Starting phenix.real_space_refine on Sun May 18 03:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6l_47572/05_2025/9e6l_47572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6l_47572/05_2025/9e6l_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_47572/05_2025/9e6l_47572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6l_47572/05_2025/9e6l_47572.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6l_47572/05_2025/9e6l_47572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6l_47572/05_2025/9e6l_47572.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ASP:plan': 2} 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: 10.22, per 1000 atoms: 0.62 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: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.85 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: 5.27 Time building geometry restraints manager: 4.47 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=" 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=" 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 bond pdb=" N ARG B 153 " pdb=" CA ARG B 153 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.23e+00 bond pdb=" N ARG B 154 " pdb=" CA ARG B 154 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.28e-02 6.10e+03 4.07e+00 bond pdb=" N ARG H 119 " pdb=" CA ARG H 119 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 3.93e+00 ... (remaining 16856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 22531 1.90 - 3.81: 275 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: 2088 0.045 - 0.090: 345 0.090 - 0.135: 161 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 400 or resid 501 through 502)) selection = (chain 'B' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'C' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'D' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'E' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'F' and (resid 81 through 400 or resid 501 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.100 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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= 0.105 Angle : 0.500 9.521 22849 Z= 0.285 Chirality : 0.040 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (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 HIS 0.002 0.000 HIS C 257 PHE 0.022 0.001 PHE A 187 TYR 0.005 0.001 TYR D 217 ARG 0.002 0.000 ARG F 308 Details of bonding type rmsd hydrogen bonds : bond 0.14964 ( 776) hydrogen bonds : angle 4.70021 ( 2172) covalent geometry : bond 0.00196 (16861) covalent geometry : angle 0.49976 (22849) *********************** 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 : 1.882 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: 0.2774 time to fit residues: 47.3727 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 : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 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 = 0.3317 r_free = 0.3317 target = 0.072008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.047716 restraints weight = 54476.379| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.55 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16861 Z= 0.232 Angle : 0.536 8.982 22849 Z= 0.282 Chirality : 0.042 0.142 2599 Planarity : 0.003 0.055 2902 Dihedral : 12.088 88.170 2661 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % Rotamer: Outliers : 0.47 % Allowed : 4.86 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.20), residues: 2072 helix: 1.89 (0.18), residues: 995 sheet: 2.44 (0.30), residues: 294 loop : 0.05 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 105 PHE 0.017 0.001 PHE A 187 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 776) hydrogen bonds : angle 4.04488 ( 2172) covalent geometry : bond 0.00533 (16861) covalent geometry : angle 0.53552 (22849) *********************** 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 100 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.905 Fit side-chains REVERT: C 383 CYS cc_start: 0.7781 (m) cc_final: 0.7418 (m) REVERT: F 89 ASN cc_start: 0.8984 (t0) cc_final: 0.8641 (t0) REVERT: F 335 MET cc_start: 0.6386 (pmm) cc_final: 0.5706 (tpt) REVERT: B 89 ASN cc_start: 0.9115 (m110) cc_final: 0.8724 (m110) REVERT: E 89 ASN cc_start: 0.9205 (m110) cc_final: 0.8993 (m-40) REVERT: A 89 ASN cc_start: 0.9049 (t0) cc_final: 0.8701 (t0) REVERT: A 345 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8716 (tt) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.2487 time to fit residues: 39.1868 Evaluate side-chains 85 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain A residue 198 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 195 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 116 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.073304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047768 restraints weight = 54761.058| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 4.70 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16861 Z= 0.128 Angle : 0.455 5.709 22849 Z= 0.242 Chirality : 0.040 0.130 2599 Planarity : 0.003 0.042 2902 Dihedral : 11.548 89.917 2661 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.99 % Rotamer: Outliers : 0.41 % Allowed : 6.44 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 2072 helix: 1.89 (0.18), residues: 997 sheet: 2.77 (0.30), residues: 282 loop : 0.08 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 257 PHE 0.015 0.001 PHE A 187 TYR 0.007 0.001 TYR D 286 ARG 0.007 0.000 ARG J 119 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 776) hydrogen bonds : angle 3.63990 ( 2172) covalent geometry : bond 0.00287 (16861) covalent geometry : angle 0.45513 (22849) *********************** 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 104 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.875 Fit side-chains REVERT: C 142 MET cc_start: 0.9089 (mmm) cc_final: 0.8788 (mmm) REVERT: C 383 CYS cc_start: 0.7758 (m) cc_final: 0.7345 (m) REVERT: F 89 ASN cc_start: 0.8945 (t0) cc_final: 0.8574 (t0) REVERT: F 335 MET cc_start: 0.6746 (pmm) cc_final: 0.6158 (tpt) REVERT: B 89 ASN cc_start: 0.9080 (m110) cc_final: 0.8674 (m110) REVERT: E 89 ASN cc_start: 0.9150 (m110) cc_final: 0.8889 (m-40) REVERT: A 89 ASN cc_start: 0.9024 (t0) cc_final: 0.8641 (t0) REVERT: A 159 CYS cc_start: 0.8103 (p) cc_final: 0.7723 (p) REVERT: A 345 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8854 (tt) REVERT: A 353 SER cc_start: 0.9273 (m) cc_final: 0.8964 (p) REVERT: D 345 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8652 (pt) outliers start: 7 outliers final: 1 residues processed: 98 average time/residue: 0.2582 time to fit residues: 41.3079 Evaluate side-chains 88 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 174 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 42 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.047028 restraints weight = 55008.434| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.48 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16861 Z= 0.239 Angle : 0.534 7.819 22849 Z= 0.282 Chirality : 0.042 0.139 2599 Planarity : 0.003 0.039 2902 Dihedral : 11.631 89.993 2661 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.55 % Rotamer: Outliers : 0.70 % Allowed : 7.50 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.20), residues: 2072 helix: 1.90 (0.18), residues: 995 sheet: 2.47 (0.31), residues: 294 loop : 0.02 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 257 PHE 0.015 0.001 PHE A 187 TYR 0.006 0.001 TYR D 286 ARG 0.005 0.000 ARG H 119 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 776) hydrogen bonds : angle 3.94132 ( 2172) covalent geometry : bond 0.00548 (16861) covalent geometry : angle 0.53425 (22849) *********************** 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 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.831 Fit side-chains REVERT: C 142 MET cc_start: 0.9023 (mmm) cc_final: 0.8774 (mmm) REVERT: C 383 CYS cc_start: 0.7796 (m) cc_final: 0.7454 (m) REVERT: F 89 ASN cc_start: 0.9007 (t0) cc_final: 0.8579 (t0) REVERT: F 335 MET cc_start: 0.6922 (pmm) cc_final: 0.6415 (tpt) REVERT: B 89 ASN cc_start: 0.9087 (m110) cc_final: 0.8699 (m110) REVERT: A 89 ASN cc_start: 0.9012 (t0) cc_final: 0.8634 (t0) REVERT: A 345 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8858 (tt) outliers start: 12 outliers final: 5 residues processed: 88 average time/residue: 0.2716 time to fit residues: 38.8601 Evaluate side-chains 81 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 ASN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.047529 restraints weight = 54475.477| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.54 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 16861 Z= 0.156 Angle : 0.474 6.602 22849 Z= 0.250 Chirality : 0.040 0.131 2599 Planarity : 0.003 0.036 2902 Dihedral : 11.550 89.726 2661 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.75 % Rotamer: Outliers : 0.47 % Allowed : 8.67 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 2072 helix: 1.90 (0.18), residues: 999 sheet: 2.54 (0.31), residues: 294 loop : 0.05 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 257 PHE 0.011 0.001 PHE D 187 TYR 0.004 0.001 TYR B 286 ARG 0.004 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 776) hydrogen bonds : angle 3.67650 ( 2172) covalent geometry : bond 0.00354 (16861) covalent geometry : angle 0.47387 (22849) *********************** 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 96 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.753 Fit side-chains REVERT: C 142 MET cc_start: 0.9004 (mmm) cc_final: 0.8769 (mmm) REVERT: C 383 CYS cc_start: 0.7748 (m) cc_final: 0.7338 (m) REVERT: F 89 ASN cc_start: 0.8970 (t0) cc_final: 0.8537 (t0) REVERT: F 335 MET cc_start: 0.6960 (pmm) cc_final: 0.6511 (tpt) REVERT: B 89 ASN cc_start: 0.9067 (m110) cc_final: 0.8702 (m110) REVERT: E 353 SER cc_start: 0.9482 (m) cc_final: 0.9192 (p) REVERT: A 89 ASN cc_start: 0.9006 (t0) cc_final: 0.8699 (t0) REVERT: A 159 CYS cc_start: 0.8243 (p) cc_final: 0.7758 (p) REVERT: A 345 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 350 MET cc_start: 0.9442 (mmm) cc_final: 0.9175 (tpt) REVERT: A 353 SER cc_start: 0.9252 (m) cc_final: 0.8954 (p) outliers start: 8 outliers final: 2 residues processed: 93 average time/residue: 0.2522 time to fit residues: 38.2829 Evaluate side-chains 84 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 125 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 64 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 144 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.044594 restraints weight = 56586.200| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 4.67 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 16861 Z= 0.355 Angle : 0.633 10.246 22849 Z= 0.330 Chirality : 0.044 0.148 2599 Planarity : 0.004 0.050 2902 Dihedral : 11.779 87.437 2661 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % Rotamer: Outliers : 0.53 % Allowed : 9.78 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2072 helix: 1.74 (0.18), residues: 983 sheet: 2.28 (0.31), residues: 294 loop : -0.11 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 196 PHE 0.011 0.001 PHE A 360 TYR 0.006 0.001 TYR C 217 ARG 0.006 0.001 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 776) hydrogen bonds : angle 4.30897 ( 2172) covalent geometry : bond 0.00810 (16861) covalent geometry : angle 0.63280 (22849) *********************** 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 84 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.825 Fit side-chains REVERT: C 315 ASP cc_start: 0.8498 (m-30) cc_final: 0.8228 (m-30) REVERT: C 383 CYS cc_start: 0.7780 (m) cc_final: 0.7458 (m) REVERT: B 89 ASN cc_start: 0.9205 (m110) cc_final: 0.8854 (m110) REVERT: B 301 MET cc_start: 0.8666 (tpt) cc_final: 0.8376 (tmm) REVERT: A 89 ASN cc_start: 0.9078 (t0) cc_final: 0.8673 (t0) REVERT: A 345 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8830 (tt) REVERT: A 350 MET cc_start: 0.9479 (mmm) cc_final: 0.9239 (tpt) REVERT: A 353 SER cc_start: 0.9317 (m) cc_final: 0.9027 (p) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.2482 time to fit residues: 34.4784 Evaluate side-chains 80 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.047469 restraints weight = 54607.899| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 4.50 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16861 Z= 0.139 Angle : 0.476 7.534 22849 Z= 0.252 Chirality : 0.040 0.133 2599 Planarity : 0.003 0.046 2902 Dihedral : 11.599 89.778 2661 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.59 % Allowed : 9.78 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.20), residues: 2072 helix: 1.85 (0.18), residues: 997 sheet: 2.70 (0.31), residues: 282 loop : 0.03 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 257 PHE 0.007 0.001 PHE F 317 TYR 0.003 0.001 TYR F 217 ARG 0.004 0.000 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 776) hydrogen bonds : angle 3.69684 ( 2172) covalent geometry : bond 0.00314 (16861) covalent geometry : angle 0.47607 (22849) *********************** 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 96 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.862 Fit side-chains REVERT: C 142 MET cc_start: 0.9446 (mmm) cc_final: 0.8757 (mmm) REVERT: C 383 CYS cc_start: 0.7706 (m) cc_final: 0.7356 (m) REVERT: F 312 ARG cc_start: 0.8405 (mpt-90) cc_final: 0.8151 (mmt90) REVERT: F 335 MET cc_start: 0.6478 (pmm) cc_final: 0.5667 (tpt) REVERT: B 89 ASN cc_start: 0.9165 (m110) cc_final: 0.8815 (m110) REVERT: A 89 ASN cc_start: 0.9081 (t0) cc_final: 0.8703 (t0) REVERT: A 159 CYS cc_start: 0.8180 (p) cc_final: 0.7672 (p) REVERT: A 345 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 350 MET cc_start: 0.9423 (mmm) cc_final: 0.9213 (tpt) REVERT: A 353 SER cc_start: 0.9245 (m) cc_final: 0.8960 (p) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.2621 time to fit residues: 39.6575 Evaluate side-chains 88 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 354 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.047050 restraints weight = 54666.014| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.42 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 16861 Z= 0.203 Angle : 0.521 7.665 22849 Z= 0.272 Chirality : 0.041 0.135 2599 Planarity : 0.003 0.045 2902 Dihedral : 11.597 89.243 2661 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.59 % Allowed : 10.08 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 2072 helix: 1.88 (0.18), residues: 991 sheet: 2.32 (0.31), residues: 294 loop : -0.02 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 257 PHE 0.006 0.001 PHE A 360 TYR 0.004 0.001 TYR F 217 ARG 0.004 0.000 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 776) hydrogen bonds : angle 3.82176 ( 2172) covalent geometry : bond 0.00464 (16861) covalent geometry : angle 0.52132 (22849) *********************** 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 95 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.716 Fit side-chains REVERT: C 142 MET cc_start: 0.9391 (mmm) cc_final: 0.8958 (mmm) REVERT: C 315 ASP cc_start: 0.8368 (m-30) cc_final: 0.8085 (m-30) REVERT: C 383 CYS cc_start: 0.7785 (m) cc_final: 0.7418 (m) REVERT: F 312 ARG cc_start: 0.8402 (mpt-90) cc_final: 0.8131 (mmt90) REVERT: F 335 MET cc_start: 0.6554 (pmm) cc_final: 0.5757 (tpt) REVERT: B 89 ASN cc_start: 0.9166 (m110) cc_final: 0.8826 (m110) REVERT: B 345 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8807 (tt) REVERT: E 350 MET cc_start: 0.9192 (mmm) cc_final: 0.8948 (mmm) REVERT: A 89 ASN cc_start: 0.9092 (t0) cc_final: 0.8736 (t0) REVERT: A 345 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8800 (tt) REVERT: A 353 SER cc_start: 0.9276 (m) cc_final: 0.8982 (p) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.2434 time to fit residues: 36.4200 Evaluate side-chains 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain 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 130 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.047713 restraints weight = 54675.776| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.63 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16861 Z= 0.166 Angle : 0.504 8.282 22849 Z= 0.262 Chirality : 0.040 0.141 2599 Planarity : 0.003 0.045 2902 Dihedral : 11.565 89.841 2661 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.64 % Allowed : 10.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.20), residues: 2072 helix: 1.88 (0.18), residues: 995 sheet: 2.60 (0.31), residues: 286 loop : 0.00 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 196 PHE 0.007 0.001 PHE D 317 TYR 0.004 0.001 TYR A 217 ARG 0.004 0.000 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 776) hydrogen bonds : angle 3.72246 ( 2172) covalent geometry : bond 0.00378 (16861) covalent geometry : angle 0.50362 (22849) *********************** 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 97 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.708 Fit side-chains REVERT: C 142 MET cc_start: 0.9325 (mmm) cc_final: 0.8869 (mmm) REVERT: C 315 ASP cc_start: 0.8342 (m-30) cc_final: 0.8070 (m-30) REVERT: C 383 CYS cc_start: 0.7732 (m) cc_final: 0.7403 (m) REVERT: F 312 ARG cc_start: 0.8416 (mpt-90) cc_final: 0.8142 (mmt90) REVERT: F 335 MET cc_start: 0.6513 (pmm) cc_final: 0.5794 (tpt) REVERT: B 89 ASN cc_start: 0.9175 (m110) cc_final: 0.8836 (m110) REVERT: B 345 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8904 (tt) REVERT: E 350 MET cc_start: 0.9125 (mmm) cc_final: 0.8898 (mmm) REVERT: A 89 ASN cc_start: 0.9095 (t0) cc_final: 0.8742 (t0) REVERT: A 159 CYS cc_start: 0.8128 (p) cc_final: 0.7640 (p) REVERT: A 353 SER cc_start: 0.9279 (m) cc_final: 0.8961 (p) outliers start: 11 outliers final: 8 residues processed: 93 average time/residue: 0.2521 time to fit residues: 38.3287 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 345 ILE 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 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 123 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.047542 restraints weight = 54846.716| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.56 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16861 Z= 0.186 Angle : 0.528 8.875 22849 Z= 0.272 Chirality : 0.040 0.136 2599 Planarity : 0.003 0.045 2902 Dihedral : 11.562 89.472 2661 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.59 % Allowed : 10.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 2072 helix: 1.86 (0.18), residues: 995 sheet: 2.39 (0.31), residues: 296 loop : -0.02 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 352 PHE 0.006 0.001 PHE D 317 TYR 0.004 0.001 TYR A 217 ARG 0.003 0.000 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 776) hydrogen bonds : angle 3.74881 ( 2172) covalent geometry : bond 0.00426 (16861) covalent geometry : angle 0.52814 (22849) ********************** 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 92 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.718 Fit side-chains REVERT: C 142 MET cc_start: 0.9307 (mmm) cc_final: 0.8690 (mmm) REVERT: C 315 ASP cc_start: 0.8362 (m-30) cc_final: 0.8092 (m-30) REVERT: C 383 CYS cc_start: 0.7744 (m) cc_final: 0.7424 (m) REVERT: F 312 ARG cc_start: 0.8418 (mpt-90) cc_final: 0.8186 (mmt90) REVERT: F 335 MET cc_start: 0.6451 (pmm) cc_final: 0.5745 (tpt) REVERT: B 89 ASN cc_start: 0.9146 (m110) cc_final: 0.8800 (m110) REVERT: B 345 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8931 (tt) REVERT: E 315 ASP cc_start: 0.8379 (p0) cc_final: 0.8166 (p0) REVERT: E 350 MET cc_start: 0.9140 (mmm) cc_final: 0.8905 (mmm) REVERT: A 89 ASN cc_start: 0.9104 (t0) cc_final: 0.8749 (t0) REVERT: A 159 CYS cc_start: 0.8140 (p) cc_final: 0.7651 (p) REVERT: A 353 SER cc_start: 0.9327 (m) cc_final: 0.9051 (p) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.2466 time to fit residues: 36.1005 Evaluate side-chains 90 residues out of total 1713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 345 ILE 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 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 194 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048014 restraints weight = 54819.310| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.63 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16861 Z= 0.146 Angle : 0.513 10.776 22849 Z= 0.262 Chirality : 0.040 0.137 2599 Planarity : 0.003 0.043 2902 Dihedral : 11.517 89.834 2661 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.47 % Allowed : 10.60 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 2072 helix: 1.88 (0.18), residues: 995 sheet: 2.70 (0.31), residues: 288 loop : 0.02 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 196 PHE 0.006 0.001 PHE F 317 TYR 0.004 0.001 TYR D 286 ARG 0.002 0.000 ARG I 119 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 776) hydrogen bonds : angle 3.61720 ( 2172) covalent geometry : bond 0.00332 (16861) covalent geometry : angle 0.51292 (22849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5525.21 seconds wall clock time: 97 minutes 15.98 seconds (5835.98 seconds total)