Starting phenix.real_space_refine on Mon Jul 6 00:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbl_13294/07_2026/7pbl_13294_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbl_13294/07_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_13294/07_2026/7pbl_13294_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbl_13294/07_2026/7pbl_13294_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbl_13294/07_2026/7pbl_13294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbl_13294/07_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-dev-6108/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: 5.48, per 1000 atoms: 0.17 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: 3.15 Conformation dependent library (CDL) restraints added in 830.1 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: 5.13 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: 6.97 Time building geometry restraints manager: 4.13 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: 56734 2.17 - 4.35: 504 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: 3.140 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: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.250 ------------------------------------------------------------------------------- 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 : 0.772 10.868 22091 Z= 0.443 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 0.77176 / 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 : 0.878 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: 0.3714 time to fit residues: 218.6604 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 : 0.842 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.116142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.081336 restraints weight = 73162.255| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.60 r_work: 0.2788 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16220 Z= 0.213 Angle : 0.681 7.001 22091 Z= 0.368 Chirality : 0.043 0.155 2488 Planarity : 0.006 0.056 2739 Dihedral : 14.534 147.576 2599 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.25 % Allowed : 6.74 % Favored : 92.01 % 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: 0.46 (0.19), residues: 1902 helix: 0.36 (0.16), residues: 1026 sheet: 0.58 (0.31), residues: 282 loop : 0.39 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00478 / 0.21 (16220) covalent geometry : angle 0.68072 / 0.37 (22091) hydrogen bonds : bond 0.08354 / 5.62 ( 779) hydrogen bonds : angle 6.04572 / 4.20 ( 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 305 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.858 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: 0.8905 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 295 GLU cc_start: 0.8371 (tt0) cc_final: 0.8007 (tp30) REVERT: A 309 MET cc_start: 0.8577 (ttm) cc_final: 0.8252 (ttp) REVERT: B 163 MET cc_start: 0.8973 (mtp) cc_final: 0.8771 (mtp) REVERT: C 81 LYS cc_start: 0.8566 (mptt) cc_final: 0.8055 (mttt) REVERT: D 290 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 135 MET cc_start: 0.1255 (mtm) cc_final: 0.0686 (mtm) REVERT: E 194 SER cc_start: 0.9221 (p) cc_final: 0.9004 (p) REVERT: E 252 ASP cc_start: 0.9014 (t0) cc_final: 0.8751 (t0) REVERT: E 290 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7483 (mm-30) REVERT: F 105 ASP cc_start: 0.8352 (m-30) cc_final: 0.8084 (m-30) REVERT: F 120 GLU cc_start: 0.8647 (tt0) cc_final: 0.8373 (tt0) REVERT: F 125 SER cc_start: 0.9181 (m) cc_final: 0.8979 (p) REVERT: F 134 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8563 (mm) REVERT: F 222 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8438 (ttm-80) REVERT: F 236 ASP cc_start: 0.7807 (m-30) cc_final: 0.7023 (p0) outliers start: 20 outliers final: 9 residues processed: 297 average time/residue: 0.3204 time to fit residues: 134.5126 Evaluate side-chains 267 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 292 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 134 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: 0.5980 chunk 121 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN D 82 GLN F 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082445 restraints weight = 73125.674| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.58 r_work: 0.2807 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 16220 Z= 0.136 Angle : 0.584 8.889 22091 Z= 0.307 Chirality : 0.041 0.140 2488 Planarity : 0.004 0.038 2739 Dihedral : 14.016 145.718 2599 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.87 % Allowed : 7.86 % Favored : 91.27 % 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: 0.88 (0.19), residues: 1902 helix: 0.77 (0.16), residues: 1029 sheet: 0.79 (0.31), residues: 270 loop : 0.43 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.017 0.001 TYR C 124 PHE 0.007 0.001 PHE C 197 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (16220) covalent geometry : angle 0.58397 / 0.31 (22091) hydrogen bonds : bond 0.06343 / 4.30 ( 779) hydrogen bonds : angle 5.42069 / 3.75 ( 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 : 0.834 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: 0.8864 (mm-30) cc_final: 0.8427 (mm-30) REVERT: A 295 GLU cc_start: 0.8438 (tt0) cc_final: 0.7985 (tp30) REVERT: A 309 MET cc_start: 0.8529 (ttm) cc_final: 0.8196 (ttp) REVERT: B 163 MET cc_start: 0.8974 (mtp) cc_final: 0.8773 (mtp) REVERT: C 81 LYS cc_start: 0.8563 (mptt) cc_final: 0.8067 (mttt) REVERT: C 272 MET cc_start: 0.8749 (mtp) cc_final: 0.8472 (mtp) REVERT: E 135 MET cc_start: 0.1133 (mtm) cc_final: 0.0819 (mtm) REVERT: E 171 ARG cc_start: 0.8475 (mmt-90) cc_final: 0.8149 (mmm-85) REVERT: E 194 SER cc_start: 0.9195 (p) cc_final: 0.8965 (p) REVERT: E 252 ASP cc_start: 0.9029 (t0) cc_final: 0.8729 (t0) REVERT: E 290 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7546 (mm-30) REVERT: F 105 ASP cc_start: 0.8389 (m-30) cc_final: 0.8104 (m-30) REVERT: F 222 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8395 (ttm-80) REVERT: F 236 ASP cc_start: 0.7868 (m-30) cc_final: 0.7022 (p0) outliers start: 14 outliers final: 11 residues processed: 281 average time/residue: 0.3255 time to fit residues: 128.1657 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 : 0.807 ------------------------------------------------------------------------------- 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 124 TYR 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 286 ASN Chi-restraints excluded: chain E residue 308 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: 5.9990 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.116938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082438 restraints weight = 73006.371| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.58 r_work: 0.2805 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3283 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= 0.137 Angle : 0.566 6.225 22091 Z= 0.296 Chirality : 0.040 0.138 2488 Planarity : 0.004 0.038 2739 Dihedral : 13.757 145.825 2599 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.94 % Allowed : 8.17 % Favored : 90.89 % 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: 1.07 (0.19), residues: 1902 helix: 1.00 (0.17), residues: 1029 sheet: 0.72 (0.31), residues: 274 loop : 0.44 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.017 0.001 TYR D 124 PHE 0.013 0.001 PHE E 152 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (16220) covalent geometry : angle 0.56568 / 0.30 (22091) hydrogen bonds : bond 0.05327 / 3.62 ( 779) hydrogen bonds : angle 5.11887 / 3.52 ( 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 288 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.850 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: 0.8887 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 295 GLU cc_start: 0.8470 (tt0) cc_final: 0.8060 (tp30) REVERT: A 309 MET cc_start: 0.8560 (ttm) cc_final: 0.8232 (ttp) REVERT: B 144 SER cc_start: 0.8451 (p) cc_final: 0.7703 (t) REVERT: B 163 MET cc_start: 0.9022 (mtp) cc_final: 0.8817 (mtp) REVERT: B 178 MET cc_start: 0.9396 (mmt) cc_final: 0.9191 (mmt) REVERT: C 81 LYS cc_start: 0.8630 (mptt) cc_final: 0.8177 (mttt) REVERT: C 272 MET cc_start: 0.8750 (mtp) cc_final: 0.8461 (mtp) REVERT: E 135 MET cc_start: 0.1159 (mtm) cc_final: 0.0816 (mtm) REVERT: E 194 SER cc_start: 0.9178 (p) cc_final: 0.8959 (p) REVERT: E 252 ASP cc_start: 0.9084 (t0) cc_final: 0.8823 (t0) REVERT: E 290 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7511 (mm-30) REVERT: F 105 ASP cc_start: 0.8395 (m-30) cc_final: 0.8118 (m-30) REVERT: F 120 GLU cc_start: 0.8678 (tt0) cc_final: 0.8412 (tt0) REVERT: F 236 ASP cc_start: 0.7977 (m-30) cc_final: 0.7151 (p0) REVERT: F 273 TYR cc_start: 0.7351 (m-80) cc_final: 0.6852 (m-80) outliers start: 15 outliers final: 13 residues processed: 282 average time/residue: 0.3227 time to fit residues: 128.8707 Evaluate side-chains 270 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 286 ASN 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 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: 0.9980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.116098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.081585 restraints weight = 73117.134| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.57 r_work: 0.2793 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16220 Z= 0.160 Angle : 0.563 6.131 22091 Z= 0.296 Chirality : 0.040 0.144 2488 Planarity : 0.004 0.039 2739 Dihedral : 13.689 149.295 2599 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.12 % Allowed : 8.86 % Favored : 90.02 % 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: 1.07 (0.19), residues: 1902 helix: 1.12 (0.17), residues: 1029 sheet: 0.59 (0.31), residues: 274 loop : 0.27 (0.24), residues: 599 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 0.003 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16220) covalent geometry : angle 0.56315 / 0.30 (22091) hydrogen bonds : bond 0.05274 / 3.59 ( 779) hydrogen bonds : angle 4.99625 / 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 278 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.812 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: A 295 GLU cc_start: 0.8537 (tt0) cc_final: 0.8195 (tp30) REVERT: A 309 MET cc_start: 0.8588 (ttm) cc_final: 0.8252 (ttp) REVERT: B 105 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8855 (m-30) REVERT: B 163 MET cc_start: 0.9061 (mtp) cc_final: 0.8851 (mtp) REVERT: B 178 MET cc_start: 0.9400 (mmt) cc_final: 0.9178 (mmt) REVERT: C 81 LYS cc_start: 0.8633 (mptt) cc_final: 0.8181 (mttt) REVERT: C 272 MET cc_start: 0.8731 (mtp) cc_final: 0.8440 (mtp) REVERT: D 252 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7332 (t0) REVERT: E 111 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7874 (mt-10) REVERT: E 135 MET cc_start: 0.1159 (mtm) cc_final: 0.0806 (mtm) REVERT: E 194 SER cc_start: 0.9176 (p) cc_final: 0.8947 (p) REVERT: E 252 ASP cc_start: 0.9090 (t0) cc_final: 0.8857 (t0) REVERT: E 290 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7507 (mm-30) REVERT: F 105 ASP cc_start: 0.8332 (m-30) cc_final: 0.8051 (m-30) REVERT: F 120 GLU cc_start: 0.8683 (tt0) cc_final: 0.8407 (tt0) REVERT: F 236 ASP cc_start: 0.7981 (m-30) cc_final: 0.7106 (p0) REVERT: F 273 TYR cc_start: 0.7484 (m-80) cc_final: 0.7078 (m-80) outliers start: 18 outliers final: 16 residues processed: 272 average time/residue: 0.3254 time to fit residues: 124.9502 Evaluate side-chains 272 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 165 SER 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 93 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 135 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.116498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.082069 restraints weight = 72833.529| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.56 r_work: 0.2801 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3574 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= 0.130 Angle : 0.544 6.098 22091 Z= 0.285 Chirality : 0.040 0.144 2488 Planarity : 0.004 0.047 2739 Dihedral : 13.609 149.184 2599 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.19 % Allowed : 9.11 % Favored : 89.71 % 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: 1.20 (0.19), residues: 1902 helix: 1.24 (0.17), residues: 1030 sheet: 0.57 (0.31), residues: 274 loop : 0.33 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 0.00286 / 0.13 (16220) covalent geometry : angle 0.54387 / 0.28 (22091) hydrogen bonds : bond 0.04830 / 3.29 ( 779) hydrogen bonds : angle 4.87280 / 3.34 ( 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 282 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.860 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: A 295 GLU cc_start: 0.8523 (tt0) cc_final: 0.8201 (tp30) REVERT: A 309 MET cc_start: 0.8574 (ttm) cc_final: 0.8238 (ttp) REVERT: B 105 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8856 (m-30) REVERT: B 178 MET cc_start: 0.9384 (mmt) cc_final: 0.9162 (mmt) REVERT: B 188 GLU cc_start: 0.8186 (mp0) cc_final: 0.7795 (mp0) REVERT: C 81 LYS cc_start: 0.8588 (mptt) cc_final: 0.8182 (mttt) REVERT: C 199 MET cc_start: 0.7891 (mmt) cc_final: 0.7685 (mmt) REVERT: C 272 MET cc_start: 0.8711 (mtp) cc_final: 0.8441 (mtp) REVERT: D 252 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7297 (t0) REVERT: E 111 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7818 (mt-10) REVERT: E 135 MET cc_start: 0.1184 (mtm) cc_final: 0.0824 (mtm) REVERT: E 194 SER cc_start: 0.9174 (p) cc_final: 0.8942 (p) REVERT: E 252 ASP cc_start: 0.9106 (t0) cc_final: 0.8843 (t0) REVERT: F 105 ASP cc_start: 0.8298 (m-30) cc_final: 0.8007 (m-30) REVERT: F 120 GLU cc_start: 0.8684 (tt0) cc_final: 0.8447 (tt0) REVERT: F 236 ASP cc_start: 0.7990 (m-30) cc_final: 0.7052 (p0) REVERT: F 273 TYR cc_start: 0.7496 (m-80) cc_final: 0.7147 (m-10) outliers start: 19 outliers final: 16 residues processed: 273 average time/residue: 0.3319 time to fit residues: 127.2249 Evaluate side-chains 273 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 160 ARG 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: 1.9990 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.116031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.081570 restraints weight = 73478.394| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.58 r_work: 0.2794 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16220 Z= 0.148 Angle : 0.553 8.873 22091 Z= 0.288 Chirality : 0.040 0.141 2488 Planarity : 0.004 0.042 2739 Dihedral : 13.573 150.558 2599 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 9.92 % Favored : 88.96 % 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: 1.20 (0.19), residues: 1902 helix: 1.30 (0.17), residues: 1030 sheet: 0.47 (0.32), residues: 264 loop : 0.26 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 267 TYR 0.016 0.001 TYR C 124 PHE 0.006 0.001 PHE F 108 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16220) covalent geometry : angle 0.55275 / 0.29 (22091) hydrogen bonds : bond 0.04815 / 3.29 ( 779) hydrogen bonds : angle 4.82368 / 3.29 ( 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 283 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.829 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 295 GLU cc_start: 0.8530 (tt0) cc_final: 0.8225 (tp30) REVERT: A 309 MET cc_start: 0.8575 (ttm) cc_final: 0.8238 (ttp) REVERT: B 105 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8874 (m-30) REVERT: B 178 MET cc_start: 0.9388 (mmt) cc_final: 0.9179 (mmt) REVERT: B 188 GLU cc_start: 0.8134 (mp0) cc_final: 0.7754 (mp0) REVERT: C 81 LYS cc_start: 0.8594 (mptt) cc_final: 0.8196 (mttt) REVERT: C 199 MET cc_start: 0.7928 (mmt) cc_final: 0.7720 (mmt) REVERT: C 272 MET cc_start: 0.8723 (mtp) cc_final: 0.8458 (mtp) REVERT: D 252 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7387 (t0) REVERT: E 111 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7906 (mt-10) REVERT: E 114 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7558 (mmp80) REVERT: E 135 MET cc_start: 0.1195 (mtm) cc_final: 0.0850 (mtm) REVERT: E 194 SER cc_start: 0.9184 (p) cc_final: 0.8949 (p) REVERT: E 252 ASP cc_start: 0.9116 (t0) cc_final: 0.8847 (t0) REVERT: F 105 ASP cc_start: 0.8302 (m-30) cc_final: 0.8023 (m-30) REVERT: F 120 GLU cc_start: 0.8697 (tt0) cc_final: 0.8454 (tt0) REVERT: F 236 ASP cc_start: 0.8033 (m-30) cc_final: 0.7034 (p0) REVERT: F 325 MET cc_start: 0.7369 (mtp) cc_final: 0.7135 (mtt) outliers start: 18 outliers final: 16 residues processed: 276 average time/residue: 0.3126 time to fit residues: 122.2740 Evaluate side-chains 273 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 308 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.115413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.081117 restraints weight = 73133.272| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.54 r_work: 0.2788 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16220 Z= 0.162 Angle : 0.561 6.713 22091 Z= 0.293 Chirality : 0.040 0.146 2488 Planarity : 0.005 0.050 2739 Dihedral : 13.553 152.218 2599 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.43 % Allowed : 9.92 % Favored : 88.65 % 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: 1.18 (0.19), residues: 1902 helix: 1.31 (0.17), residues: 1030 sheet: 0.44 (0.32), residues: 264 loop : 0.21 (0.24), residues: 608 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 0.007 0.001 PHE F 108 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (16220) covalent geometry : angle 0.56128 / 0.29 (22091) hydrogen bonds : bond 0.04854 / 3.32 ( 779) hydrogen bonds : angle 4.79448 / 3.28 ( 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 287 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.891 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: A 295 GLU cc_start: 0.8527 (tt0) cc_final: 0.8286 (tp30) REVERT: A 309 MET cc_start: 0.8570 (ttm) cc_final: 0.8232 (ttp) REVERT: B 105 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8864 (m-30) REVERT: B 178 MET cc_start: 0.9395 (mmt) cc_final: 0.9187 (mmt) REVERT: B 188 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 81 LYS cc_start: 0.8616 (mptt) cc_final: 0.8209 (mttt) REVERT: C 272 MET cc_start: 0.8705 (mtp) cc_final: 0.8439 (mtp) REVERT: D 252 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7382 (t0) REVERT: E 111 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7956 (mt-10) REVERT: E 114 ARG cc_start: 0.7852 (mmp80) cc_final: 0.7570 (mmp80) REVERT: E 135 MET cc_start: 0.1232 (mtm) cc_final: 0.0890 (mtm) REVERT: E 194 SER cc_start: 0.9193 (p) cc_final: 0.8970 (p) REVERT: E 252 ASP cc_start: 0.9121 (t0) cc_final: 0.8855 (t0) REVERT: F 105 ASP cc_start: 0.8281 (m-30) cc_final: 0.8002 (m-30) REVERT: F 236 ASP cc_start: 0.8033 (m-30) cc_final: 0.7028 (p0) outliers start: 23 outliers final: 20 residues processed: 278 average time/residue: 0.3394 time to fit residues: 134.0470 Evaluate side-chains 277 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 272 MET 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 Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.116056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.081551 restraints weight = 73273.088| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.58 r_work: 0.2797 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16220 Z= 0.130 Angle : 0.552 8.208 22091 Z= 0.286 Chirality : 0.040 0.146 2488 Planarity : 0.004 0.044 2739 Dihedral : 13.517 150.914 2599 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.31 % Allowed : 10.11 % Favored : 88.58 % 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: 1.26 (0.19), residues: 1902 helix: 1.37 (0.17), residues: 1032 sheet: 0.45 (0.32), residues: 264 loop : 0.28 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 267 TYR 0.016 0.001 TYR D 124 PHE 0.008 0.001 PHE F 307 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16220) covalent geometry : angle 0.55217 / 0.29 (22091) hydrogen bonds : bond 0.04559 / 3.12 ( 779) hydrogen bonds : angle 4.73073 / 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 282 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 0.865 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: 0.8518 (tt0) cc_final: 0.8304 (tp30) REVERT: A 309 MET cc_start: 0.8564 (ttm) cc_final: 0.8226 (ttp) REVERT: B 105 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: B 178 MET cc_start: 0.9386 (mmt) cc_final: 0.9175 (mmt) REVERT: B 188 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 81 LYS cc_start: 0.8646 (mptt) cc_final: 0.8243 (mttt) REVERT: C 272 MET cc_start: 0.8695 (mtp) cc_final: 0.8434 (mtp) REVERT: D 252 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7356 (t0) REVERT: E 114 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7585 (mmp80) REVERT: E 194 SER cc_start: 0.9169 (p) cc_final: 0.8934 (p) REVERT: E 252 ASP cc_start: 0.9133 (t0) cc_final: 0.8862 (t0) REVERT: F 105 ASP cc_start: 0.8274 (m-30) cc_final: 0.7990 (m-30) REVERT: F 236 ASP cc_start: 0.8028 (m-30) cc_final: 0.7024 (p0) outliers start: 21 outliers final: 16 residues processed: 271 average time/residue: 0.3270 time to fit residues: 125.6558 Evaluate side-chains 275 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 252 ASP Chi-restraints excluded: chain D residue 272 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.115524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.081193 restraints weight = 73018.518| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.54 r_work: 0.2791 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3906 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= 0.155 Angle : 0.562 8.346 22091 Z= 0.293 Chirality : 0.040 0.144 2488 Planarity : 0.005 0.045 2739 Dihedral : 13.514 151.880 2599 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 10.79 % 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: 1.21 (0.19), residues: 1902 helix: 1.35 (0.17), residues: 1032 sheet: 0.37 (0.32), residues: 264 loop : 0.25 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 196 TYR 0.017 0.001 TYR C 124 PHE 0.007 0.001 PHE F 108 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16220) covalent geometry : angle 0.56237 / 0.29 (22091) hydrogen bonds : bond 0.04651 / 3.18 ( 779) hydrogen bonds : angle 4.73566 / 3.24 ( 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 279 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.898 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 295 GLU cc_start: 0.8495 (tt0) cc_final: 0.8273 (tp30) REVERT: A 309 MET cc_start: 0.8567 (ttm) cc_final: 0.8228 (ttp) REVERT: B 105 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (m-30) REVERT: B 178 MET cc_start: 0.9382 (mmt) cc_final: 0.9161 (mmt) REVERT: B 188 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 81 LYS cc_start: 0.8666 (mptt) cc_final: 0.8258 (mttt) REVERT: C 272 MET cc_start: 0.8705 (mtp) cc_final: 0.8440 (mtp) REVERT: D 252 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7392 (t0) REVERT: E 194 SER cc_start: 0.9177 (p) cc_final: 0.8951 (p) REVERT: E 252 ASP cc_start: 0.9125 (t0) cc_final: 0.8781 (t0) REVERT: F 105 ASP cc_start: 0.8280 (m-30) cc_final: 0.7993 (m-30) REVERT: F 236 ASP cc_start: 0.8031 (m-30) cc_final: 0.7016 (p0) outliers start: 20 outliers final: 16 residues processed: 270 average time/residue: 0.3325 time to fit residues: 127.2876 Evaluate side-chains 274 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 199 MET 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 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: 0.9980 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 179 optimal weight: 0.2980 chunk 136 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.116357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.082018 restraints weight = 73047.105| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.55 r_work: 0.2805 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16220 Z= 0.119 Angle : 0.545 8.288 22091 Z= 0.281 Chirality : 0.039 0.131 2488 Planarity : 0.004 0.044 2739 Dihedral : 13.464 149.649 2599 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.19 % Allowed : 11.23 % Favored : 87.59 % 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: 1.35 (0.19), residues: 1902 helix: 1.44 (0.17), residues: 1033 sheet: 0.46 (0.32), residues: 270 loop : 0.34 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 0.00267 / 0.12 (16220) covalent geometry : angle 0.54473 / 0.28 (22091) hydrogen bonds : bond 0.04274 / 2.93 ( 779) hydrogen bonds : angle 4.65307 / 3.18 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8608.90 seconds wall clock time: 146 minutes 3.57 seconds (8763.57 seconds total)