Starting phenix.real_space_refine on Mon Jul 6 00:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbs_13301/07_2026/7pbs_13301_neut_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 47 5.49 5 Mg 5 5.21 5 S 102 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3152 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31328 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: 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} Time building chain proxies: 4.59, per 1000 atoms: 0.15 Number of scatterers: 31328 At special positions: 0 Unit cell: (123.2, 137.5, 107.8, 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 102 16.00 P 47 15.00 Mg 5 11.99 O 3152 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 950.9 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: 104 helices and 21 sheets defined 60.1% alpha, 11.4% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.617A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.559A 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 100 removed outlier: 3.654A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.413A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (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 198 removed outlier: 3.590A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.612A 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 288 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.783A 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: 3.585A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.522A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (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 100 removed outlier: 3.605A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.565A pdb=" N MET B 115 " --> pdb=" O ILE B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.524A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.515A pdb=" N TYR B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.505A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A 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 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.539A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 129 removed outlier: 4.137A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.555A 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 removed outlier: 3.519A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.787A 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: 3.691A 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 288 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.780A 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 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: 3.720A 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 130 removed outlier: 4.435A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.593A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.667A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.578A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 234 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.575A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.512A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.557A 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 48 removed outlier: 3.532A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.544A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.658A 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: 3.743A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.816A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.736A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 removed outlier: 3.746A pdb=" N ASN E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) 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: 3.712A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.703A 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 100 removed outlier: 3.713A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.483A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.542A pdb=" N PHE F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 213 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.528A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.573A 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 200 through 201 removed outlier: 7.008A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.408A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.349A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.441A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.340A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.189A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.507A pdb=" N LYS F 81 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP F 110 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR F 83 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC2, first strand: chain 'F' and resid 200 through 201 removed outlier: 7.085A pdb=" N THR F 200 " --> pdb=" O ILE F 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 308 through 311 775 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.71 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15439 1.05 - 1.28: 2655 1.28 - 1.50: 6782 1.50 - 1.72: 6592 1.72 - 1.94: 199 Bond restraints: 31667 Sorted by residual: bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.569 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.570 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 31662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 56769 2.28 - 4.57: 478 4.57 - 6.85: 38 6.85 - 9.13: 25 9.13 - 11.41: 11 Bond angle restraints: 57321 Sorted by residual: angle pdb=" O4' DC V 6 " pdb=" C1' DC V 6 " pdb=" N1 DC V 6 " ideal model delta sigma weight residual 108.00 111.24 -3.24 7.00e-01 2.04e+00 2.14e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT V 7 " pdb=" C4 DT V 7 " pdb=" O4 DT V 7 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT V 14 " pdb=" C4 DT V 14 " pdb=" O4 DT V 14 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.59e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 ... (remaining 57316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 14120 31.42 - 62.84: 611 62.84 - 94.26: 57 94.26 - 125.68: 0 125.68 - 157.10: 1 Dihedral angle restraints: 14789 sinusoidal: 8520 harmonic: 6269 Sorted by residual: 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 97.10 -157.10 1 2.00e+01 2.50e-03 4.61e+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 -90.39 -59.61 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP D 133 " pdb=" CB ASP D 133 " pdb=" CG ASP D 133 " pdb=" OD1 ASP D 133 " ideal model delta sinusoidal sigma weight residual -30.00 -86.49 56.49 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 14786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2251 0.085 - 0.170: 223 0.170 - 0.254: 9 0.254 - 0.339: 4 0.339 - 0.424: 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 -2.76 -0.42 2.00e-01 2.50e+01 4.49e+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 1.87e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.145 9.50e-02 1.11e+02 6.91e-02 5.71e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.099 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.312 9.50e-02 1.11e+02 1.13e-01 5.48e+01 pdb=" NE ARG E 160 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.168 9.50e-02 1.11e+02 7.21e-02 4.99e+01 pdb=" NE ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.083 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.084 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 760 2.13 - 2.75: 56501 2.75 - 3.37: 84017 3.37 - 3.98: 108550 3.98 - 4.60: 175860 Nonbonded interactions: 425688 Sorted by model distance: nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.516 2.450 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.525 2.450 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.534 2.450 nonbonded pdb=" HZ3 LYS D 46 " pdb=" O GLU D 75 " model vdw 1.538 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.568 2.450 ... (remaining 425683 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: 3.350 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: 0.180 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.440 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.006 0.104 16228 Z= 0.320 Angle : 0.826 11.413 22105 Z= 0.465 Chirality : 0.050 0.424 2488 Planarity : 0.011 0.137 2739 Dihedral : 15.479 157.097 6377 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.25 % Allowed : 1.37 % Favored : 98.38 % 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: -0.18 (0.18), residues: 1902 helix: -0.48 (0.15), residues: 1018 sheet: 0.80 (0.30), residues: 309 loop : 0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C 114 TYR 0.025 0.005 TYR E 273 PHE 0.020 0.003 PHE A 25 HIS 0.012 0.003 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.32 (16228) covalent geometry : angle 0.82629 / 0.46 (22105) hydrogen bonds : bond 0.24351 / 16.05 ( 800) hydrogen bonds : angle 8.57410 / 6.15 ( 2276) *********************** 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 424 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 420 time to evaluate : 0.623 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 33 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7428 (mttt) REVERT: A 43 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 131 TYR cc_start: 0.8742 (p90) cc_final: 0.7984 (p90) REVERT: A 160 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7771 (ptp-170) REVERT: A 234 MET cc_start: 0.7411 (ptp) cc_final: 0.7067 (ptp) REVERT: A 252 ASP cc_start: 0.7867 (t0) cc_final: 0.7416 (t0) REVERT: A 282 THR cc_start: 0.8514 (m) cc_final: 0.8033 (p) REVERT: A 292 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6967 (tt0) REVERT: A 309 MET cc_start: 0.7326 (ttm) cc_final: 0.7122 (ttt) REVERT: A 325 MET cc_start: 0.7672 (mmm) cc_final: 0.7250 (mmt) REVERT: B 49 ASP cc_start: 0.7720 (t0) cc_final: 0.7439 (t0) REVERT: B 102 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6946 (mt-10) REVERT: B 178 MET cc_start: 0.8658 (mmm) cc_final: 0.7603 (mmt) REVERT: B 199 MET cc_start: 0.7852 (mmp) cc_final: 0.7278 (tpt) REVERT: B 234 MET cc_start: 0.8341 (mmp) cc_final: 0.8124 (mmm) REVERT: C 47 LEU cc_start: 0.8037 (tp) cc_final: 0.7701 (mt) REVERT: C 260 TYR cc_start: 0.7683 (t80) cc_final: 0.7360 (t80) REVERT: D 78 VAL cc_start: 0.7517 (t) cc_final: 0.7270 (p) REVERT: D 264 LYS cc_start: 0.7838 (tttt) cc_final: 0.7482 (ttpt) REVERT: D 292 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7162 (mp0) REVERT: D 309 MET cc_start: 0.7813 (mtp) cc_final: 0.7580 (mtp) REVERT: D 330 THR cc_start: 0.6052 (m) cc_final: 0.5665 (p) REVERT: E 76 MET cc_start: 0.8489 (mmm) cc_final: 0.7798 (mmt) REVERT: E 89 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6160 (mm-30) REVERT: E 111 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7734 (mt-10) REVERT: E 125 SER cc_start: 0.7697 (m) cc_final: 0.7494 (t) REVERT: E 143 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6012 (mtm110) REVERT: E 179 GLU cc_start: 0.7682 (pt0) cc_final: 0.7456 (pt0) REVERT: E 242 LYS cc_start: 0.7315 (pttm) cc_final: 0.6655 (tppt) REVERT: E 267 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6663 (ttp-110) REVERT: E 299 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6124 (mt-10) REVERT: E 301 TYR cc_start: 0.7101 (t80) cc_final: 0.6824 (t80) REVERT: F 102 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6767 (mp0) REVERT: F 125 SER cc_start: 0.8456 (m) cc_final: 0.8214 (p) REVERT: F 143 ARG cc_start: 0.7562 (ptt90) cc_final: 0.7229 (ptt-90) REVERT: F 144 SER cc_start: 0.8630 (p) cc_final: 0.8350 (t) REVERT: F 199 MET cc_start: 0.7222 (tpp) cc_final: 0.6662 (tpp) REVERT: F 267 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5890 (ttp80) REVERT: F 286 ASN cc_start: 0.7162 (m-40) cc_final: 0.6900 (m110) outliers start: 4 outliers final: 1 residues processed: 421 average time/residue: 0.3154 time to fit residues: 187.2923 Evaluate side-chains 275 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN D 232 GLN D 286 ASN E 166 ASN F 23 GLN F 113 HIS F 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.094958 restraints weight = 65998.243| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.96 r_work: 0.2833 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16228 Z= 0.171 Angle : 0.644 8.135 22105 Z= 0.353 Chirality : 0.043 0.176 2488 Planarity : 0.006 0.070 2739 Dihedral : 14.780 140.200 2653 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.94 % Allowed : 5.68 % Favored : 93.39 % 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: 0.70 (0.19), residues: 1902 helix: 0.47 (0.16), residues: 1046 sheet: 1.24 (0.31), residues: 272 loop : 0.36 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 218 TYR 0.012 0.001 TYR E 273 PHE 0.011 0.001 PHE D 172 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (16228) covalent geometry : angle 0.64415 / 0.35 (22105) hydrogen bonds : bond 0.07224 / 4.86 ( 800) hydrogen bonds : angle 6.08791 / 4.35 ( 2276) *********************** 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 282 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 0.673 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: A 131 TYR cc_start: 0.9051 (p90) cc_final: 0.8566 (p90) REVERT: A 160 ARG cc_start: 0.8552 (ptp90) cc_final: 0.8266 (ptp-170) REVERT: A 234 MET cc_start: 0.8084 (ptp) cc_final: 0.7656 (ptp) REVERT: A 252 ASP cc_start: 0.7996 (t0) cc_final: 0.7414 (t0) REVERT: A 282 THR cc_start: 0.8327 (m) cc_final: 0.8078 (p) REVERT: A 309 MET cc_start: 0.8018 (ttm) cc_final: 0.7807 (ttt) REVERT: A 325 MET cc_start: 0.7701 (mmm) cc_final: 0.7347 (mmt) REVERT: B 49 ASP cc_start: 0.8325 (t0) cc_final: 0.8035 (t0) REVERT: B 102 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7272 (mt-10) REVERT: B 178 MET cc_start: 0.8944 (mmm) cc_final: 0.8072 (mmt) REVERT: B 199 MET cc_start: 0.8190 (mmp) cc_final: 0.7602 (tpt) REVERT: C 260 TYR cc_start: 0.7835 (t80) cc_final: 0.7581 (t80) REVERT: D 78 VAL cc_start: 0.7725 (t) cc_final: 0.7480 (p) REVERT: D 117 MET cc_start: 0.6810 (ttm) cc_final: 0.6498 (mtp) REVERT: D 272 MET cc_start: 0.8808 (mmm) cc_final: 0.8546 (mmm) REVERT: D 292 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7715 (mp0) REVERT: D 330 THR cc_start: 0.6164 (m) cc_final: 0.5826 (p) REVERT: E 84 SER cc_start: 0.8508 (p) cc_final: 0.8155 (t) REVERT: E 89 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6237 (mm-30) REVERT: E 135 MET cc_start: 0.5813 (mmm) cc_final: 0.5411 (mmm) REVERT: E 143 ARG cc_start: 0.6216 (mtm180) cc_final: 0.5628 (mtm110) REVERT: E 255 HIS cc_start: 0.6764 (p-80) cc_final: 0.6064 (m90) REVERT: E 267 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.6824 (ttp-110) REVERT: E 301 TYR cc_start: 0.7282 (t80) cc_final: 0.6902 (t80) REVERT: F 102 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7166 (mp0) REVERT: F 143 ARG cc_start: 0.7860 (ptt90) cc_final: 0.7484 (ptt-90) REVERT: F 144 SER cc_start: 0.8761 (p) cc_final: 0.8489 (t) REVERT: F 195 GLU cc_start: 0.7386 (tp30) cc_final: 0.7076 (tm-30) REVERT: F 267 ARG cc_start: 0.6653 (ttm170) cc_final: 0.6006 (ttp80) outliers start: 15 outliers final: 12 residues processed: 276 average time/residue: 0.2690 time to fit residues: 108.1914 Evaluate side-chains 254 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094176 restraints weight = 66512.812| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.87 r_work: 0.2810 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16228 Z= 0.172 Angle : 0.571 6.183 22105 Z= 0.308 Chirality : 0.041 0.152 2488 Planarity : 0.005 0.063 2739 Dihedral : 14.191 143.227 2653 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.81 % Allowed : 6.43 % Favored : 92.76 % 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: 0.75 (0.19), residues: 1902 helix: 0.64 (0.16), residues: 1049 sheet: 0.98 (0.31), residues: 272 loop : 0.29 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 312 TYR 0.013 0.001 TYR E 298 PHE 0.007 0.001 PHE E 58 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (16228) covalent geometry : angle 0.57083 / 0.31 (22105) hydrogen bonds : bond 0.06362 / 4.34 ( 800) hydrogen bonds : angle 5.53237 / 3.94 ( 2276) *********************** 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 262 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8565 (ptp90) cc_final: 0.8241 (ptp-170) REVERT: A 234 MET cc_start: 0.8165 (ptp) cc_final: 0.7733 (ptp) REVERT: A 252 ASP cc_start: 0.7877 (t0) cc_final: 0.7317 (t0) REVERT: A 282 THR cc_start: 0.8304 (m) cc_final: 0.8085 (p) REVERT: B 102 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7259 (mt-10) REVERT: B 128 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: B 199 MET cc_start: 0.8232 (mmp) cc_final: 0.7531 (tpt) REVERT: D 78 VAL cc_start: 0.7787 (t) cc_final: 0.7514 (p) REVERT: D 117 MET cc_start: 0.6815 (ttm) cc_final: 0.6606 (mtp) REVERT: D 130 TYR cc_start: 0.5462 (m-80) cc_final: 0.5215 (m-80) REVERT: D 272 MET cc_start: 0.8819 (mmm) cc_final: 0.8573 (mmm) REVERT: D 292 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7726 (mp0) REVERT: D 330 THR cc_start: 0.6258 (m) cc_final: 0.5882 (p) REVERT: E 84 SER cc_start: 0.8423 (p) cc_final: 0.8076 (t) REVERT: E 89 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6244 (mm-30) REVERT: E 143 ARG cc_start: 0.6394 (mtm180) cc_final: 0.6062 (mtm110) REVERT: E 255 HIS cc_start: 0.6887 (p-80) cc_final: 0.6222 (m90) REVERT: E 267 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.6856 (ttp-110) REVERT: E 301 TYR cc_start: 0.7442 (t80) cc_final: 0.7006 (t80) REVERT: F 102 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7250 (mp0) REVERT: F 143 ARG cc_start: 0.7922 (ptt90) cc_final: 0.7607 (ptt-90) outliers start: 13 outliers final: 10 residues processed: 255 average time/residue: 0.2988 time to fit residues: 110.1203 Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 234 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092823 restraints weight = 65502.841| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.96 r_work: 0.2813 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16228 Z= 0.142 Angle : 0.540 6.321 22105 Z= 0.291 Chirality : 0.041 0.148 2488 Planarity : 0.005 0.054 2739 Dihedral : 13.936 143.699 2653 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.06 % Allowed : 6.92 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1902 helix: 0.82 (0.16), residues: 1049 sheet: 0.86 (0.30), residues: 272 loop : 0.21 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 160 TYR 0.015 0.001 TYR A 322 PHE 0.006 0.001 PHE B 58 HIS 0.012 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16228) covalent geometry : angle 0.53992 / 0.29 (22105) hydrogen bonds : bond 0.05240 / 3.54 ( 800) hydrogen bonds : angle 5.19494 / 3.70 ( 2276) *********************** 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 262 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8553 (ptp90) cc_final: 0.8212 (ptp-170) REVERT: A 234 MET cc_start: 0.8057 (ptp) cc_final: 0.7506 (ptp) REVERT: A 252 ASP cc_start: 0.8011 (t0) cc_final: 0.7459 (t0) REVERT: A 325 MET cc_start: 0.7793 (mmp) cc_final: 0.7388 (mmp) REVERT: B 102 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7474 (mt-10) REVERT: B 128 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: B 199 MET cc_start: 0.8255 (mmp) cc_final: 0.7544 (tpt) REVERT: D 78 VAL cc_start: 0.7806 (t) cc_final: 0.7550 (p) REVERT: D 130 TYR cc_start: 0.5709 (m-80) cc_final: 0.5423 (m-80) REVERT: D 272 MET cc_start: 0.8829 (mmm) cc_final: 0.8569 (mmm) REVERT: D 292 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7794 (mp0) REVERT: D 330 THR cc_start: 0.6564 (m) cc_final: 0.6189 (p) REVERT: E 84 SER cc_start: 0.8462 (p) cc_final: 0.8152 (t) REVERT: E 89 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6095 (mm-30) REVERT: E 101 LEU cc_start: 0.7641 (mt) cc_final: 0.7409 (mt) REVERT: E 143 ARG cc_start: 0.6412 (mtm180) cc_final: 0.6088 (mtm110) REVERT: E 234 MET cc_start: 0.6802 (mpp) cc_final: 0.6601 (mpp) REVERT: E 255 HIS cc_start: 0.6891 (p-80) cc_final: 0.6268 (m90) REVERT: E 267 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.6877 (ttp-110) REVERT: E 301 TYR cc_start: 0.7487 (t80) cc_final: 0.7186 (t80) REVERT: F 102 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7288 (mp0) REVERT: F 121 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8501 (mm-30) REVERT: F 143 ARG cc_start: 0.7943 (ptt90) cc_final: 0.7668 (ptt-90) outliers start: 17 outliers final: 12 residues processed: 255 average time/residue: 0.3021 time to fit residues: 112.1258 Evaluate side-chains 250 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 136 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.091339 restraints weight = 66256.286| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.00 r_work: 0.2787 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16228 Z= 0.195 Angle : 0.568 6.045 22105 Z= 0.305 Chirality : 0.042 0.153 2488 Planarity : 0.005 0.054 2739 Dihedral : 14.068 150.278 2653 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.94 % Allowed : 7.67 % Favored : 91.39 % 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: 0.70 (0.19), residues: 1902 helix: 0.81 (0.16), residues: 1048 sheet: 0.69 (0.30), residues: 274 loop : -0.05 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 312 TYR 0.011 0.001 TYR F 298 PHE 0.009 0.001 PHE B 152 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (16228) covalent geometry : angle 0.56794 / 0.31 (22105) hydrogen bonds : bond 0.05569 / 3.79 ( 800) hydrogen bonds : angle 5.13006 / 3.65 ( 2276) *********************** 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 256 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8087 (p) cc_final: 0.7885 (t) REVERT: A 160 ARG cc_start: 0.8542 (ptp90) cc_final: 0.8186 (ptp-170) REVERT: A 234 MET cc_start: 0.8141 (ptp) cc_final: 0.7563 (ptp) REVERT: A 252 ASP cc_start: 0.7871 (t0) cc_final: 0.7429 (t0) REVERT: B 102 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7489 (mt-10) REVERT: B 128 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: B 199 MET cc_start: 0.8302 (mmp) cc_final: 0.7524 (tpt) REVERT: C 100 ASP cc_start: 0.7030 (t0) cc_final: 0.6819 (t0) REVERT: D 78 VAL cc_start: 0.7902 (t) cc_final: 0.7619 (p) REVERT: D 272 MET cc_start: 0.8826 (mmm) cc_final: 0.8566 (mmm) REVERT: D 292 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7883 (mp0) REVERT: D 330 THR cc_start: 0.6631 (m) cc_final: 0.6279 (p) REVERT: E 84 SER cc_start: 0.8438 (p) cc_final: 0.8143 (t) REVERT: E 89 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6268 (mm-30) REVERT: E 143 ARG cc_start: 0.6495 (mtm180) cc_final: 0.6147 (mtm110) REVERT: E 255 HIS cc_start: 0.7015 (p-80) cc_final: 0.6256 (m90) REVERT: E 260 TYR cc_start: 0.7199 (t80) cc_final: 0.6754 (t80) REVERT: E 267 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6823 (ttp-110) REVERT: E 301 TYR cc_start: 0.7450 (t80) cc_final: 0.7102 (t80) REVERT: E 309 MET cc_start: 0.4678 (ptt) cc_final: 0.4467 (ptt) REVERT: F 102 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7281 (mp0) REVERT: F 121 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8549 (mm-30) outliers start: 15 outliers final: 12 residues processed: 248 average time/residue: 0.2896 time to fit residues: 104.3754 Evaluate side-chains 246 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.091996 restraints weight = 65811.798| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.01 r_work: 0.2840 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16228 Z= 0.143 Angle : 0.533 5.947 22105 Z= 0.287 Chirality : 0.040 0.171 2488 Planarity : 0.005 0.049 2739 Dihedral : 14.006 150.142 2653 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.87 % Allowed : 8.23 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1902 helix: 0.92 (0.16), residues: 1049 sheet: 0.69 (0.30), residues: 274 loop : -0.00 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.010 0.001 TYR D 131 PHE 0.007 0.001 PHE B 58 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16228) covalent geometry : angle 0.53266 / 0.29 (22105) hydrogen bonds : bond 0.05073 / 3.45 ( 800) hydrogen bonds : angle 5.01677 / 3.57 ( 2276) *********************** 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 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8540 (ptp90) cc_final: 0.8176 (ptp-170) REVERT: A 234 MET cc_start: 0.8125 (ptp) cc_final: 0.7548 (ptp) REVERT: A 252 ASP cc_start: 0.7872 (t0) cc_final: 0.7330 (t0) REVERT: B 102 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7496 (mt-10) REVERT: B 128 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: B 199 MET cc_start: 0.8331 (mmp) cc_final: 0.7545 (tpt) REVERT: B 242 LYS cc_start: 0.7960 (tppt) cc_final: 0.7478 (tppt) REVERT: D 78 VAL cc_start: 0.7904 (t) cc_final: 0.7625 (p) REVERT: D 272 MET cc_start: 0.8752 (mmm) cc_final: 0.8457 (mmm) REVERT: D 292 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7877 (mp0) REVERT: E 84 SER cc_start: 0.8466 (p) cc_final: 0.8238 (t) REVERT: E 89 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6249 (mm-30) REVERT: E 101 LEU cc_start: 0.7728 (mt) cc_final: 0.7496 (mt) REVERT: E 143 ARG cc_start: 0.6464 (mtm180) cc_final: 0.6127 (mtm110) REVERT: E 255 HIS cc_start: 0.7018 (p-80) cc_final: 0.6266 (m90) REVERT: E 267 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6874 (ttp-110) REVERT: E 301 TYR cc_start: 0.7487 (t80) cc_final: 0.7164 (t80) REVERT: E 309 MET cc_start: 0.4678 (ptt) cc_final: 0.4466 (ptt) REVERT: F 102 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7305 (mp0) outliers start: 14 outliers final: 12 residues processed: 243 average time/residue: 0.2881 time to fit residues: 101.6719 Evaluate side-chains 244 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 79 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092149 restraints weight = 65737.910| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.96 r_work: 0.2818 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.135 Angle : 0.510 6.048 22105 Z= 0.273 Chirality : 0.040 0.172 2488 Planarity : 0.005 0.044 2739 Dihedral : 13.884 150.966 2653 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.00 % Allowed : 8.67 % Favored : 90.33 % 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: 1.03 (0.19), residues: 1902 helix: 1.12 (0.16), residues: 1046 sheet: 0.66 (0.30), residues: 274 loop : 0.08 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 291 TYR 0.012 0.001 TYR A 322 PHE 0.007 0.001 PHE A 152 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16228) covalent geometry : angle 0.50960 / 0.27 (22105) hydrogen bonds : bond 0.04638 / 3.13 ( 800) hydrogen bonds : angle 4.87838 / 3.47 ( 2276) *********************** 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 252 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8211 (m-30) cc_final: 0.7899 (t70) REVERT: A 160 ARG cc_start: 0.8506 (ptp90) cc_final: 0.8138 (ptp-170) REVERT: A 234 MET cc_start: 0.7989 (ptp) cc_final: 0.7476 (ptp) REVERT: A 252 ASP cc_start: 0.7865 (t0) cc_final: 0.7324 (t0) REVERT: B 102 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7510 (mt-10) REVERT: B 128 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 199 MET cc_start: 0.8385 (mmp) cc_final: 0.7600 (tpt) REVERT: B 242 LYS cc_start: 0.7976 (tppt) cc_final: 0.7482 (tppt) REVERT: D 78 VAL cc_start: 0.7901 (t) cc_final: 0.7617 (p) REVERT: D 272 MET cc_start: 0.8792 (mmm) cc_final: 0.8485 (mmm) REVERT: D 292 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7894 (mp0) REVERT: E 89 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6259 (mm-30) REVERT: E 101 LEU cc_start: 0.7743 (mt) cc_final: 0.7490 (mt) REVERT: E 143 ARG cc_start: 0.6465 (mtm180) cc_final: 0.6120 (mtm110) REVERT: E 255 HIS cc_start: 0.7061 (p-80) cc_final: 0.6298 (m90) REVERT: E 260 TYR cc_start: 0.7201 (t80) cc_final: 0.6800 (t80) REVERT: E 267 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6921 (ttp-110) REVERT: E 301 TYR cc_start: 0.7517 (t80) cc_final: 0.7226 (t80) REVERT: E 309 MET cc_start: 0.4672 (ptt) cc_final: 0.4435 (ptt) REVERT: F 47 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8422 (mp) REVERT: F 102 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7316 (mp0) REVERT: F 309 MET cc_start: 0.7494 (tpp) cc_final: 0.6992 (ttm) outliers start: 16 outliers final: 14 residues processed: 243 average time/residue: 0.2875 time to fit residues: 101.0483 Evaluate side-chains 248 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091953 restraints weight = 65596.417| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.96 r_work: 0.2864 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16228 Z= 0.159 Angle : 0.524 6.878 22105 Z= 0.281 Chirality : 0.040 0.141 2488 Planarity : 0.005 0.045 2739 Dihedral : 13.911 153.191 2653 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.00 % Allowed : 9.11 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1902 helix: 1.09 (0.16), residues: 1046 sheet: 0.55 (0.30), residues: 264 loop : 0.00 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.011 0.001 TYR D 131 PHE 0.007 0.001 PHE A 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (16228) covalent geometry : angle 0.52401 / 0.28 (22105) hydrogen bonds : bond 0.04835 / 3.29 ( 800) hydrogen bonds : angle 4.88426 / 3.47 ( 2276) *********************** 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 249 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8231 (m-30) cc_final: 0.7917 (t70) REVERT: A 160 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8135 (ptp-170) REVERT: A 234 MET cc_start: 0.8085 (ptp) cc_final: 0.7518 (ptp) REVERT: A 252 ASP cc_start: 0.7861 (t0) cc_final: 0.7314 (t0) REVERT: B 102 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7507 (mt-10) REVERT: B 128 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: B 199 MET cc_start: 0.8397 (mmp) cc_final: 0.7610 (tpt) REVERT: B 242 LYS cc_start: 0.7966 (tppt) cc_final: 0.7471 (tppt) REVERT: D 292 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7890 (mp0) REVERT: E 89 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6259 (mm-30) REVERT: E 101 LEU cc_start: 0.7759 (mt) cc_final: 0.7504 (mt) REVERT: E 143 ARG cc_start: 0.6471 (mtm180) cc_final: 0.6123 (mtm110) REVERT: E 255 HIS cc_start: 0.7178 (p-80) cc_final: 0.6318 (m90) REVERT: E 260 TYR cc_start: 0.7213 (t80) cc_final: 0.6806 (t80) REVERT: E 267 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6915 (ttp-110) REVERT: E 301 TYR cc_start: 0.7520 (t80) cc_final: 0.7230 (t80) REVERT: F 47 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8397 (mp) REVERT: F 102 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7365 (mp0) outliers start: 16 outliers final: 12 residues processed: 240 average time/residue: 0.2774 time to fit residues: 96.1737 Evaluate side-chains 243 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 26 optimal weight: 0.0270 chunk 62 optimal weight: 0.0000 chunk 122 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 187 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.092943 restraints weight = 65455.722| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.98 r_work: 0.2843 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16228 Z= 0.097 Angle : 0.476 7.477 22105 Z= 0.255 Chirality : 0.039 0.138 2488 Planarity : 0.004 0.036 2739 Dihedral : 13.745 149.481 2653 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.81 % Allowed : 9.48 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 1902 helix: 1.35 (0.17), residues: 1046 sheet: 0.67 (0.29), residues: 274 loop : 0.23 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.013 0.001 TYR A 322 PHE 0.005 0.001 PHE C 58 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (16228) covalent geometry : angle 0.47600 / 0.25 (22105) hydrogen bonds : bond 0.04021 / 2.71 ( 800) hydrogen bonds : angle 4.70562 / 3.34 ( 2276) *********************** 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 255 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8183 (m-30) cc_final: 0.7909 (t70) REVERT: A 111 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7651 (mp0) REVERT: A 160 ARG cc_start: 0.8492 (ptp90) cc_final: 0.8083 (ptp-170) REVERT: A 234 MET cc_start: 0.8002 (ptp) cc_final: 0.7536 (ptp) REVERT: A 252 ASP cc_start: 0.7962 (t0) cc_final: 0.7389 (t0) REVERT: B 102 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7507 (mt-10) REVERT: B 128 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: B 199 MET cc_start: 0.8447 (mmp) cc_final: 0.7765 (tpt) REVERT: B 242 LYS cc_start: 0.7903 (tppt) cc_final: 0.7429 (tppt) REVERT: D 272 MET cc_start: 0.8770 (mmm) cc_final: 0.8467 (mmm) REVERT: D 292 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7875 (mp0) REVERT: E 89 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6407 (mm-30) REVERT: E 101 LEU cc_start: 0.7655 (mt) cc_final: 0.7374 (mt) REVERT: E 143 ARG cc_start: 0.6480 (mtm180) cc_final: 0.6142 (mtm110) REVERT: E 240 ASP cc_start: 0.7019 (m-30) cc_final: 0.6255 (t70) REVERT: E 255 HIS cc_start: 0.7144 (p-80) cc_final: 0.6337 (m90) REVERT: E 260 TYR cc_start: 0.7158 (t80) cc_final: 0.6785 (t80) REVERT: E 267 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.6929 (ttp-110) REVERT: E 301 TYR cc_start: 0.7505 (t80) cc_final: 0.7234 (t80) REVERT: E 309 MET cc_start: 0.4524 (ptt) cc_final: 0.4314 (ptt) REVERT: F 47 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (mp) REVERT: F 102 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7370 (mp0) REVERT: F 135 MET cc_start: 0.7946 (mmm) cc_final: 0.7111 (mmt) REVERT: F 309 MET cc_start: 0.7511 (tpp) cc_final: 0.7001 (ttm) outliers start: 13 outliers final: 7 residues processed: 249 average time/residue: 0.2925 time to fit residues: 105.8799 Evaluate side-chains 240 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.089889 restraints weight = 65903.575| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.02 r_work: 0.2827 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16228 Z= 0.123 Angle : 0.490 7.054 22105 Z= 0.262 Chirality : 0.039 0.136 2488 Planarity : 0.005 0.045 2739 Dihedral : 13.767 150.682 2653 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.69 % Allowed : 9.61 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 1902 helix: 1.39 (0.17), residues: 1046 sheet: 0.55 (0.30), residues: 264 loop : 0.17 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 312 TYR 0.013 0.001 TYR A 322 PHE 0.006 0.001 PHE A 152 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (16228) covalent geometry : angle 0.49015 / 0.26 (22105) hydrogen bonds : bond 0.04217 / 2.84 ( 800) hydrogen bonds : angle 4.70798 / 3.35 ( 2276) ********************** 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 244 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 233 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8233 (m-30) cc_final: 0.7921 (t70) REVERT: A 111 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7670 (mp0) REVERT: A 160 ARG cc_start: 0.8487 (ptp90) cc_final: 0.8078 (ptp-170) REVERT: A 234 MET cc_start: 0.8014 (ptp) cc_final: 0.7516 (ptp) REVERT: A 252 ASP cc_start: 0.7881 (t0) cc_final: 0.7327 (t0) REVERT: B 102 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7491 (mt-10) REVERT: B 128 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: B 199 MET cc_start: 0.8450 (mmp) cc_final: 0.7684 (tpt) REVERT: B 242 LYS cc_start: 0.7889 (tppt) cc_final: 0.7401 (tppt) REVERT: D 272 MET cc_start: 0.8808 (mmm) cc_final: 0.8509 (mmm) REVERT: D 292 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7885 (mp0) REVERT: E 89 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6378 (mm-30) REVERT: E 101 LEU cc_start: 0.7658 (mt) cc_final: 0.7374 (mt) REVERT: E 143 ARG cc_start: 0.6483 (mtm180) cc_final: 0.6128 (mtm110) REVERT: E 240 ASP cc_start: 0.7021 (m-30) cc_final: 0.6245 (t70) REVERT: E 255 HIS cc_start: 0.7163 (p-80) cc_final: 0.6322 (m90) REVERT: E 260 TYR cc_start: 0.7192 (t80) cc_final: 0.6831 (t80) REVERT: E 267 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6904 (ttp-110) REVERT: E 301 TYR cc_start: 0.7505 (t80) cc_final: 0.7236 (t80) REVERT: F 47 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8376 (mp) REVERT: F 102 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7417 (mp0) REVERT: F 135 MET cc_start: 0.7986 (mmm) cc_final: 0.7266 (mmt) REVERT: F 309 MET cc_start: 0.7537 (tpp) cc_final: 0.7021 (ttm) outliers start: 11 outliers final: 7 residues processed: 238 average time/residue: 0.3056 time to fit residues: 105.4326 Evaluate side-chains 242 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 233 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 134 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091091 restraints weight = 66261.497| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.05 r_work: 0.2816 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.146 Angle : 0.510 7.633 22105 Z= 0.273 Chirality : 0.040 0.140 2488 Planarity : 0.005 0.041 2739 Dihedral : 13.823 154.795 2653 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.69 % Allowed : 9.67 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1902 helix: 1.33 (0.17), residues: 1046 sheet: 0.51 (0.30), residues: 264 loop : 0.10 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 312 TYR 0.013 0.001 TYR A 322 PHE 0.007 0.001 PHE C 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16228) covalent geometry : angle 0.51039 / 0.27 (22105) hydrogen bonds : bond 0.04499 / 3.02 ( 800) hydrogen bonds : angle 4.73722 / 3.36 ( 2276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6839.70 seconds wall clock time: 116 minutes 29.40 seconds (6989.40 seconds total)