Starting phenix.real_space_refine on Mon Sep 14 15:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbq_13299/09_2026/7pbq_13299_neut_trim.cif" } resolution = 3.1 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 46 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3150 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 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31323 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: 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: "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: 5.55, per 1000 atoms: 0.18 Number of scatterers: 31323 At special positions: 0 Unit cell: (125.35, 139.52, 109, 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 101 16.00 P 46 15.00 Mg 4 11.99 O 3150 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: 3.00 Conformation dependent library (CDL) restraints added in 753.7 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: 103 helices and 18 sheets defined 59.0% alpha, 10.9% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.532A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.829A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (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 99 removed outlier: 3.549A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (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: 4.027A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.544A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.658A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.681A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.641A 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 49 removed outlier: 3.589A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.571A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.556A 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 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.439A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.518A 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 removed outlier: 3.501A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.575A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.671A pdb=" N ASP B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.624A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.527A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.625A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.528A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.582A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (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 removed outlier: 3.511A pdb=" N GLU C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.976A 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: 3.785A 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: 3.820A 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: 3.532A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 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 100 removed outlier: 3.663A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.613A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.606A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.201A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.809A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 232 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: 3.594A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.649A 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 90 through 100 removed outlier: 3.559A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.821A 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 130 removed outlier: 3.510A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.191A 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 Processing helix chain 'E' and resid 202 through 212 removed outlier: 3.741A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.510A pdb=" N LYS E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.536A 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 removed outlier: 3.545A pdb=" N GLY E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 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: 3.601A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 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: 3.795A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.280A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.548A 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 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 213 removed outlier: 3.646A pdb=" N ARG F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) 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 removed outlier: 3.711A pdb=" N TYR F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.649A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 removed outlier: 3.608A pdb=" N VAL F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 304 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: 6.499A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.647A 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: 6.479A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.636A 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: 6.311A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (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: 6.296A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 136 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: 6.460A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (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 308 through 311 Processing sheet with id=AB7, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.214A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AB9, first strand: chain 'F' and resid 308 through 310 760 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 7.10 Time building geometry restraints manager: 4.12 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: 6784 1.50 - 1.72: 6587 1.72 - 1.95: 198 Bond restraints: 31663 Sorted by residual: bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.572 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 0.860 0.100 2.00e-02 2.50e+03 2.51e+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 A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 56662 2.15 - 4.31: 574 4.31 - 6.46: 48 6.46 - 8.62: 15 8.62 - 10.77: 15 Bond angle restraints: 57314 Sorted by residual: angle pdb=" O4' DT V 7 " pdb=" C1' DT V 7 " pdb=" N1 DT V 7 " ideal model delta sigma weight residual 108.00 111.81 -3.81 7.00e-01 2.04e+00 2.96e+01 angle pdb=" C4' DA U 2 " pdb=" O4' DA U 2 " pdb=" C1' DA U 2 " ideal model delta sigma weight residual 110.10 105.06 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 110.85 -2.85 7.00e-01 2.04e+00 1.66e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" O5' DA U 2 " pdb=" C5' DA U 2 " pdb=" C4' DA U 2 " ideal model delta sigma weight residual 109.40 112.59 -3.19 8.00e-01 1.56e+00 1.59e+01 ... (remaining 57309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.66: 14159 32.66 - 65.32: 565 65.32 - 97.98: 36 97.98 - 130.64: 0 130.64 - 163.30: 2 Dihedral angle restraints: 14762 sinusoidal: 8493 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 -60.00 103.30 -163.30 1 2.00e+01 2.50e-03 4.70e+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 -60.00 100.63 -160.63 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C1' ADP E 600 " pdb=" C4' ADP E 600 " pdb=" O4' ADP E 600 " pdb=" C5' ADP E 600 " ideal model delta sinusoidal sigma weight residual -150.00 -92.23 -57.77 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 14759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2241 0.080 - 0.160: 236 0.160 - 0.240: 7 0.240 - 0.320: 3 0.320 - 0.400: 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 -2.74 -0.40 2.00e-01 2.50e+01 4.00e+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 -2.65 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.392 9.50e-02 1.11e+02 1.39e-01 7.05e+01 pdb=" NE ARG E 160 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.100 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.203 9.50e-02 1.11e+02 8.38e-02 5.92e+01 pdb=" NE ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.090 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.055 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 169 " -0.166 9.50e-02 1.11e+02 6.78e-02 3.80e+01 pdb=" NE ARG C 169 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 169 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 169 " 0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG C 169 " -0.029 2.00e-02 2.50e+03 pdb="HH11 ARG C 169 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG C 169 " -0.075 2.00e-02 2.50e+03 pdb="HH21 ARG C 169 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 169 " 0.030 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 654 2.13 - 2.75: 55143 2.75 - 3.36: 82517 3.36 - 3.98: 105528 3.98 - 4.60: 171716 Nonbonded interactions: 415558 Sorted by model distance: nonbonded pdb="HH22 ARG F 214 " pdb=" OD2 ASP F 262 " model vdw 1.510 2.450 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU A 299 " pdb="HH11 ARG A 315 " model vdw 1.578 2.450 nonbonded pdb=" O ALA E 138 " pdb=" HG1 THR E 141 " model vdw 1.601 2.450 ... (remaining 415553 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.420 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 16224 Z= 0.276 Angle : 0.808 10.773 22098 Z= 0.466 Chirality : 0.048 0.400 2488 Planarity : 0.010 0.134 2739 Dihedral : 15.090 163.296 6350 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.19 % Allowed : 1.19 % Favored : 98.63 % 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: -0.62 (0.18), residues: 1902 helix: -0.85 (0.14), residues: 1004 sheet: 0.63 (0.29), residues: 318 loop : 0.25 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 171 TYR 0.027 0.004 TYR D 327 PHE 0.023 0.003 PHE A 25 HIS 0.016 0.003 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.28 (16224) covalent geometry : angle 0.80795 / 0.47 (22098) hydrogen bonds : bond 0.26322 / 17.35 ( 790) hydrogen bonds : angle 8.49758 / 6.17 ( 2250) *********************** 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 482 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 479 time to evaluate : 0.727 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: A 99 ASN cc_start: 0.8548 (m-40) cc_final: 0.8197 (m-40) REVERT: B 110 ASP cc_start: 0.7843 (t0) cc_final: 0.7636 (t0) REVERT: B 325 MET cc_start: 0.8563 (mmm) cc_final: 0.8118 (mmp) REVERT: C 125 SER cc_start: 0.8513 (m) cc_final: 0.8224 (p) REVERT: C 178 MET cc_start: 0.9154 (mmt) cc_final: 0.8641 (mmt) REVERT: C 199 MET cc_start: 0.7646 (mmp) cc_final: 0.7391 (mmt) REVERT: C 297 MET cc_start: 0.9060 (ttt) cc_final: 0.8832 (ttm) REVERT: D 58 PHE cc_start: 0.7770 (m-80) cc_final: 0.7379 (m-80) REVERT: D 250 MET cc_start: 0.8433 (ttp) cc_final: 0.8207 (ttp) REVERT: D 269 MET cc_start: 0.8636 (mtp) cc_final: 0.8396 (mtm) REVERT: D 313 THR cc_start: 0.8252 (m) cc_final: 0.8022 (m) REVERT: E 105 ASP cc_start: 0.7654 (m-30) cc_final: 0.7415 (m-30) REVERT: E 111 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7518 (mt-10) REVERT: E 163 MET cc_start: 0.7378 (mmp) cc_final: 0.7046 (mmp) REVERT: E 165 SER cc_start: 0.7385 (t) cc_final: 0.7132 (m) REVERT: E 204 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 243 ILE cc_start: 0.8848 (mm) cc_final: 0.8605 (mt) REVERT: F 117 MET cc_start: 0.7773 (tpt) cc_final: 0.7529 (tpt) REVERT: F 284 SER cc_start: 0.8901 (m) cc_final: 0.8553 (t) REVERT: F 292 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7673 (mm-30) REVERT: F 296 ASP cc_start: 0.7881 (m-30) cc_final: 0.7678 (m-30) outliers start: 3 outliers final: 1 residues processed: 481 average time/residue: 0.3913 time to fit residues: 257.8320 Evaluate side-chains 328 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 166 ASN C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.078383 restraints weight = 74228.074| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.25 r_work: 0.2816 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16224 Z= 0.181 Angle : 0.681 6.717 22098 Z= 0.372 Chirality : 0.043 0.182 2488 Planarity : 0.006 0.086 2739 Dihedral : 14.312 161.788 2626 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.25 % Allowed : 7.74 % Favored : 91.02 % 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: 0.36 (0.19), residues: 1902 helix: 0.29 (0.16), residues: 1037 sheet: 0.99 (0.30), residues: 281 loop : 0.06 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 214 TYR 0.013 0.001 TYR E 230 PHE 0.009 0.001 PHE F 197 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (16224) covalent geometry : angle 0.68135 / 0.37 (22098) hydrogen bonds : bond 0.08006 / 5.27 ( 790) hydrogen bonds : angle 6.03167 / 4.33 ( 2250) *********************** 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 352 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 332 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8772 (m-40) cc_final: 0.8344 (m-40) REVERT: B 99 ASN cc_start: 0.8254 (t0) cc_final: 0.7923 (t0) REVERT: B 200 THR cc_start: 0.8735 (t) cc_final: 0.8500 (p) REVERT: B 312 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7281 (ttt-90) REVERT: C 90 LYS cc_start: 0.8374 (pttt) cc_final: 0.8140 (ptpp) REVERT: C 125 SER cc_start: 0.8874 (m) cc_final: 0.8512 (p) REVERT: C 178 MET cc_start: 0.9368 (mmt) cc_final: 0.8962 (mmt) REVERT: C 297 MET cc_start: 0.9322 (ttt) cc_final: 0.9104 (ttm) REVERT: D 26 LYS cc_start: 0.8684 (tppp) cc_final: 0.8473 (mppt) REVERT: D 58 PHE cc_start: 0.8358 (m-80) cc_final: 0.8090 (m-80) REVERT: D 110 ASP cc_start: 0.8230 (t0) cc_final: 0.7991 (t0) REVERT: D 169 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7811 (ttm-80) REVERT: D 313 THR cc_start: 0.8405 (m) cc_final: 0.8113 (m) REVERT: E 243 ILE cc_start: 0.8613 (mm) cc_final: 0.8389 (mt) REVERT: F 89 GLU cc_start: 0.7904 (pm20) cc_final: 0.7668 (pm20) REVERT: F 117 MET cc_start: 0.7610 (tpt) cc_final: 0.7253 (tpt) REVERT: F 163 MET cc_start: 0.7949 (tpp) cc_final: 0.7733 (tpp) REVERT: F 292 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8150 (mm-30) outliers start: 20 outliers final: 14 residues processed: 343 average time/residue: 0.3594 time to fit residues: 174.1768 Evaluate side-chains 320 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 306 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 246 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 = 0.3359 r_free = 0.3359 target = 0.105279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080052 restraints weight = 74221.274| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.25 r_work: 0.2820 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16224 Z= 0.140 Angle : 0.571 8.902 22098 Z= 0.306 Chirality : 0.041 0.141 2488 Planarity : 0.005 0.044 2739 Dihedral : 13.854 168.319 2626 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.06 % Allowed : 8.67 % Favored : 90.27 % 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: 0.68 (0.19), residues: 1902 helix: 0.68 (0.16), residues: 1041 sheet: 0.93 (0.30), residues: 281 loop : 0.03 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.024 0.001 TYR E 230 PHE 0.009 0.001 PHE A 25 HIS 0.003 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (16224) covalent geometry : angle 0.57114 / 0.31 (22098) hydrogen bonds : bond 0.06312 / 4.13 ( 790) hydrogen bonds : angle 5.34036 / 3.84 ( 2250) *********************** 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 352 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 335 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: A 99 ASN cc_start: 0.8741 (m-40) cc_final: 0.8456 (m-40) REVERT: B 117 MET cc_start: 0.8117 (tpp) cc_final: 0.7753 (tpp) REVERT: B 200 THR cc_start: 0.8659 (t) cc_final: 0.8423 (p) REVERT: B 312 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7318 (ttt-90) REVERT: B 325 MET cc_start: 0.8875 (mmm) cc_final: 0.8656 (mmp) REVERT: C 90 LYS cc_start: 0.8369 (pttt) cc_final: 0.8147 (ptpp) REVERT: C 178 MET cc_start: 0.9333 (mmt) cc_final: 0.8909 (mmt) REVERT: C 297 MET cc_start: 0.9308 (ttt) cc_final: 0.9087 (ttm) REVERT: D 26 LYS cc_start: 0.8689 (tppp) cc_final: 0.8473 (mppt) REVERT: D 58 PHE cc_start: 0.8390 (m-80) cc_final: 0.8087 (m-80) REVERT: D 169 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7848 (ttm-80) REVERT: D 313 THR cc_start: 0.8341 (m) cc_final: 0.8085 (m) REVERT: E 105 ASP cc_start: 0.8490 (m-30) cc_final: 0.8204 (m-30) REVERT: E 188 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 243 ILE cc_start: 0.8554 (mm) cc_final: 0.8335 (mt) REVERT: E 327 TYR cc_start: 0.7866 (m-80) cc_final: 0.7387 (m-80) REVERT: F 89 GLU cc_start: 0.7926 (pm20) cc_final: 0.7635 (pm20) REVERT: F 117 MET cc_start: 0.7617 (tpt) cc_final: 0.7144 (tpt) REVERT: F 163 MET cc_start: 0.7833 (tpp) cc_final: 0.7620 (tpp) REVERT: F 292 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8162 (mm-30) outliers start: 17 outliers final: 11 residues processed: 342 average time/residue: 0.3528 time to fit residues: 170.3919 Evaluate side-chains 335 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 324 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.078526 restraints weight = 74311.645| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.26 r_work: 0.2799 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16224 Z= 0.204 Angle : 0.592 6.389 22098 Z= 0.319 Chirality : 0.042 0.147 2488 Planarity : 0.005 0.041 2739 Dihedral : 13.856 177.069 2626 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.25 % Allowed : 9.17 % Favored : 89.58 % 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: 0.62 (0.19), residues: 1902 helix: 0.72 (0.16), residues: 1044 sheet: 0.91 (0.30), residues: 279 loop : -0.19 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 218 TYR 0.020 0.001 TYR A 298 PHE 0.008 0.001 PHE A 25 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (16224) covalent geometry : angle 0.59207 / 0.32 (22098) hydrogen bonds : bond 0.05950 / 3.94 ( 790) hydrogen bonds : angle 5.22747 / 3.74 ( 2250) *********************** 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 348 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 328 time to evaluate : 0.849 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 99 ASN cc_start: 0.8682 (m-40) cc_final: 0.8322 (m110) REVERT: A 252 ASP cc_start: 0.8289 (t0) cc_final: 0.7988 (t0) REVERT: A 296 ASP cc_start: 0.7972 (m-30) cc_final: 0.7770 (m-30) REVERT: B 99 ASN cc_start: 0.8334 (t0) cc_final: 0.7994 (t0) REVERT: B 117 MET cc_start: 0.8173 (tpp) cc_final: 0.7812 (tpp) REVERT: B 200 THR cc_start: 0.8718 (t) cc_final: 0.8495 (p) REVERT: B 312 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7364 (ttt-90) REVERT: B 325 MET cc_start: 0.8925 (mmm) cc_final: 0.8715 (mmp) REVERT: C 90 LYS cc_start: 0.8414 (pttt) cc_final: 0.8112 (ptpp) REVERT: C 178 MET cc_start: 0.9344 (mmt) cc_final: 0.8891 (mmt) REVERT: C 297 MET cc_start: 0.9324 (ttt) cc_final: 0.9114 (ttm) REVERT: D 26 LYS cc_start: 0.8681 (tppp) cc_final: 0.8475 (mppt) REVERT: D 313 THR cc_start: 0.8359 (m) cc_final: 0.8091 (m) REVERT: E 105 ASP cc_start: 0.8356 (m-30) cc_final: 0.8151 (m-30) REVERT: E 188 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7434 (tm-30) REVERT: E 243 ILE cc_start: 0.8609 (mm) cc_final: 0.8379 (mt) REVERT: E 327 TYR cc_start: 0.7868 (m-80) cc_final: 0.7421 (m-80) REVERT: F 89 GLU cc_start: 0.7983 (pm20) cc_final: 0.7615 (pm20) REVERT: F 117 MET cc_start: 0.7597 (tpt) cc_final: 0.7082 (tpt) REVERT: F 163 MET cc_start: 0.8001 (tpp) cc_final: 0.7757 (tpp) REVERT: F 292 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8199 (mm-30) outliers start: 20 outliers final: 16 residues processed: 335 average time/residue: 0.3630 time to fit residues: 170.4989 Evaluate side-chains 338 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.079426 restraints weight = 74205.571| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.25 r_work: 0.2790 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16224 Z= 0.135 Angle : 0.553 6.414 22098 Z= 0.295 Chirality : 0.040 0.148 2488 Planarity : 0.005 0.044 2739 Dihedral : 13.761 177.197 2626 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.06 % Allowed : 10.23 % Favored : 88.71 % 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: 0.79 (0.19), residues: 1902 helix: 0.88 (0.16), residues: 1045 sheet: 0.92 (0.30), residues: 275 loop : -0.12 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.014 0.001 TYR A 298 PHE 0.008 0.001 PHE E 58 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (16224) covalent geometry : angle 0.55273 / 0.30 (22098) hydrogen bonds : bond 0.05275 / 3.47 ( 790) hydrogen bonds : angle 5.03821 / 3.61 ( 2250) *********************** 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 350 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 333 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8614 (m-40) cc_final: 0.8327 (m110) REVERT: B 99 ASN cc_start: 0.8374 (t0) cc_final: 0.7990 (t0) REVERT: B 117 MET cc_start: 0.8148 (tpp) cc_final: 0.7801 (tpp) REVERT: B 200 THR cc_start: 0.8713 (t) cc_final: 0.8489 (p) REVERT: B 325 MET cc_start: 0.8923 (mmm) cc_final: 0.8700 (mmp) REVERT: C 90 LYS cc_start: 0.8368 (pttt) cc_final: 0.8080 (ptpp) REVERT: C 178 MET cc_start: 0.9330 (mmt) cc_final: 0.8875 (mmt) REVERT: D 110 ASP cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) REVERT: E 105 ASP cc_start: 0.8380 (m-30) cc_final: 0.8160 (m-30) REVERT: E 188 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7480 (tm-30) REVERT: E 243 ILE cc_start: 0.8583 (mm) cc_final: 0.8347 (mt) REVERT: E 327 TYR cc_start: 0.7848 (m-80) cc_final: 0.7330 (m-80) REVERT: F 89 GLU cc_start: 0.7964 (pm20) cc_final: 0.7543 (pm20) REVERT: F 163 MET cc_start: 0.7983 (tpp) cc_final: 0.7756 (tpp) REVERT: F 292 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8189 (mm-30) outliers start: 17 outliers final: 13 residues processed: 340 average time/residue: 0.3669 time to fit residues: 174.6135 Evaluate side-chains 337 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 324 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.0060 chunk 133 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.079046 restraints weight = 73882.109| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.25 r_work: 0.2814 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16224 Z= 0.141 Angle : 0.546 6.365 22098 Z= 0.291 Chirality : 0.040 0.144 2488 Planarity : 0.005 0.059 2739 Dihedral : 13.731 179.248 2624 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.19 % Allowed : 10.61 % Favored : 88.21 % 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: 0.90 (0.19), residues: 1902 helix: 1.00 (0.16), residues: 1045 sheet: 0.91 (0.31), residues: 273 loop : -0.11 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 218 TYR 0.011 0.001 TYR C 124 PHE 0.007 0.001 PHE E 58 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16224) covalent geometry : angle 0.54632 / 0.29 (22098) hydrogen bonds : bond 0.04991 / 3.29 ( 790) hydrogen bonds : angle 4.93428 / 3.54 ( 2250) *********************** 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 346 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8658 (m-40) cc_final: 0.8412 (m110) REVERT: B 99 ASN cc_start: 0.8378 (t0) cc_final: 0.8105 (t0) REVERT: B 117 MET cc_start: 0.8169 (tpp) cc_final: 0.7820 (tpp) REVERT: B 325 MET cc_start: 0.8924 (mmm) cc_final: 0.8693 (mmp) REVERT: C 178 MET cc_start: 0.9330 (mmt) cc_final: 0.8808 (mmt) REVERT: D 24 TYR cc_start: 0.7410 (m-80) cc_final: 0.7132 (m-80) REVERT: D 110 ASP cc_start: 0.8244 (t0) cc_final: 0.7867 (t0) REVERT: E 105 ASP cc_start: 0.8363 (m-30) cc_final: 0.8129 (m-30) REVERT: E 188 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7475 (tm-30) REVERT: E 243 ILE cc_start: 0.8598 (mm) cc_final: 0.8357 (mt) REVERT: E 327 TYR cc_start: 0.7829 (m-80) cc_final: 0.7310 (m-80) REVERT: F 89 GLU cc_start: 0.7956 (pm20) cc_final: 0.7574 (pm20) REVERT: F 163 MET cc_start: 0.7997 (tpp) cc_final: 0.7759 (tpp) REVERT: F 292 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8213 (mm-30) outliers start: 19 outliers final: 15 residues processed: 332 average time/residue: 0.3615 time to fit residues: 168.3718 Evaluate side-chains 333 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 318 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 129 optimal weight: 0.7980 chunk 40 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.079637 restraints weight = 74062.283| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.25 r_work: 0.2820 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16224 Z= 0.116 Angle : 0.536 6.371 22098 Z= 0.284 Chirality : 0.039 0.144 2488 Planarity : 0.005 0.049 2739 Dihedral : 13.684 178.538 2624 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.00 % Allowed : 10.79 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1902 helix: 1.12 (0.17), residues: 1046 sheet: 0.93 (0.31), residues: 273 loop : -0.03 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 291 TYR 0.010 0.001 TYR D 131 PHE 0.009 0.001 PHE E 197 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (16224) covalent geometry : angle 0.53608 / 0.28 (22098) hydrogen bonds : bond 0.04671 / 3.10 ( 790) hydrogen bonds : angle 4.82744 / 3.47 ( 2250) *********************** 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 346 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 330 time to evaluate : 0.925 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 99 ASN cc_start: 0.8639 (m-40) cc_final: 0.8421 (m110) REVERT: B 90 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8188 (mtmm) REVERT: B 99 ASN cc_start: 0.8360 (t0) cc_final: 0.8076 (t0) REVERT: B 117 MET cc_start: 0.8142 (tpp) cc_final: 0.7800 (tpp) REVERT: B 325 MET cc_start: 0.8911 (mmm) cc_final: 0.8674 (mmp) REVERT: C 178 MET cc_start: 0.9326 (mmt) cc_final: 0.8803 (mmt) REVERT: D 110 ASP cc_start: 0.8253 (t0) cc_final: 0.7865 (t0) REVERT: E 105 ASP cc_start: 0.8389 (m-30) cc_final: 0.8152 (m-30) REVERT: E 148 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: E 188 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7514 (tm-30) REVERT: E 243 ILE cc_start: 0.8600 (mm) cc_final: 0.8345 (mt) REVERT: E 327 TYR cc_start: 0.7839 (m-80) cc_final: 0.7208 (m-80) REVERT: F 163 MET cc_start: 0.7995 (tpp) cc_final: 0.7748 (tpp) REVERT: F 291 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7899 (ttm170) REVERT: F 292 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8175 (mm-30) outliers start: 16 outliers final: 14 residues processed: 335 average time/residue: 0.3610 time to fit residues: 169.7574 Evaluate side-chains 328 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 313 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.079608 restraints weight = 74258.278| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.23 r_work: 0.2815 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16224 Z= 0.138 Angle : 0.541 6.675 22098 Z= 0.286 Chirality : 0.040 0.139 2488 Planarity : 0.005 0.049 2739 Dihedral : 13.685 178.728 2624 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 1.11 (0.19), residues: 1902 helix: 1.20 (0.17), residues: 1047 sheet: 0.91 (0.31), residues: 273 loop : -0.04 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 291 TYR 0.011 0.001 TYR D 24 PHE 0.009 0.001 PHE D 25 HIS 0.003 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16224) covalent geometry : angle 0.54140 / 0.29 (22098) hydrogen bonds : bond 0.04634 / 3.06 ( 790) hydrogen bonds : angle 4.78308 / 3.43 ( 2250) *********************** 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 332 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 313 time to evaluate : 0.884 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 99 ASN cc_start: 0.8644 (m-40) cc_final: 0.8413 (m110) REVERT: A 252 ASP cc_start: 0.8305 (t0) cc_final: 0.8036 (t0) REVERT: B 90 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8198 (mtmm) REVERT: B 117 MET cc_start: 0.8143 (tpp) cc_final: 0.7817 (tpp) REVERT: B 325 MET cc_start: 0.8918 (mmm) cc_final: 0.8678 (mmp) REVERT: C 178 MET cc_start: 0.9317 (mmt) cc_final: 0.8802 (mmt) REVERT: D 110 ASP cc_start: 0.8261 (t0) cc_final: 0.7857 (t0) REVERT: E 105 ASP cc_start: 0.8400 (m-30) cc_final: 0.8153 (m-30) REVERT: E 148 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: E 188 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7526 (tm-30) REVERT: E 243 ILE cc_start: 0.8621 (mm) cc_final: 0.8361 (mt) REVERT: E 285 VAL cc_start: 0.7431 (t) cc_final: 0.7095 (m) REVERT: E 295 GLU cc_start: 0.8208 (tt0) cc_final: 0.7934 (mt-10) REVERT: E 327 TYR cc_start: 0.7838 (m-80) cc_final: 0.7228 (m-80) REVERT: F 89 GLU cc_start: 0.7809 (pm20) cc_final: 0.7565 (pm20) REVERT: F 163 MET cc_start: 0.7956 (tpp) cc_final: 0.7726 (tpp) REVERT: F 291 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7953 (ttm170) REVERT: F 292 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8203 (mm-30) outliers start: 19 outliers final: 17 residues processed: 319 average time/residue: 0.3512 time to fit residues: 158.9474 Evaluate side-chains 330 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 312 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 189 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 183 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.080173 restraints weight = 73880.692| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.26 r_work: 0.2825 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16224 Z= 0.111 Angle : 0.525 6.382 22098 Z= 0.276 Chirality : 0.039 0.143 2488 Planarity : 0.005 0.048 2739 Dihedral : 13.652 179.465 2624 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.06 % Allowed : 11.67 % Favored : 87.27 % 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: 1.24 (0.19), residues: 1902 helix: 1.29 (0.17), residues: 1048 sheet: 0.94 (0.30), residues: 273 loop : 0.06 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 218 TYR 0.010 0.001 TYR E 260 PHE 0.006 0.001 PHE E 58 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (16224) covalent geometry : angle 0.52531 / 0.28 (22098) hydrogen bonds : bond 0.04295 / 2.83 ( 790) hydrogen bonds : angle 4.70042 / 3.38 ( 2250) *********************** 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 332 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 0.983 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 99 ASN cc_start: 0.8633 (m-40) cc_final: 0.8431 (m110) REVERT: B 90 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8225 (mtmm) REVERT: B 117 MET cc_start: 0.8119 (tpp) cc_final: 0.7822 (tpp) REVERT: B 325 MET cc_start: 0.8854 (mmm) cc_final: 0.8611 (mmp) REVERT: C 50 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7879 (mm-30) REVERT: C 178 MET cc_start: 0.9306 (mmt) cc_final: 0.8784 (mmt) REVERT: D 24 TYR cc_start: 0.7546 (m-80) cc_final: 0.7318 (m-10) REVERT: E 105 ASP cc_start: 0.8387 (m-30) cc_final: 0.8128 (m-30) REVERT: E 148 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: E 243 ILE cc_start: 0.8543 (mm) cc_final: 0.8286 (mt) REVERT: E 285 VAL cc_start: 0.7416 (t) cc_final: 0.7087 (m) REVERT: E 295 GLU cc_start: 0.8176 (tt0) cc_final: 0.7924 (mt-10) REVERT: E 327 TYR cc_start: 0.7803 (m-80) cc_final: 0.7009 (m-80) REVERT: F 163 MET cc_start: 0.7946 (tpp) cc_final: 0.7707 (tpp) REVERT: F 291 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7952 (ttm170) REVERT: F 292 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8195 (mm-30) outliers start: 17 outliers final: 16 residues processed: 321 average time/residue: 0.3567 time to fit residues: 162.6408 Evaluate side-chains 330 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 313 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 114 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 144 optimal weight: 0.0020 chunk 88 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080458 restraints weight = 74242.198| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.27 r_work: 0.2810 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16224 Z= 0.112 Angle : 0.529 7.034 22098 Z= 0.277 Chirality : 0.039 0.145 2488 Planarity : 0.005 0.052 2739 Dihedral : 13.616 179.546 2624 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.06 % Allowed : 11.73 % Favored : 87.21 % 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: 1.39 (0.17), residues: 1049 sheet: 0.88 (0.30), residues: 275 loop : 0.15 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 218 TYR 0.017 0.001 TYR E 230 PHE 0.006 0.001 PHE D 25 HIS 0.002 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16224) covalent geometry : angle 0.52859 / 0.28 (22098) hydrogen bonds : bond 0.04126 / 2.72 ( 790) hydrogen bonds : angle 4.63729 / 3.33 ( 2250) ********************** 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 330 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 313 time to evaluate : 0.697 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 99 ASN cc_start: 0.8618 (m-40) cc_final: 0.8417 (m110) REVERT: B 90 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8222 (mtmm) REVERT: B 117 MET cc_start: 0.8148 (tpp) cc_final: 0.7862 (tpp) REVERT: B 325 MET cc_start: 0.8824 (mmm) cc_final: 0.8594 (mmp) REVERT: C 50 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7885 (mm-30) REVERT: C 178 MET cc_start: 0.9294 (mmt) cc_final: 0.8723 (mmt) REVERT: E 105 ASP cc_start: 0.8374 (m-30) cc_final: 0.8130 (m-30) REVERT: E 148 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: E 241 ASP cc_start: 0.7723 (p0) cc_final: 0.7116 (t0) REVERT: E 252 ASP cc_start: 0.8927 (t70) cc_final: 0.8671 (t0) REVERT: E 285 VAL cc_start: 0.7408 (t) cc_final: 0.7072 (m) REVERT: E 295 GLU cc_start: 0.8168 (tt0) cc_final: 0.7917 (mt-10) REVERT: E 327 TYR cc_start: 0.7793 (m-80) cc_final: 0.7029 (m-80) REVERT: F 163 MET cc_start: 0.7956 (tpp) cc_final: 0.7714 (tpp) REVERT: F 291 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7964 (ttm170) REVERT: F 292 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8226 (mm-30) outliers start: 17 outliers final: 16 residues processed: 319 average time/residue: 0.3539 time to fit residues: 159.7730 Evaluate side-chains 331 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 115 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 116 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 189 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.080000 restraints weight = 74246.788| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.26 r_work: 0.2792 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16224 Z= 0.125 Angle : 0.533 6.349 22098 Z= 0.279 Chirality : 0.039 0.147 2488 Planarity : 0.005 0.054 2739 Dihedral : 13.594 177.456 2624 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.12 % Allowed : 11.60 % Favored : 87.27 % 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: 1.36 (0.19), residues: 1902 helix: 1.40 (0.17), residues: 1049 sheet: 0.90 (0.30), residues: 276 loop : 0.17 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 218 TYR 0.012 0.001 TYR E 230 PHE 0.007 0.001 PHE E 197 HIS 0.002 0.001 HIS F 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16224) covalent geometry : angle 0.53323 / 0.28 (22098) hydrogen bonds : bond 0.04252 / 2.81 ( 790) hydrogen bonds : angle 4.63857 / 3.33 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8747.18 seconds wall clock time: 148 minutes 29.81 seconds (8909.81 seconds total)