 / 3.18 ( 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 106 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.521 Fit side-chains REVERT: C 307 MET cc_start: 0.9482 (mmm) cc_final: 0.8905 (mmt) REVERT: C 350 MET cc_start: 0.9405 (mmm) cc_final: 0.9204 (tpt) REVERT: C 383 CYS cc_start: 0.7781 (m) cc_final: 0.7434 (m) REVERT: F 89 ASN cc_start: 0.9016 (t0) cc_final: 0.8662 (t0) REVERT: F 335 MET cc_start: 0.6442 (pmm) cc_final: 0.5833 (tpt) REVERT: B 89 ASN cc_start: 0.9106 (m110) cc_final: 0.8692 (m110) REVERT: E 89 ASN cc_start: 0.9132 (m110) cc_final: 0.8913 (m-40) REVERT: A 89 ASN cc_start: 0.9061 (t0) cc_final: 0.8689 (t0) REVERT: A 159 CYS cc_start: 0.8063 (p) cc_final: 0.7670 (p) REVERT: A 345 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8719 (tt) outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 0.1025 time to fit residues: 16.7486 Evaluate side-chains 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 6.9990 chunk 73 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.071813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.047584 restraints weight = 54830.404| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.55 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16861 Z= 0.210 Angle : 0.510 6.612 22849 Z= 0.271 Chirality : 0.041 0.162 2599 Planarity : 0.003 0.043 2902 Dihedral : 11.915 89.948 2661 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.75 % Rotamer: Outliers : 0.59 % Allowed : 6.33 % Favored : 93.09 % 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: 1.93 (0.20), residues: 2072 helix: 1.92 (0.18), residues: 995 sheet: 2.44 (0.30), residues: 294 loop : 0.03 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 154 TYR 0.007 0.001 TYR B 217 PHE 0.015 0.001 PHE A 187 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (16861) covalent geometry : angle 0.51018 / 0.27 (22849) hydrogen bonds : bond 0.03724 / 2.60 ( 776) hydrogen bonds : angle 3.85227 / 3.18 ( 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 98 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.624 Fit side-chains REVERT: C 142 MET cc_start: 0.9179 (mmm) cc_final: 0.8753 (mmm) REVERT: C 350 MET cc_start: 0.9399 (mmm) cc_final: 0.8951 (mmm) REVERT: C 383 CYS cc_start: 0.7764 (m) cc_final: 0.7363 (m) REVERT: F 89 ASN cc_start: 0.9005 (t0) cc_final: 0.8638 (t0) REVERT: F 335 MET cc_start: 0.6769 (pmm) cc_final: 0.6162 (tpt) REVERT: B 89 ASN cc_start: 0.9101 (m110) cc_final: 0.8694 (m110) REVERT: E 89 ASN cc_start: 0.9205 (m110) cc_final: 0.8950 (m-40) REVERT: A 89 ASN cc_start: 0.9024 (t0) cc_final: 0.8639 (t0) REVERT: A 345 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8845 (tt) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.1010 time to fit residues: 15.4014 Evaluate side-chains 85 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 354 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 155 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.047036 restraints weight = 54813.668| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.55 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16861 Z= 0.221 Angle : 0.516 7.825 22849 Z= 0.273 Chirality : 0.041 0.143 2599 Planarity : 0.003 0.041 2902 Dihedral : 11.826 89.918 2661 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Rotamer: Outliers : 0.70 % Allowed : 7.73 % Favored : 91.56 % 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: 1.87 (0.20), residues: 2072 helix: 1.87 (0.18), residues: 995 sheet: 2.39 (0.30), residues: 294 loop : -0.01 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 119 TYR 0.007 0.001 TYR C 217 PHE 0.014 0.001 PHE A 187 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (16861) covalent geometry : angle 0.51642 / 0.27 (22849) hydrogen bonds : bond 0.03649 / 2.55 ( 776) hydrogen bonds : angle 3.86499 / 3.20 ( 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 94 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: C 142 MET cc_start: 0.9174 (mmm) cc_final: 0.8787 (mmm) REVERT: C 350 MET cc_start: 0.9434 (mmm) cc_final: 0.9200 (tpp) REVERT: C 383 CYS cc_start: 0.7786 (m) cc_final: 0.7457 (m) REVERT: F 89 ASN cc_start: 0.9010 (t0) cc_final: 0.8632 (t0) REVERT: B 89 ASN cc_start: 0.9102 (m110) cc_final: 0.8707 (m110) REVERT: A 89 ASN cc_start: 0.9018 (t0) cc_final: 0.8622 (t0) REVERT: A 345 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (tt) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.1151 time to fit residues: 16.3459 Evaluate side-chains 85 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 354 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 138 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 50.0000 chunk 84 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 182 optimal weight: 0.0670 chunk 115 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.073044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.049086 restraints weight = 53735.139| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 4.52 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16861 Z= 0.088 Angle : 0.451 9.632 22849 Z= 0.239 Chirality : 0.039 0.141 2599 Planarity : 0.003 0.037 2902 Dihedral : 11.697 89.586 2661 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.08 % Rotamer: Outliers : 0.70 % Allowed : 8.14 % Favored : 91.15 % 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: 2.02 (0.20), residues: 2072 helix: 1.90 (0.18), residues: 1001 sheet: 2.86 (0.31), residues: 282 loop : 0.05 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 119 TYR 0.004 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 0.00179 / 0.09 (16861) covalent geometry : angle 0.45140 / 0.24 (22849) hydrogen bonds : bond 0.02749 / 1.91 ( 776) hydrogen bonds : angle 3.50031 / 2.93 ( 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 110 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.624 Fit side-chains REVERT: C 142 MET cc_start: 0.9056 (mmm) cc_final: 0.8760 (mmm) REVERT: C 307 MET cc_start: 0.9538 (mmm) cc_final: 0.9334 (mmt) REVERT: C 350 MET cc_start: 0.9430 (mmm) cc_final: 0.9192 (tpp) REVERT: C 383 CYS cc_start: 0.7748 (m) cc_final: 0.7321 (m) REVERT: F 89 ASN cc_start: 0.8962 (t0) cc_final: 0.8560 (t0) REVERT: F 335 MET cc_start: 0.6227 (pmm) cc_final: 0.5408 (tpt) REVERT: B 89 ASN cc_start: 0.9072 (m110) cc_final: 0.8704 (m110) REVERT: B 345 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8745 (tt) REVERT: E 350 MET cc_start: 0.9342 (mmm) cc_final: 0.9083 (tpt) REVERT: E 353 SER cc_start: 0.9470 (m) cc_final: 0.9228 (p) REVERT: A 89 ASN cc_start: 0.9008 (t0) cc_final: 0.8667 (t0) REVERT: A 159 CYS cc_start: 0.8074 (p) cc_final: 0.7658 (p) REVERT: A 345 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 350 MET cc_start: 0.9342 (mmm) cc_final: 0.9088 (tpt) REVERT: A 353 SER cc_start: 0.9261 (m) cc_final: 0.8890 (p) outliers start: 12 outliers final: 2 residues processed: 104 average time/residue: 0.1073 time to fit residues: 18.2131 Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.072196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.048134 restraints weight = 54482.195| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.47 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16861 Z= 0.150 Angle : 0.476 8.381 22849 Z= 0.249 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.043 2902 Dihedral : 11.691 89.948 2661 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.60 % Rotamer: Outliers : 0.59 % Allowed : 8.90 % Favored : 90.51 % 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: 2.05 (0.20), residues: 2072 helix: 1.93 (0.18), residues: 1007 sheet: 2.56 (0.31), residues: 298 loop : 0.14 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 119 TYR 0.005 0.001 TYR D 286 PHE 0.009 0.001 PHE E 274 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16861) covalent geometry : angle 0.47589 / 0.25 (22849) hydrogen bonds : bond 0.03087 / 2.15 ( 776) hydrogen bonds : angle 3.58670 / 3.00 ( 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 99 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.590 Fit side-chains REVERT: C 142 MET cc_start: 0.9129 (mmm) cc_final: 0.8772 (mmm) REVERT: C 383 CYS cc_start: 0.7811 (m) cc_final: 0.7387 (m) REVERT: F 89 ASN cc_start: 0.8949 (t0) cc_final: 0.8528 (t0) REVERT: F 335 MET cc_start: 0.6521 (pmm) cc_final: 0.5758 (tpt) REVERT: B 89 ASN cc_start: 0.9120 (m110) cc_final: 0.8746 (m110) REVERT: B 345 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8849 (tt) REVERT: E 353 SER cc_start: 0.9483 (m) cc_final: 0.9281 (p) REVERT: A 89 ASN cc_start: 0.9043 (t0) cc_final: 0.8663 (t0) REVERT: A 159 CYS cc_start: 0.8186 (p) cc_final: 0.7705 (p) REVERT: A 307 MET cc_start: 0.9554 (mmm) cc_final: 0.9302 (mmt) REVERT: A 345 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 350 MET cc_start: 0.9330 (mmm) cc_final: 0.8728 (mmm) REVERT: A 353 SER cc_start: 0.9344 (m) cc_final: 0.9059 (p) outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 0.1056 time to fit residues: 16.3622 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 91 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 61 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.072216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.048147 restraints weight = 54163.499| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.50 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16861 Z= 0.145 Angle : 0.472 10.525 22849 Z= 0.248 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.040 2902 Dihedral : 11.686 89.392 2661 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.89 % Rotamer: Outliers : 0.59 % Allowed : 9.37 % Favored : 90.04 % 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: 1007 sheet: 2.55 (0.31), residues: 300 loop : 0.13 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 119 TYR 0.006 0.001 TYR D 286 PHE 0.013 0.001 PHE E 274 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16861) covalent geometry : angle 0.47153 / 0.25 (22849) hydrogen bonds : bond 0.02997 / 2.09 ( 776) hydrogen bonds : angle 3.55976 / 2.99 ( 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 95 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.620 Fit side-chains REVERT: C 142 MET cc_start: 0.9108 (mmm) cc_final: 0.8828 (mmm) REVERT: C 350 MET cc_start: 0.9429 (mmm) cc_final: 0.9159 (mmm) REVERT: C 383 CYS cc_start: 0.7793 (m) cc_final: 0.7393 (m) REVERT: F 89 ASN cc_start: 0.8904 (t0) cc_final: 0.8455 (t0) REVERT: F 335 MET cc_start: 0.6688 (pmm) cc_final: 0.6008 (tpt) REVERT: B 89 ASN cc_start: 0.9085 (m110) cc_final: 0.8694 (m110) REVERT: B 345 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8804 (tt) REVERT: E 353 SER cc_start: 0.9474 (m) cc_final: 0.9232 (p) REVERT: A 89 ASN cc_start: 0.9047 (t0) cc_final: 0.8657 (t0) REVERT: A 159 CYS cc_start: 0.8179 (p) cc_final: 0.7743 (p) REVERT: A 307 MET cc_start: 0.9569 (mmm) cc_final: 0.9166 (mmt) REVERT: A 345 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8722 (tt) REVERT: A 350 MET cc_start: 0.9335 (mmm) cc_final: 0.9128 (tpt) REVERT: A 353 SER cc_start: 0.9328 (m) cc_final: 0.9035 (p) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.1040 time to fit residues: 15.5091 Evaluate side-chains 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.072409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.048259 restraints weight = 54603.533| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 4.51 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16861 Z= 0.129 Angle : 0.461 8.066 22849 Z= 0.243 Chirality : 0.040 0.138 2599 Planarity : 0.003 0.038 2902 Dihedral : 11.671 89.240 2661 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.89 % Rotamer: Outliers : 0.59 % Allowed : 9.84 % Favored : 89.57 % 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: 2.09 (0.20), residues: 2072 helix: 1.97 (0.18), residues: 1001 sheet: 2.60 (0.31), residues: 300 loop : 0.15 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 119 TYR 0.006 0.001 TYR D 286 PHE 0.014 0.001 PHE E 274 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16861) covalent geometry : angle 0.46078 / 0.24 (22849) hydrogen bonds : bond 0.02885 / 2.01 ( 776) hydrogen bonds : angle 3.51870 / 2.95 ( 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 97 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.426 Fit side-chains REVERT: C 142 MET cc_start: 0.9088 (mmm) cc_final: 0.8866 (mmm) REVERT: C 383 CYS cc_start: 0.7788 (m) cc_final: 0.7374 (m) REVERT: F 89 ASN cc_start: 0.8893 (t0) cc_final: 0.8439 (t0) REVERT: F 335 MET cc_start: 0.6631 (pmm) cc_final: 0.5973 (tpt) REVERT: B 89 ASN cc_start: 0.9093 (m110) cc_final: 0.8710 (m110) REVERT: B 345 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8787 (tt) REVERT: E 353 SER cc_start: 0.9459 (m) cc_final: 0.9208 (p) REVERT: A 89 ASN cc_start: 0.9043 (t0) cc_final: 0.8663 (t0) REVERT: A 159 CYS cc_start: 0.8176 (p) cc_final: 0.7743 (p) REVERT: A 345 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 353 SER cc_start: 0.9336 (m) cc_final: 0.9011 (p) REVERT: D 350 MET cc_start: 0.9415 (tpp) cc_final: 0.9112 (mmm) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.1031 time to fit residues: 15.7896 Evaluate side-chains 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 84 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 chunk 178 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.071875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.047766 restraints weight = 54471.064| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 4.50 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16861 Z= 0.173 Angle : 0.499 8.513 22849 Z= 0.260 Chirality : 0.040 0.153 2599 Planarity : 0.003 0.036 2902 Dihedral : 11.703 89.820 2661 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Rotamer: Outliers : 0.53 % Allowed : 10.19 % Favored : 89.28 % 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: 2.04 (0.20), residues: 2072 helix: 1.97 (0.18), residues: 1001 sheet: 2.34 (0.31), residues: 308 loop : 0.14 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.004 0.001 TYR C 217 PHE 0.011 0.001 PHE E 274 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (16861) covalent geometry : angle 0.49944 / 0.26 (22849) hydrogen bonds : bond 0.03193 / 2.22 ( 776) hydrogen bonds : angle 3.64008 / 3.04 ( 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 91 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.608 Fit side-chains REVERT: C 142 MET cc_start: 0.9099 (mmm) cc_final: 0.8842 (mmm) REVERT: C 383 CYS cc_start: 0.7821 (m) cc_final: 0.7396 (m) REVERT: F 89 ASN cc_start: 0.8911 (t0) cc_final: 0.8444 (t0) REVERT: F 335 MET cc_start: 0.6700 (pmm) cc_final: 0.6024 (tpt) REVERT: B 89 ASN cc_start: 0.9102 (m110) cc_final: 0.8720 (m110) REVERT: B 345 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8820 (tt) REVERT: E 353 SER cc_start: 0.9460 (m) cc_final: 0.9223 (p) REVERT: A 89 ASN cc_start: 0.9043 (t0) cc_final: 0.8654 (t0) REVERT: A 159 CYS cc_start: 0.8283 (p) cc_final: 0.7837 (p) REVERT: A 353 SER cc_start: 0.9330 (m) cc_final: 0.8991 (p) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.0966 time to fit residues: 14.3778 Evaluate side-chains 88 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 338 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 159 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 195 optimal weight: 0.2980 chunk 175 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.073022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.048903 restraints weight = 54158.102| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.47 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1753 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= 0.102 Angle : 0.479 9.618 22849 Z= 0.247 Chirality : 0.040 0.181 2599 Planarity : 0.003 0.036 2902 Dihedral : 11.664 88.907 2661 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.13 % Rotamer: Outliers : 0.29 % Allowed : 10.60 % Favored : 89.10 % 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: 2.12 (0.20), residues: 2072 helix: 1.93 (0.18), residues: 1001 sheet: 2.80 (0.31), residues: 298 loop : 0.18 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 308 TYR 0.004 0.001 TYR D 286 PHE 0.013 0.001 PHE E 274 HIS 0.002 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (16861) covalent geometry : angle 0.47903 / 0.25 (22849) hydrogen bonds : bond 0.02655 / 1.84 ( 776) hydrogen bonds : angle 3.48083 / 2.92 ( 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 93 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.529 Fit side-chains REVERT: C 142 MET cc_start: 0.9090 (mmm) cc_final: 0.8887 (mmm) REVERT: C 383 CYS cc_start: 0.7822 (m) cc_final: 0.7374 (m) REVERT: F 89 ASN cc_start: 0.8838 (t0) cc_final: 0.8348 (t0) REVERT: F 335 MET cc_start: 0.6685 (pmm) cc_final: 0.6043 (tpt) REVERT: B 89 ASN cc_start: 0.9048 (m110) cc_final: 0.8761 (m-40) REVERT: B 345 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8748 (tt) REVERT: E 353 SER cc_start: 0.9425 (m) cc_final: 0.9182 (p) REVERT: A 89 ASN cc_start: 0.9049 (t0) cc_final: 0.8661 (t0) REVERT: A 159 CYS cc_start: 0.8143 (p) cc_final: 0.7715 (p) REVERT: A 293 ARG cc_start: 0.3901 (ttt180) cc_final: 0.3684 (ttt180) REVERT: A 353 SER cc_start: 0.9248 (m) cc_final: 0.8979 (p) REVERT: D 277 ILE cc_start: 0.9061 (mt) cc_final: 0.8839 (tt) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.1042 time to fit residues: 15.6536 Evaluate side-chains 88 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 338 ASN Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 177 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.072112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048076 restraints weight = 54494.312| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 4.46 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 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 : 0.004 0.041 16861 Z= 0.165 Angle : 0.514 10.821 22849 Z= 0.262 Chirality : 0.040 0.158 2599 Planarity : 0.003 0.034 2902 Dihedral : 11.686 89.752 2661 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % Rotamer: Outliers : 0.53 % Allowed : 10.66 % Favored : 88.81 % 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: 2.09 (0.20), residues: 2072 helix: 1.97 (0.18), residues: 1001 sheet: 2.44 (0.31), residues: 310 loop : 0.18 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 119 TYR 0.004 0.001 TYR B 286 PHE 0.011 0.001 PHE E 274 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (16861) covalent geometry : angle 0.51358 / 0.26 (22849) hydrogen bonds : bond 0.03113 / 2.19 ( 776) hydrogen bonds : angle 3.61093 / 3.02 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.60 seconds wall clock time: 42 minutes 29.31 seconds (2549.31 seconds total)