Starting phenix.real_space_refine on Mon Sep 14 15:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbl_13294/09_2026/7pbl_13294.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 45 5.49 5 Mg 3 5.21 5 S 100 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3148 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31318 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.15 Number of scatterers: 31318 At special positions: 0 Unit cell: (124.26, 138.43, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 45 15.00 Mg 3 11.99 O 3148 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 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: 2.23 Conformation dependent library (CDL) restraints added in 751.6 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 19 sheets defined 59.5% alpha, 11.2% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.607A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.654A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.631A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.894A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.760A pdb=" N MET A 163 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.765A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.576A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.614A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.514A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 3.615A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.623A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.552A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.782A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.598A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.566A pdb=" N MET B 115 " --> pdb=" O ILE B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.566A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.506A pdb=" N ASP B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.598A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.512A pdb=" N TYR B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.553A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.659A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.619A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 removed outlier: 3.511A pdb=" N MET C 115 " --> pdb=" O ILE C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 116 through 130 removed outlier: 4.004A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 212 removed outlier: 3.586A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.697A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.783A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.738A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.511A pdb=" N ALA D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.706A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.667A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.588A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.093A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.676A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 removed outlier: 3.558A pdb=" N TYR D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.661A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.516A pdb=" N TYR D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.736A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.573A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.726A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.587A pdb=" N GLU E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.830A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 removed outlier: 3.527A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.819A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 297 Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.545A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.574A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.696A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.627A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.521A pdb=" N LEU F 164 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.543A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 56 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.457A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.409A pdb=" N LYS C 81 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP C 110 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C 83 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 56 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.258A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 137 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.557A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 201 removed outlier: 6.988A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB8, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.295A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'F' and resid 308 through 311 752 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.33 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15439 1.06 - 1.28: 2655 1.28 - 1.50: 6776 1.50 - 1.73: 6592 1.73 - 1.95: 197 Bond restraints: 31659 Sorted by residual: bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 56733 2.17 - 4.35: 505 4.35 - 6.52: 42 6.52 - 8.69: 16 8.69 - 10.87: 11 Bond angle restraints: 57307 Sorted by residual: angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.72 4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 110.99 -2.99 7.00e-01 2.04e+00 1.83e+01 angle pdb=" C4' DT V 15 " pdb=" O4' DT V 15 " pdb=" C1' DT V 15 " ideal model delta sigma weight residual 110.10 105.98 4.12 1.00e+00 1.00e+00 1.70e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.56e+01 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 14130 31.95 - 63.90: 561 63.90 - 95.84: 41 95.84 - 127.79: 1 127.79 - 159.74: 2 Dihedral angle restraints: 14735 sinusoidal: 8466 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 99.74 -159.74 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 81.44 -141.44 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 36.91 -96.91 1 2.00e+01 2.50e-03 2.69e+01 ... (remaining 14732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2210 0.074 - 0.148: 260 0.148 - 0.221: 14 0.221 - 0.295: 3 0.295 - 0.369: 1 Chirality restraints: 2488 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.70 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.143 9.50e-02 1.11e+02 6.44e-02 4.44e+01 pdb=" NE ARG A 192 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 192 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 192 " -0.051 2.00e-02 2.50e+03 pdb="HH21 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 192 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 232 " -0.044 2.00e-02 2.50e+03 5.42e-02 4.40e+01 pdb=" CD GLN D 232 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN D 232 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN D 232 " 0.085 2.00e-02 2.50e+03 pdb="HE21 GLN D 232 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 232 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.043 2.00e-02 2.50e+03 5.29e-02 4.20e+01 pdb=" CD GLN C 31 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.083 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.081 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 567 2.11 - 2.73: 52994 2.73 - 3.35: 83924 3.35 - 3.98: 106426 3.98 - 4.60: 172380 Nonbonded interactions: 416291 Sorted by model distance: nonbonded pdb=" OE1 GLU D 121 " pdb=" HH TYR D 124 " model vdw 1.487 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.518 2.450 nonbonded pdb=" HZ1 LYS F 81 " pdb=" O ASP F 100 " model vdw 1.543 2.450 nonbonded pdb=" HZ3 LYS E 90 " pdb=" OD1 ASP E 93 " model vdw 1.562 2.450 nonbonded pdb=" O ALA F 138 " pdb=" HG1 THR F 141 " model vdw 1.569 2.450 ... (remaining 416286 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 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 3.000 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: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.910 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.005 0.101 16220 Z= 0.256 Angle : 0.773 10.868 22091 Z= 0.444 Chirality : 0.047 0.369 2488 Planarity : 0.010 0.132 2739 Dihedral : 15.024 159.741 6323 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 1902 helix: -0.88 (0.14), residues: 1009 sheet: 0.16 (0.28), residues: 322 loop : 0.57 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.003 ARG F 312 TYR 0.036 0.005 TYR E 131 PHE 0.018 0.003 PHE F 25 HIS 0.013 0.003 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.26 (16220) covalent geometry : angle 0.77271 / 0.44 (22091) hydrogen bonds : bond 0.24952 / 16.56 ( 779) hydrogen bonds : angle 8.33347 / 5.83 ( 2223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 256 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 49 ASP cc_start: 0.7646 (t0) cc_final: 0.7397 (t0) REVERT: C 124 TYR cc_start: 0.8404 (p90) cc_final: 0.8159 (p90) REVERT: D 245 ASP cc_start: 0.7716 (m-30) cc_final: 0.7297 (m-30) REVERT: D 250 MET cc_start: 0.8836 (ttp) cc_final: 0.8600 (ttp) REVERT: D 290 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 305 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8256 (mtpp) REVERT: D 309 MET cc_start: 0.8673 (mtp) cc_final: 0.8459 (mtm) REVERT: E 135 MET cc_start: 0.1184 (mtm) cc_final: 0.0910 (mtm) REVERT: E 291 ARG cc_start: 0.8214 (ptm-80) cc_final: 0.7851 (ptm160) REVERT: F 125 SER cc_start: 0.9078 (m) cc_final: 0.8856 (p) REVERT: F 222 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8301 (ttm-80) REVERT: F 236 ASP cc_start: 0.7209 (m-30) cc_final: 0.6636 (p0) outliers start: 1 outliers final: 1 residues processed: 427 average time/residue: 0.3410 time to fit residues: 201.9704 Evaluate side-chains 276 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 286 ASN C 82 GLN D 82 GLN E 31 GLN F 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081420 restraints weight = 73142.526| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.58 r_work: 0.2788 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16220 Z= 0.216 Angle : 0.687 6.871 22091 Z= 0.373 Chirality : 0.044 0.151 2488 Planarity : 0.006 0.050 2739 Dihedral : 14.507 147.048 2599 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.31 % Allowed : 6.61 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1902 helix: 0.39 (0.16), residues: 1028 sheet: 0.58 (0.31), residues: 282 loop : 0.39 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 267 TYR 0.025 0.001 TYR C 124 PHE 0.007 0.001 PHE C 25 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (16220) covalent geometry : angle 0.68730 / 0.37 (22091) hydrogen bonds : bond 0.07854 / 5.29 ( 779) hydrogen bonds : angle 5.97137 / 4.15 ( 2223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8451 (mm-30) REVERT: A 295 GLU cc_start: 0.8376 (tt0) cc_final: 0.8000 (tp30) REVERT: C 81 LYS cc_start: 0.8555 (mptt) cc_final: 0.8046 (mttt) REVERT: D 252 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (t70) REVERT: D 290 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 135 MET cc_start: 0.1234 (mtm) cc_final: 0.0670 (mtm) REVERT: E 252 ASP cc_start: 0.9027 (t0) cc_final: 0.8733 (t0) REVERT: E 290 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7479 (mm-30) REVERT: F 105 ASP cc_start: 0.8384 (m-30) cc_final: 0.8112 (m-30) REVERT: F 120 GLU cc_start: 0.8649 (tt0) cc_final: 0.8363 (tt0) REVERT: F 125 SER cc_start: 0.9184 (m) cc_final: 0.8980 (p) REVERT: F 222 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8415 (ttm-80) REVERT: F 236 ASP cc_start: 0.7802 (m-30) cc_final: 0.7021 (p0) outliers start: 21 outliers final: 10 residues processed: 297 average time/residue: 0.3258 time to fit residues: 136.4385 Evaluate side-chains 271 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 44 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 134 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.082612 restraints weight = 73053.222| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.59 r_work: 0.2812 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16220 Z= 0.130 Angle : 0.583 9.218 22091 Z= 0.306 Chirality : 0.041 0.138 2488 Planarity : 0.004 0.038 2739 Dihedral : 13.976 145.107 2599 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.87 % Allowed : 7.99 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1902 helix: 0.79 (0.16), residues: 1029 sheet: 0.69 (0.31), residues: 280 loop : 0.48 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.006 0.001 PHE C 197 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (16220) covalent geometry : angle 0.58266 / 0.31 (22091) hydrogen bonds : bond 0.06273 / 4.25 ( 779) hydrogen bonds : angle 5.40230 / 3.73 ( 2223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 295 GLU cc_start: 0.8433 (tt0) cc_final: 0.7981 (tp30) REVERT: A 309 MET cc_start: 0.8519 (ttm) cc_final: 0.8187 (ttp) REVERT: C 81 LYS cc_start: 0.8563 (mptt) cc_final: 0.8058 (mttt) REVERT: C 272 MET cc_start: 0.8723 (mtp) cc_final: 0.8453 (mtp) REVERT: E 135 MET cc_start: 0.1139 (mtm) cc_final: 0.0809 (mtm) REVERT: E 171 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8234 (mmm-85) REVERT: E 252 ASP cc_start: 0.9031 (t0) cc_final: 0.8716 (t0) REVERT: E 290 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7505 (mm-30) REVERT: F 105 ASP cc_start: 0.8379 (m-30) cc_final: 0.8098 (m-30) REVERT: F 222 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8397 (ttm-80) REVERT: F 236 ASP cc_start: 0.7879 (m-30) cc_final: 0.7061 (p0) outliers start: 14 outliers final: 11 residues processed: 281 average time/residue: 0.3321 time to fit residues: 131.6175 Evaluate side-chains 265 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.082261 restraints weight = 73090.897| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.56 r_work: 0.2803 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16220 Z= 0.148 Angle : 0.574 6.221 22091 Z= 0.301 Chirality : 0.041 0.142 2488 Planarity : 0.004 0.038 2739 Dihedral : 13.773 145.998 2599 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.19 % Allowed : 8.36 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1902 helix: 0.97 (0.17), residues: 1030 sheet: 0.73 (0.31), residues: 274 loop : 0.41 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.014 0.001 PHE E 152 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16220) covalent geometry : angle 0.57366 / 0.30 (22091) hydrogen bonds : bond 0.05505 / 3.74 ( 779) hydrogen bonds : angle 5.16397 / 3.56 ( 2223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8447 (mm-30) REVERT: A 295 GLU cc_start: 0.8480 (tt0) cc_final: 0.8063 (tp30) REVERT: A 309 MET cc_start: 0.8562 (ttm) cc_final: 0.8234 (ttp) REVERT: B 144 SER cc_start: 0.8399 (p) cc_final: 0.7658 (t) REVERT: B 178 MET cc_start: 0.9400 (mmt) cc_final: 0.9197 (mmt) REVERT: C 81 LYS cc_start: 0.8629 (mptt) cc_final: 0.8172 (mttt) REVERT: C 272 MET cc_start: 0.8741 (mtp) cc_final: 0.8462 (mtp) REVERT: D 252 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7393 (t0) REVERT: E 127 MET cc_start: 0.8122 (mtm) cc_final: 0.7918 (mtm) REVERT: E 135 MET cc_start: 0.1141 (mtm) cc_final: 0.0791 (mtm) REVERT: E 171 ARG cc_start: 0.8447 (mmt-90) cc_final: 0.8145 (mmm-85) REVERT: E 252 ASP cc_start: 0.9089 (t0) cc_final: 0.8827 (t0) REVERT: E 290 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7491 (mm-30) REVERT: F 105 ASP cc_start: 0.8411 (m-30) cc_final: 0.8103 (m-30) REVERT: F 120 GLU cc_start: 0.8681 (tt0) cc_final: 0.8394 (tt0) REVERT: F 236 ASP cc_start: 0.7973 (m-30) cc_final: 0.7153 (p0) outliers start: 19 outliers final: 15 residues processed: 280 average time/residue: 0.3534 time to fit residues: 140.0791 Evaluate side-chains 270 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 HIS D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.081914 restraints weight = 73245.620| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.54 r_work: 0.2804 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16220 Z= 0.152 Angle : 0.562 6.141 22091 Z= 0.295 Chirality : 0.040 0.146 2488 Planarity : 0.004 0.039 2739 Dihedral : 13.684 148.636 2599 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.94 % Allowed : 9.11 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1902 helix: 1.09 (0.17), residues: 1029 sheet: 0.62 (0.31), residues: 272 loop : 0.30 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.006 0.001 PHE F 108 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16220) covalent geometry : angle 0.56208 / 0.30 (22091) hydrogen bonds : bond 0.05243 / 3.57 ( 779) hydrogen bonds : angle 5.00019 / 3.42 ( 2223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8522 (tt0) cc_final: 0.8182 (tp30) REVERT: A 309 MET cc_start: 0.8544 (ttm) cc_final: 0.8210 (ttp) REVERT: B 105 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8823 (m-30) REVERT: C 81 LYS cc_start: 0.8634 (mptt) cc_final: 0.8179 (mttt) REVERT: C 272 MET cc_start: 0.8704 (mtp) cc_final: 0.8408 (mtp) REVERT: D 252 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7398 (t0) REVERT: E 111 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 127 MET cc_start: 0.8097 (mtm) cc_final: 0.7884 (mtm) REVERT: E 135 MET cc_start: 0.1170 (mtm) cc_final: 0.0777 (mtm) REVERT: E 163 MET cc_start: 0.8197 (mmm) cc_final: 0.7981 (mmp) REVERT: E 171 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8131 (mmm-85) REVERT: E 252 ASP cc_start: 0.9096 (t0) cc_final: 0.8867 (t0) REVERT: E 290 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7496 (mm-30) REVERT: F 105 ASP cc_start: 0.8328 (m-30) cc_final: 0.8035 (m-30) REVERT: F 236 ASP cc_start: 0.7931 (m-30) cc_final: 0.7082 (p0) outliers start: 15 outliers final: 13 residues processed: 271 average time/residue: 0.3543 time to fit residues: 135.4573 Evaluate side-chains 263 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 135 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.0030 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.082212 restraints weight = 73019.556| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.57 r_work: 0.2807 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16220 Z= 0.129 Angle : 0.548 6.103 22091 Z= 0.286 Chirality : 0.040 0.145 2488 Planarity : 0.004 0.040 2739 Dihedral : 13.592 148.798 2599 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.12 % Allowed : 9.23 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1902 helix: 1.23 (0.17), residues: 1030 sheet: 0.62 (0.31), residues: 272 loop : 0.32 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 267 TYR 0.016 0.001 TYR D 124 PHE 0.006 0.001 PHE F 108 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16220) covalent geometry : angle 0.54790 / 0.29 (22091) hydrogen bonds : bond 0.04751 / 3.24 ( 779) hydrogen bonds : angle 4.84828 / 3.32 ( 2223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8377 (mm-30) REVERT: A 309 MET cc_start: 0.8551 (ttm) cc_final: 0.8214 (ttp) REVERT: B 105 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8843 (m-30) REVERT: B 188 GLU cc_start: 0.8175 (mp0) cc_final: 0.7784 (mp0) REVERT: C 81 LYS cc_start: 0.8592 (mptt) cc_final: 0.8179 (mttt) REVERT: C 272 MET cc_start: 0.8686 (mtp) cc_final: 0.8411 (mtp) REVERT: D 252 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7342 (t0) REVERT: E 135 MET cc_start: 0.1175 (mtm) cc_final: 0.0752 (mtm) REVERT: E 171 ARG cc_start: 0.8429 (mmt-90) cc_final: 0.8185 (mmm-85) REVERT: E 252 ASP cc_start: 0.9118 (t0) cc_final: 0.8852 (t0) REVERT: E 290 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7474 (mm-30) REVERT: F 105 ASP cc_start: 0.8289 (m-30) cc_final: 0.7999 (m-30) REVERT: F 120 GLU cc_start: 0.8676 (tt0) cc_final: 0.8419 (tt0) REVERT: F 236 ASP cc_start: 0.7943 (m-30) cc_final: 0.7041 (p0) outliers start: 18 outliers final: 14 residues processed: 272 average time/residue: 0.3484 time to fit residues: 134.4784 Evaluate side-chains 267 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 53 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN E 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.081916 restraints weight = 73474.661| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.57 r_work: 0.2804 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16220 Z= 0.137 Angle : 0.547 7.776 22091 Z= 0.285 Chirality : 0.040 0.137 2488 Planarity : 0.004 0.046 2739 Dihedral : 13.545 149.526 2599 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.87 % Allowed : 10.04 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 1902 helix: 1.30 (0.17), residues: 1030 sheet: 0.52 (0.32), residues: 262 loop : 0.31 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 267 TYR 0.017 0.001 TYR A 322 PHE 0.006 0.001 PHE F 108 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16220) covalent geometry : angle 0.54728 / 0.28 (22091) hydrogen bonds : bond 0.04653 / 3.18 ( 779) hydrogen bonds : angle 4.78005 / 3.26 ( 2223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8337 (mm-30) REVERT: A 295 GLU cc_start: 0.8537 (tt0) cc_final: 0.8175 (tp30) REVERT: A 309 MET cc_start: 0.8560 (ttm) cc_final: 0.8223 (ttp) REVERT: B 105 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8859 (m-30) REVERT: B 188 GLU cc_start: 0.8112 (mp0) cc_final: 0.7731 (mp0) REVERT: C 81 LYS cc_start: 0.8600 (mptt) cc_final: 0.8195 (mttt) REVERT: C 199 MET cc_start: 0.7929 (mmt) cc_final: 0.7719 (mmt) REVERT: C 272 MET cc_start: 0.8687 (mtp) cc_final: 0.8423 (mtp) REVERT: D 252 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7349 (t0) REVERT: E 111 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7907 (mt-10) REVERT: E 114 ARG cc_start: 0.7825 (mmp80) cc_final: 0.7539 (mmp80) REVERT: E 135 MET cc_start: 0.1195 (mtm) cc_final: 0.0788 (mtm) REVERT: E 171 ARG cc_start: 0.8428 (mmt-90) cc_final: 0.8148 (mmm-85) REVERT: E 252 ASP cc_start: 0.9129 (t0) cc_final: 0.8861 (t0) REVERT: F 105 ASP cc_start: 0.8291 (m-30) cc_final: 0.8000 (m-30) REVERT: F 120 GLU cc_start: 0.8687 (tt0) cc_final: 0.8432 (tt0) REVERT: F 236 ASP cc_start: 0.7992 (m-30) cc_final: 0.7036 (p0) outliers start: 14 outliers final: 10 residues processed: 268 average time/residue: 0.3589 time to fit residues: 136.4337 Evaluate side-chains 267 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 53 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081370 restraints weight = 73261.582| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.57 r_work: 0.2795 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16220 Z= 0.161 Angle : 0.561 8.559 22091 Z= 0.291 Chirality : 0.040 0.146 2488 Planarity : 0.005 0.049 2739 Dihedral : 13.538 151.393 2599 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.31 % Allowed : 10.17 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1902 helix: 1.32 (0.17), residues: 1030 sheet: 0.49 (0.32), residues: 262 loop : 0.24 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 267 TYR 0.017 0.001 TYR C 124 PHE 0.007 0.001 PHE F 108 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16220) covalent geometry : angle 0.56144 / 0.29 (22091) hydrogen bonds : bond 0.04756 / 3.25 ( 779) hydrogen bonds : angle 4.76638 / 3.26 ( 2223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8557 (tt0) cc_final: 0.8266 (tp30) REVERT: A 309 MET cc_start: 0.8575 (ttm) cc_final: 0.8236 (ttp) REVERT: B 105 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8863 (m-30) REVERT: B 188 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: C 81 LYS cc_start: 0.8598 (mptt) cc_final: 0.8187 (mttt) REVERT: C 272 MET cc_start: 0.8722 (mtp) cc_final: 0.8455 (mtp) REVERT: D 252 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7445 (t0) REVERT: E 111 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7950 (mt-10) REVERT: E 114 ARG cc_start: 0.7833 (mmp80) cc_final: 0.7575 (mmp80) REVERT: E 135 MET cc_start: 0.1223 (mtm) cc_final: 0.0836 (mtm) REVERT: E 171 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8152 (mmm-85) REVERT: E 252 ASP cc_start: 0.9129 (t0) cc_final: 0.8861 (t0) REVERT: F 105 ASP cc_start: 0.8276 (m-30) cc_final: 0.7996 (m-30) REVERT: F 120 GLU cc_start: 0.8706 (tt0) cc_final: 0.8459 (tt0) REVERT: F 236 ASP cc_start: 0.7979 (m-30) cc_final: 0.6990 (p0) outliers start: 21 outliers final: 18 residues processed: 268 average time/residue: 0.3616 time to fit residues: 137.3017 Evaluate side-chains 268 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 125 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081401 restraints weight = 73415.778| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.58 r_work: 0.2795 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16220 Z= 0.146 Angle : 0.555 8.095 22091 Z= 0.288 Chirality : 0.040 0.146 2488 Planarity : 0.004 0.044 2739 Dihedral : 13.517 150.980 2599 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.50 % Allowed : 10.11 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1902 helix: 1.34 (0.17), residues: 1032 sheet: 0.54 (0.32), residues: 268 loop : 0.25 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 267 TYR 0.016 0.001 TYR C 124 PHE 0.007 0.001 PHE F 108 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16220) covalent geometry : angle 0.55498 / 0.29 (22091) hydrogen bonds : bond 0.04622 / 3.16 ( 779) hydrogen bonds : angle 4.73049 / 3.23 ( 2223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8546 (tt0) cc_final: 0.8267 (tp30) REVERT: A 309 MET cc_start: 0.8569 (ttm) cc_final: 0.8231 (ttp) REVERT: B 105 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: B 188 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 81 LYS cc_start: 0.8650 (mptt) cc_final: 0.8228 (mttt) REVERT: C 272 MET cc_start: 0.8692 (mtp) cc_final: 0.8429 (mtp) REVERT: D 252 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7455 (t0) REVERT: D 272 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7696 (ttm) REVERT: E 111 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7950 (mt-10) REVERT: E 114 ARG cc_start: 0.7820 (mmp80) cc_final: 0.7561 (mmp80) REVERT: E 135 MET cc_start: 0.1224 (mtm) cc_final: 0.0829 (mtm) REVERT: E 171 ARG cc_start: 0.8473 (mmt-90) cc_final: 0.8160 (mmm-85) REVERT: E 252 ASP cc_start: 0.9140 (t0) cc_final: 0.8874 (t0) REVERT: F 105 ASP cc_start: 0.8274 (m-30) cc_final: 0.7991 (m-30) REVERT: F 236 ASP cc_start: 0.8006 (m-30) cc_final: 0.7001 (p0) REVERT: F 286 ASN cc_start: 0.6771 (t0) cc_final: 0.6522 (m-40) outliers start: 24 outliers final: 18 residues processed: 264 average time/residue: 0.3657 time to fit residues: 136.3791 Evaluate side-chains 270 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 53 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.082268 restraints weight = 72972.830| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.56 r_work: 0.2813 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16220 Z= 0.118 Angle : 0.546 8.200 22091 Z= 0.281 Chirality : 0.040 0.155 2488 Planarity : 0.004 0.065 2739 Dihedral : 13.460 148.377 2599 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.25 % Allowed : 10.67 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 1902 helix: 1.43 (0.17), residues: 1033 sheet: 0.56 (0.32), residues: 268 loop : 0.38 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 267 TYR 0.015 0.001 TYR D 124 PHE 0.006 0.001 PHE F 108 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16220) covalent geometry : angle 0.54612 / 0.28 (22091) hydrogen bonds : bond 0.04221 / 2.89 ( 779) hydrogen bonds : angle 4.64598 / 3.17 ( 2223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLU cc_start: 0.8526 (tt0) cc_final: 0.8262 (tp30) REVERT: A 309 MET cc_start: 0.8559 (ttm) cc_final: 0.8226 (ttp) REVERT: B 105 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8844 (m-30) REVERT: B 188 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: C 81 LYS cc_start: 0.8643 (mptt) cc_final: 0.8232 (mttt) REVERT: C 272 MET cc_start: 0.8663 (mtp) cc_final: 0.8399 (mtp) REVERT: D 121 GLU cc_start: 0.8336 (mp0) cc_final: 0.8108 (mm-30) REVERT: D 252 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7434 (t0) REVERT: D 272 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7626 (ttm) REVERT: E 111 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7964 (mt-10) REVERT: E 114 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7618 (mmp80) REVERT: E 135 MET cc_start: 0.1278 (mtm) cc_final: 0.0885 (mtm) REVERT: E 163 MET cc_start: 0.8249 (mmm) cc_final: 0.7985 (mmp) REVERT: E 171 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8155 (mmm-85) REVERT: E 252 ASP cc_start: 0.9136 (t0) cc_final: 0.8864 (t0) REVERT: F 105 ASP cc_start: 0.8268 (m-30) cc_final: 0.7988 (m-30) REVERT: F 236 ASP cc_start: 0.8026 (m-30) cc_final: 0.7029 (p0) REVERT: F 286 ASN cc_start: 0.6773 (t0) cc_final: 0.6520 (m-40) REVERT: F 305 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8471 (mtpp) outliers start: 20 outliers final: 14 residues processed: 263 average time/residue: 0.3484 time to fit residues: 129.9713 Evaluate side-chains 269 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 82 GLN B 324 HIS D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.081140 restraints weight = 73307.778| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.56 r_work: 0.2793 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16220 Z= 0.168 Angle : 0.560 8.280 22091 Z= 0.290 Chirality : 0.040 0.128 2488 Planarity : 0.005 0.058 2739 Dihedral : 13.475 151.389 2599 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.31 % Allowed : 10.73 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.19), residues: 1902 helix: 1.38 (0.17), residues: 1034 sheet: 0.49 (0.32), residues: 270 loop : 0.27 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 267 TYR 0.018 0.001 TYR C 124 PHE 0.007 0.001 PHE F 108 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16220) covalent geometry : angle 0.56019 / 0.29 (22091) hydrogen bonds : bond 0.04586 / 3.14 ( 779) hydrogen bonds : angle 4.68924 / 3.20 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8587.12 seconds wall clock time: 145 minutes 55.72 seconds (8755.72 seconds total)