Starting phenix.real_space_refine on Thu Jun 4 15:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.map" model { file = "/net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iik_60596/06_2026/9iik_60596.cif" } resolution = 4.12 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= 0.029 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 8865 2.51 5 N 2431 2.21 5 O 2631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14001 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3925 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3900 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 461} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2340 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 292} Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3821 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 459} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.24 Number of scatterers: 14001 At special positions: 0 Unit cell: (102.343, 147.59, 258.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 2 15.00 O 2631 8.00 N 2431 7.00 C 8865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 219 " - pdb=" SG CYS G 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS G 237 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.03 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: 1.11 Conformation dependent library (CDL) restraints added in 665.2 milliseconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3294 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 24 sheets defined 21.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.678A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.075A pdb=" N ASN E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 290 Proline residue: E 224 - end of helix Proline residue: E 233 - end of helix removed outlier: 3.710A pdb=" N GLU E 254 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 removed outlier: 3.631A pdb=" N ALA E 309 " --> pdb=" O PRO E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 388 through 391 Processing helix chain 'G' and resid 221 through 253 removed outlier: 3.558A pdb=" N ILE G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE G 232 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Proline residue: G 233 - end of helix removed outlier: 3.706A pdb=" N LYS G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G 244 " --> pdb=" O TRP G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 295 removed outlier: 4.038A pdb=" N THR G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.734A pdb=" N PHE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 305 Proline residue: C 228 - end of helix Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 219 through 293 Proline residue: D 228 - end of helix removed outlier: 3.549A pdb=" N ARG D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.811A pdb=" N TYR D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 removed outlier: 4.035A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 54 through 56 removed outlier: 3.945A pdb=" N GLU E 35 " --> pdb=" O GLN E 100 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN E 100 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 39 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY E 93 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU E 112 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 138 through 142 removed outlier: 5.473A pdb=" N ILE E 138 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR E 177 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG E 140 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 175 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET E 174 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET E 166 " --> pdb=" O MET E 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 147 through 151 Processing sheet with id=AA5, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.832A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE G 469 " --> pdb=" O VAL G 322 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 322 " --> pdb=" O ILE G 469 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 297 through 299 removed outlier: 3.832A pdb=" N LEU E 297 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU G 297 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN G 437 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N HIS G 443 " --> pdb=" O ASN G 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 304 through 305 removed outlier: 4.906A pdb=" N LEU E 348 " --> pdb=" O ASP E 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 315 removed outlier: 3.742A pdb=" N TRP E 360 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASN E 437 " --> pdb=" O HIS E 443 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS E 443 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 13 removed outlier: 4.153A pdb=" N ILE G 11 " --> pdb=" O HIS G 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 113 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP G 106 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA G 108 " --> pdb=" O CYS G 97 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG G 96 " --> pdb=" O PHE G 39 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE G 39 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 68 through 71 Processing sheet with id=AB2, first strand: chain 'G' and resid 122 through 129 removed outlier: 6.408A pdb=" N ARG G 134 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS G 128 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY G 132 " --> pdb=" O HIS G 128 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 135 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 179 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER G 139 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL G 175 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY G 141 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE G 173 " --> pdb=" O GLY G 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 147 through 151 Processing sheet with id=AB4, first strand: chain 'G' and resid 304 through 305 removed outlier: 4.632A pdb=" N LEU G 348 " --> pdb=" O ASP G 305 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 349 " --> pdb=" O PRO G 458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.833A pdb=" N LYS C 79 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP C 73 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 14 removed outlier: 5.660A pdb=" N SER C 40 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 46 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.772A pdb=" N VAL C 166 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.565A pdb=" N VAL C 175 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR C 140 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA C 177 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG C 138 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 179 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU C 136 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET C 181 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C 134 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP D 150 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 157 through 158 removed outlier: 4.698A pdb=" N TRP C 150 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 157 through 158 removed outlier: 4.698A pdb=" N TRP C 150 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N VAL D 123 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER C 205 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL D 125 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER C 207 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLY D 127 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N HIS D 134 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 5 removed outlier: 7.361A pdb=" N ALA D 81 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG D 72 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE D 70 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 14 removed outlier: 5.718A pdb=" N ILE D 11 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA D 115 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA D 13 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU D 36 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D 49 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP D 38 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 45 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 324 through 326 Processing sheet with id=AC5, first strand: chain 'D' and resid 354 through 356 removed outlier: 3.627A pdb=" N THR D 420 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 365 through 371 removed outlier: 6.077A pdb=" N ASN D 446 " --> pdb=" O HIS D 452 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS D 452 " --> pdb=" O ASN D 446 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4344 1.34 - 1.46: 2470 1.46 - 1.58: 7390 1.58 - 1.70: 3 1.70 - 1.82: 106 Bond restraints: 14313 Sorted by residual: bond pdb=" C27 H6P D 501 " pdb=" C30 H6P D 501 " ideal model delta sigma weight residual 1.334 1.528 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" N VAL E 216 " pdb=" CA VAL E 216 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" O16 H6P D 501 " pdb=" P13 H6P D 501 " ideal model delta sigma weight residual 1.594 1.648 -0.054 2.00e-02 2.50e+03 7.43e+00 bond pdb=" N SER E 215 " pdb=" CA SER E 215 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.16e-02 7.43e+03 6.13e+00 bond pdb=" O16 H6P D 501 " pdb=" P17 H6P D 501 " ideal model delta sigma weight residual 1.697 1.650 0.047 2.00e-02 2.50e+03 5.59e+00 ... (remaining 14308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 19259 3.24 - 6.47: 122 6.47 - 9.71: 11 9.71 - 12.95: 1 12.95 - 16.18: 4 Bond angle restraints: 19397 Sorted by residual: angle pdb=" C21 H6P D 501 " pdb=" C30 H6P D 501 " pdb=" C27 H6P D 501 " ideal model delta sigma weight residual 125.58 109.40 16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" C28 H6P D 501 " pdb=" C27 H6P D 501 " pdb=" C30 H6P D 501 " ideal model delta sigma weight residual 127.23 112.53 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" CA SER G 211 " pdb=" C SER G 211 " pdb=" N PHE G 212 " ideal model delta sigma weight residual 117.72 124.00 -6.28 1.31e+00 5.83e-01 2.30e+01 angle pdb=" N GLY D 127 " pdb=" CA GLY D 127 " pdb=" C GLY D 127 " ideal model delta sigma weight residual 111.21 116.04 -4.83 1.04e+00 9.25e-01 2.16e+01 angle pdb=" P13 H6P D 501 " pdb=" O16 H6P D 501 " pdb=" P17 H6P D 501 " ideal model delta sigma weight residual 135.28 122.04 13.24 3.00e+00 1.11e-01 1.95e+01 ... (remaining 19392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.95: 8266 25.95 - 51.90: 384 51.90 - 77.85: 25 77.85 - 103.80: 9 103.80 - 129.75: 2 Dihedral angle restraints: 8686 sinusoidal: 3569 harmonic: 5117 Sorted by residual: dihedral pdb=" CA ARG E 293 " pdb=" C ARG E 293 " pdb=" N ARG E 294 " pdb=" CA ARG E 294 " ideal model delta harmonic sigma weight residual -180.00 -139.02 -40.98 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CB CYS E 219 " pdb=" SG CYS E 219 " pdb=" SG CYS G 219 " pdb=" CB CYS G 219 " ideal model delta sinusoidal sigma weight residual 93.00 38.05 54.95 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA ARG E 294 " pdb=" C ARG E 294 " pdb=" N THR E 295 " pdb=" CA THR E 295 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1745 0.058 - 0.117: 349 0.117 - 0.175: 32 0.175 - 0.233: 1 0.233 - 0.292: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CB ILE G 193 " pdb=" CA ILE G 193 " pdb=" CG1 ILE G 193 " pdb=" CG2 ILE G 193 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL E 216 " pdb=" N VAL E 216 " pdb=" C VAL E 216 " pdb=" CB VAL E 216 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ILE E 388 " pdb=" N ILE E 388 " pdb=" C ILE E 388 " pdb=" CB ILE E 388 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 2125 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 H6P D 501 " 0.034 2.00e-02 2.50e+03 2.68e-01 9.00e+02 pdb=" C27 H6P D 501 " -0.443 2.00e-02 2.50e+03 pdb=" C28 H6P D 501 " 0.213 2.00e-02 2.50e+03 pdb=" C30 H6P D 501 " 0.319 2.00e-02 2.50e+03 pdb=" C31 H6P D 501 " -0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 242 " 0.028 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP D 242 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 242 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 242 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 242 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 242 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 242 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 242 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 242 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 242 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 21 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO D 22 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " 0.037 5.00e-02 4.00e+02 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 920 2.73 - 3.27: 14571 3.27 - 3.82: 23893 3.82 - 4.36: 27375 4.36 - 4.90: 45677 Nonbonded interactions: 112436 Sorted by model distance: nonbonded pdb=" NH1 ARG C 243 " pdb=" OE1 GLN C 244 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG G 40 " pdb=" O GLN G 90 " model vdw 2.202 3.120 nonbonded pdb=" ND2 ASN C 120 " pdb=" O THR D 203 " model vdw 2.209 3.120 nonbonded pdb=" OG SER E 316 " pdb=" OD1 ASP E 318 " model vdw 2.213 3.040 nonbonded pdb=" O ALA D 222 " pdb=" OG1 THR D 226 " model vdw 2.214 3.040 ... (remaining 112431 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 'E' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 323 \ or (resid 324 and (name N or name CA or name C or name O or name CB )) or resid \ 325 through 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 through 492)) selection = (chain 'G' and (resid 1 through 215 or (resid 216 and (name N or name CA or name \ C or name O or name CB )) or resid 217 through 370 or (resid 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 492)) } 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 group one per residue 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: 12.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.220 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.003 0.194 14323 Z= 0.173 Angle : 0.728 16.185 19417 Z= 0.383 Chirality : 0.046 0.292 2128 Planarity : 0.007 0.268 2521 Dihedral : 14.185 129.745 5362 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.02 % Favored : 95.70 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.08 (0.20), residues: 1766 helix: 2.28 (0.29), residues: 312 sheet: -0.13 (0.22), residues: 553 loop : -0.58 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 259 TYR 0.025 0.001 TYR E 359 PHE 0.022 0.002 PHE D 240 TRP 0.073 0.002 TRP D 242 HIS 0.004 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (14313) covalent geometry : angle 0.72803 / 0.38 (19397) SS BOND : bond 0.00510 / 0.24 ( 10) SS BOND : angle 0.63426 / 0.38 ( 20) hydrogen bonds : bond 0.16972 / 11.35 ( 609) hydrogen bonds : angle 7.37129 / 4.97 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 174 MET cc_start: 0.7982 (mpp) cc_final: 0.7267 (tpt) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1437 time to fit residues: 15.6098 Evaluate side-chains 48 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 GLN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN G 391 ASN G 399 HIS C 149 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.036610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026582 restraints weight = 214596.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.026880 restraints weight = 134226.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.026760 restraints weight = 107807.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.026860 restraints weight = 103547.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.026919 restraints weight = 90659.898| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.055 14323 Z= 0.413 Angle : 0.881 9.348 19417 Z= 0.456 Chirality : 0.048 0.283 2128 Planarity : 0.007 0.127 2521 Dihedral : 6.928 92.658 1958 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.00 % Favored : 93.71 % Rotamer: Outliers : 0.46 % Allowed : 8.28 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.44 (0.20), residues: 1766 helix: 1.64 (0.26), residues: 312 sheet: -0.59 (0.21), residues: 575 loop : -0.73 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 77 TYR 0.041 0.003 TYR C 290 PHE 0.027 0.003 PHE D 349 TRP 0.037 0.003 TRP D 242 HIS 0.015 0.003 HIS G 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.41 (14313) covalent geometry : angle 0.88047 / 0.46 (19397) SS BOND : bond 0.00606 / 0.30 ( 10) SS BOND : angle 1.04100 / 0.69 ( 20) hydrogen bonds : bond 0.06238 / 4.12 ( 609) hydrogen bonds : angle 6.62817 / 4.52 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 125 MET cc_start: 0.9633 (mmp) cc_final: 0.9237 (mmm) REVERT: G 174 MET cc_start: 0.8670 (mpp) cc_final: 0.8376 (tpt) REVERT: G 327 PHE cc_start: 0.9627 (m-80) cc_final: 0.9281 (t80) REVERT: G 350 ARG cc_start: 0.9262 (ptt90) cc_final: 0.9053 (tmm-80) REVERT: C 29 MET cc_start: 0.9005 (tmm) cc_final: 0.8788 (tmm) outliers start: 7 outliers final: 1 residues processed: 55 average time/residue: 0.1261 time to fit residues: 10.4781 Evaluate side-chains 42 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS C 147 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.037569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.026672 restraints weight = 206882.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.027361 restraints weight = 125253.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.027811 restraints weight = 90744.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.028080 restraints weight = 73572.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.028266 restraints weight = 64443.573| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14323 Z= 0.143 Angle : 0.628 8.270 19417 Z= 0.332 Chirality : 0.046 0.221 2128 Planarity : 0.005 0.053 2521 Dihedral : 6.231 70.644 1958 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.28 % Favored : 96.55 % Rotamer: Outliers : 0.20 % Allowed : 3.09 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.12 (0.20), residues: 1766 helix: 1.94 (0.27), residues: 327 sheet: -0.39 (0.22), residues: 554 loop : -0.58 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 293 TYR 0.042 0.002 TYR C 290 PHE 0.022 0.002 PHE D 349 TRP 0.027 0.002 TRP D 242 HIS 0.009 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14313) covalent geometry : angle 0.62809 / 0.33 (19397) SS BOND : bond 0.00631 / 0.31 ( 10) SS BOND : angle 0.85320 / 0.63 ( 20) hydrogen bonds : bond 0.04775 / 3.09 ( 609) hydrogen bonds : angle 5.90509 / 3.97 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.8510 (mpp) cc_final: 0.8236 (mpp) REVERT: E 125 MET cc_start: 0.9501 (mmp) cc_final: 0.9021 (mmm) REVERT: G 174 MET cc_start: 0.8634 (mpp) cc_final: 0.8339 (tpt) REVERT: G 231 MET cc_start: 0.5021 (tpt) cc_final: 0.4570 (tmm) REVERT: C 29 MET cc_start: 0.9011 (tmm) cc_final: 0.8769 (tmm) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.1412 time to fit residues: 10.2047 Evaluate side-chains 43 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 147 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 391 ASN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.036853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.025940 restraints weight = 207668.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.026590 restraints weight = 127850.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.027026 restraints weight = 93799.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.027237 restraints weight = 76294.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.027438 restraints weight = 67698.277| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14323 Z= 0.194 Angle : 0.620 8.010 19417 Z= 0.327 Chirality : 0.044 0.216 2128 Planarity : 0.005 0.049 2521 Dihedral : 5.958 52.872 1958 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.21 (0.20), residues: 1766 helix: 1.83 (0.26), residues: 326 sheet: -0.50 (0.22), residues: 561 loop : -0.57 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 151 TYR 0.040 0.002 TYR C 290 PHE 0.014 0.002 PHE D 104 TRP 0.023 0.002 TRP D 242 HIS 0.006 0.001 HIS G 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (14313) covalent geometry : angle 0.62009 / 0.33 (19397) SS BOND : bond 0.00686 / 0.35 ( 10) SS BOND : angle 0.88231 / 0.69 ( 20) hydrogen bonds : bond 0.04549 / 2.94 ( 609) hydrogen bonds : angle 5.76310 / 3.87 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: E 125 MET cc_start: 0.9515 (mmp) cc_final: 0.9050 (mmm) REVERT: G 174 MET cc_start: 0.8624 (mpp) cc_final: 0.8378 (tpt) REVERT: G 189 MET cc_start: 0.9376 (mmp) cc_final: 0.8648 (tpt) REVERT: G 231 MET cc_start: 0.5142 (tpt) cc_final: 0.4722 (tmm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1256 time to fit residues: 8.9927 Evaluate side-chains 39 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 41 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.036831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.026208 restraints weight = 215062.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.026902 restraints weight = 129257.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.027343 restraints weight = 93331.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.027616 restraints weight = 75548.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.027798 restraints weight = 65868.624| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14323 Z= 0.152 Angle : 0.595 7.961 19417 Z= 0.315 Chirality : 0.044 0.214 2128 Planarity : 0.004 0.049 2521 Dihedral : 5.385 48.473 1958 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer: Outliers : 0.13 % Allowed : 2.04 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.13 (0.20), residues: 1766 helix: 1.80 (0.27), residues: 331 sheet: -0.47 (0.22), residues: 561 loop : -0.48 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 44 TYR 0.039 0.002 TYR C 290 PHE 0.013 0.001 PHE E 327 TRP 0.021 0.001 TRP D 242 HIS 0.005 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (14313) covalent geometry : angle 0.59507 / 0.31 (19397) SS BOND : bond 0.00466 / 0.23 ( 10) SS BOND : angle 0.80676 / 0.64 ( 20) hydrogen bonds : bond 0.04338 / 2.81 ( 609) hydrogen bonds : angle 5.58904 / 3.74 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.8819 (mpp) cc_final: 0.8400 (mpp) REVERT: E 125 MET cc_start: 0.9451 (mmp) cc_final: 0.9016 (mmp) REVERT: G 34 MET cc_start: 0.8110 (ppp) cc_final: 0.7802 (ppp) REVERT: G 174 MET cc_start: 0.8587 (mpp) cc_final: 0.8338 (tpt) REVERT: G 189 MET cc_start: 0.9335 (mmp) cc_final: 0.8614 (tpt) REVERT: G 231 MET cc_start: 0.5168 (tpt) cc_final: 0.4745 (tmm) REVERT: C 29 MET cc_start: 0.8762 (tmm) cc_final: 0.8454 (tmm) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.1119 time to fit residues: 7.9601 Evaluate side-chains 40 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 49 optimal weight: 20.0000 chunk 147 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.036096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.026006 restraints weight = 211485.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.026294 restraints weight = 136717.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.026329 restraints weight = 101097.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.026418 restraints weight = 92822.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.026405 restraints weight = 80071.784| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14323 Z= 0.202 Angle : 0.628 7.855 19417 Z= 0.330 Chirality : 0.045 0.229 2128 Planarity : 0.005 0.049 2521 Dihedral : 5.470 51.705 1958 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.20 (0.20), residues: 1766 helix: 1.78 (0.27), residues: 331 sheet: -0.57 (0.21), residues: 560 loop : -0.49 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 291 TYR 0.042 0.002 TYR C 290 PHE 0.017 0.002 PHE D 212 TRP 0.021 0.002 TRP D 242 HIS 0.007 0.002 HIS G 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (14313) covalent geometry : angle 0.62795 / 0.33 (19397) SS BOND : bond 0.00391 / 0.20 ( 10) SS BOND : angle 0.79557 / 0.65 ( 20) hydrogen bonds : bond 0.04459 / 2.88 ( 609) hydrogen bonds : angle 5.67279 / 3.79 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.8864 (mpp) cc_final: 0.8466 (mpp) REVERT: E 125 MET cc_start: 0.9562 (mmp) cc_final: 0.9061 (mmp) REVERT: G 189 MET cc_start: 0.9464 (mmp) cc_final: 0.8777 (tpt) REVERT: G 231 MET cc_start: 0.5584 (tpt) cc_final: 0.5154 (tmm) REVERT: G 350 ARG cc_start: 0.9219 (ptt90) cc_final: 0.9011 (tmm-80) REVERT: C 29 MET cc_start: 0.8806 (tmm) cc_final: 0.8454 (tmm) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.1124 time to fit residues: 8.1101 Evaluate side-chains 40 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 41 optimal weight: 0.0270 chunk 168 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 399 HIS D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.036665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.026518 restraints weight = 212485.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.027157 restraints weight = 124760.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.027031 restraints weight = 85075.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.027087 restraints weight = 86982.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.027176 restraints weight = 75719.456| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14323 Z= 0.130 Angle : 0.600 7.216 19417 Z= 0.316 Chirality : 0.045 0.342 2128 Planarity : 0.004 0.048 2521 Dihedral : 5.300 59.498 1958 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.07 (0.20), residues: 1766 helix: 1.83 (0.27), residues: 327 sheet: -0.43 (0.22), residues: 554 loop : -0.42 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 151 TYR 0.034 0.002 TYR C 290 PHE 0.014 0.001 PHE D 99 TRP 0.021 0.001 TRP D 242 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (14313) covalent geometry : angle 0.59979 / 0.32 (19397) SS BOND : bond 0.00368 / 0.18 ( 10) SS BOND : angle 0.59877 / 0.46 ( 20) hydrogen bonds : bond 0.04223 / 2.72 ( 609) hydrogen bonds : angle 5.47484 / 3.65 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.8873 (mpp) cc_final: 0.8482 (mpp) REVERT: E 125 MET cc_start: 0.9569 (mmp) cc_final: 0.9055 (mmp) REVERT: G 34 MET cc_start: 0.8397 (ppp) cc_final: 0.8178 (ppp) REVERT: G 189 MET cc_start: 0.9501 (mmp) cc_final: 0.8798 (tpt) REVERT: G 231 MET cc_start: 0.5797 (tpt) cc_final: 0.5374 (tmm) REVERT: C 29 MET cc_start: 0.8855 (tmm) cc_final: 0.8552 (ppp) REVERT: C 281 GLU cc_start: 0.9174 (mp0) cc_final: 0.8936 (mp0) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1121 time to fit residues: 7.9392 Evaluate side-chains 40 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.2980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.036129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.025975 restraints weight = 212745.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.026598 restraints weight = 127562.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.026453 restraints weight = 88797.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.026546 restraints weight = 88920.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.026574 restraints weight = 76099.925| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14323 Z= 0.171 Angle : 0.607 7.439 19417 Z= 0.318 Chirality : 0.045 0.303 2128 Planarity : 0.004 0.046 2521 Dihedral : 5.351 55.633 1958 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.16 (0.20), residues: 1766 helix: 1.62 (0.27), residues: 335 sheet: -0.44 (0.22), residues: 557 loop : -0.48 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 151 TYR 0.033 0.002 TYR C 290 PHE 0.017 0.001 PHE D 212 TRP 0.021 0.002 TRP D 242 HIS 0.005 0.001 HIS D 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (14313) covalent geometry : angle 0.60655 / 0.32 (19397) SS BOND : bond 0.00365 / 0.18 ( 10) SS BOND : angle 0.56722 / 0.47 ( 20) hydrogen bonds : bond 0.04236 / 2.73 ( 609) hydrogen bonds : angle 5.51320 / 3.68 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 61 MET cc_start: 0.8929 (mpp) cc_final: 0.8525 (mpp) REVERT: E 125 MET cc_start: 0.9543 (mmp) cc_final: 0.9035 (mmp) REVERT: G 34 MET cc_start: 0.8368 (ppp) cc_final: 0.8109 (ppp) REVERT: G 166 MET cc_start: 0.9606 (pmm) cc_final: 0.9095 (pmm) REVERT: G 174 MET cc_start: 0.8889 (mmm) cc_final: 0.8266 (mpp) REVERT: G 189 MET cc_start: 0.9474 (mmp) cc_final: 0.8801 (tpt) REVERT: G 231 MET cc_start: 0.5956 (tpt) cc_final: 0.5525 (tmm) REVERT: G 350 ARG cc_start: 0.9249 (ptt90) cc_final: 0.9019 (tmm-80) REVERT: C 29 MET cc_start: 0.8878 (tmm) cc_final: 0.8470 (ppp) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1089 time to fit residues: 7.6258 Evaluate side-chains 39 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 5 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 171 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.036361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.026223 restraints weight = 213164.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.026915 restraints weight = 125810.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.026792 restraints weight = 83740.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.026844 restraints weight = 86102.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.026925 restraints weight = 74634.577| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14323 Z= 0.130 Angle : 0.587 7.038 19417 Z= 0.308 Chirality : 0.045 0.281 2128 Planarity : 0.004 0.047 2521 Dihedral : 5.238 59.486 1958 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.79 % Favored : 96.04 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.09 (0.20), residues: 1766 helix: 1.70 (0.27), residues: 335 sheet: -0.40 (0.22), residues: 553 loop : -0.43 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 140 TYR 0.029 0.001 TYR C 290 PHE 0.015 0.001 PHE E 327 TRP 0.023 0.002 TRP D 242 HIS 0.004 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (14313) covalent geometry : angle 0.58710 / 0.31 (19397) SS BOND : bond 0.00361 / 0.18 ( 10) SS BOND : angle 0.54511 / 0.41 ( 20) hydrogen bonds : bond 0.04080 / 2.63 ( 609) hydrogen bonds : angle 5.34432 / 3.56 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: E 61 MET cc_start: 0.8871 (mpp) cc_final: 0.8556 (mpp) REVERT: E 125 MET cc_start: 0.9508 (mmp) cc_final: 0.9001 (mmp) REVERT: G 34 MET cc_start: 0.8347 (ppp) cc_final: 0.8109 (ppp) REVERT: G 166 MET cc_start: 0.9617 (pmm) cc_final: 0.9275 (pmm) REVERT: G 174 MET cc_start: 0.8863 (mmm) cc_final: 0.8316 (mpp) REVERT: G 189 MET cc_start: 0.9441 (mmp) cc_final: 0.8780 (tpt) REVERT: G 231 MET cc_start: 0.5945 (tpt) cc_final: 0.5537 (tmm) REVERT: C 29 MET cc_start: 0.9011 (tmm) cc_final: 0.8803 (ppp) REVERT: C 34 MET cc_start: 0.8719 (mpp) cc_final: 0.8173 (ptm) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1134 time to fit residues: 7.6167 Evaluate side-chains 39 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.035605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.025674 restraints weight = 215488.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.025919 restraints weight = 134910.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.025951 restraints weight = 101406.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.026029 restraints weight = 92547.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.026059 restraints weight = 80802.094| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14323 Z= 0.195 Angle : 0.630 9.168 19417 Z= 0.330 Chirality : 0.045 0.293 2128 Planarity : 0.005 0.045 2521 Dihedral : 5.426 53.615 1958 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1766 helix: 1.70 (0.27), residues: 330 sheet: -0.53 (0.22), residues: 551 loop : -0.46 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 140 TYR 0.033 0.002 TYR C 290 PHE 0.020 0.002 PHE D 212 TRP 0.026 0.002 TRP D 242 HIS 0.007 0.002 HIS G 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (14313) covalent geometry : angle 0.62980 / 0.33 (19397) SS BOND : bond 0.00325 / 0.16 ( 10) SS BOND : angle 0.59651 / 0.49 ( 20) hydrogen bonds : bond 0.04236 / 2.75 ( 609) hydrogen bonds : angle 5.55057 / 3.70 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: E 61 MET cc_start: 0.8841 (mpp) cc_final: 0.8446 (mpp) REVERT: E 125 MET cc_start: 0.9513 (mmp) cc_final: 0.9029 (mmp) REVERT: G 34 MET cc_start: 0.8263 (ppp) cc_final: 0.8038 (ppp) REVERT: G 166 MET cc_start: 0.9634 (pmm) cc_final: 0.9037 (pmm) REVERT: G 174 MET cc_start: 0.8936 (mmm) cc_final: 0.8221 (mpp) REVERT: G 189 MET cc_start: 0.9495 (mmp) cc_final: 0.8860 (tpt) REVERT: G 231 MET cc_start: 0.6099 (tpt) cc_final: 0.5710 (tmm) REVERT: C 29 MET cc_start: 0.8853 (tmm) cc_final: 0.8606 (ppp) REVERT: C 34 MET cc_start: 0.8863 (mpp) cc_final: 0.8107 (ptm) REVERT: C 281 GLU cc_start: 0.9297 (mp0) cc_final: 0.8997 (mp0) REVERT: D 269 MET cc_start: 0.9290 (mmm) cc_final: 0.9081 (mmt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1066 time to fit residues: 7.1601 Evaluate side-chains 40 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 HIS G 344 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.036005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.025973 restraints weight = 212495.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.026586 restraints weight = 127322.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.026453 restraints weight = 87912.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.026546 restraints weight = 85107.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.026570 restraints weight = 74105.815| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14323 Z= 0.128 Angle : 0.602 9.346 19417 Z= 0.319 Chirality : 0.045 0.276 2128 Planarity : 0.004 0.047 2521 Dihedral : 5.289 58.685 1958 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.07 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.06 (0.20), residues: 1766 helix: 1.78 (0.27), residues: 330 sheet: -0.40 (0.22), residues: 548 loop : -0.42 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 140 TYR 0.026 0.001 TYR D 290 PHE 0.015 0.001 PHE E 327 TRP 0.023 0.002 TRP D 242 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (14313) covalent geometry : angle 0.60214 / 0.32 (19397) SS BOND : bond 0.00328 / 0.16 ( 10) SS BOND : angle 0.54914 / 0.43 ( 20) hydrogen bonds : bond 0.04008 / 2.58 ( 609) hydrogen bonds : angle 5.42762 / 3.63 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.16 seconds wall clock time: 47 minutes 21.88 seconds (2841.88 seconds total)