Starting phenix.real_space_refine on Fri Jul 3 04:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2c_14461/07_2026/7z2c_14461.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 5940 2.51 5 N 1637 2.21 5 O 1833 1.98 5 H 2554 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12037 Number of models: 1 Model: "" Number of chains: 5 Chain: "K" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5287 Classifications: {'peptide': 347} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 338} Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.54, per 1000 atoms: 0.21 Number of scatterers: 12037 At special positions: 0 Unit cell: (111.3, 109.2, 78.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 65 16.00 P 6 15.00 Mg 2 11.99 O 1833 8.00 N 1637 7.00 C 5940 6.00 H 2554 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 499.7 milliseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 52.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 46 through 53 Processing helix chain 'K' and resid 70 through 77 Processing helix chain 'K' and resid 79 through 88 Processing helix chain 'K' and resid 103 through 109 Processing helix chain 'K' and resid 115 through 133 removed outlier: 3.559A pdb=" N MET K 120 " --> pdb=" O GLY K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 160 Processing helix chain 'K' and resid 185 through 198 removed outlier: 3.840A pdb=" N ARG K 198 " --> pdb=" O HIS K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 287 Processing helix chain 'K' and resid 295 through 298 Processing helix chain 'K' and resid 299 through 310 removed outlier: 4.794A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER K 308 " --> pdb=" O LEU K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 343 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.608A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.078A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.524A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.408A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.997A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.602A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.591A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.623A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.080A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.910A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.429A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.486A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.294A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.545A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.812A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.603A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 282' Processing helix chain 'H' and resid 287 through 297 removed outlier: 3.549A pdb=" N ASP H 297 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 4.205A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.123A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 4.071A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.068A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 93 " --> pdb=" O VAL K 316 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE K 318 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE K 95 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN K 320 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR K 97 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER K 92 " --> pdb=" O CYS K 241 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE K 243 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL K 94 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 63 through 65 removed outlier: 9.068A pdb=" N TYR K 63 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL K 8 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE K 65 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE K 10 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 93 " --> pdb=" O VAL K 316 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE K 318 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE K 95 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN K 320 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR K 97 " --> pdb=" O ASN K 320 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER K 92 " --> pdb=" O CYS K 241 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE K 243 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL K 94 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.536A pdb=" N MET K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'K' and resid 202 through 205 removed outlier: 4.718A pdb=" N THR K 205 " --> pdb=" O LYS K 209 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS K 209 " --> pdb=" O THR K 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.018A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.816A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.171A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1464 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: 2.32 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2548 1.13 - 1.31: 1627 1.31 - 1.48: 3878 1.48 - 1.66: 4066 1.66 - 1.83: 105 Bond restraints: 12224 Sorted by residual: bond pdb=" NE ARG K 297 " pdb=" HE ARG K 297 " ideal model delta sigma weight residual 0.860 1.050 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" NH1 ARG K 213 " pdb="HH11 ARG K 213 " ideal model delta sigma weight residual 0.860 1.044 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" NE2 HIS K 194 " pdb=" HE2 HIS K 194 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" NE ARG K 53 " pdb=" HE ARG K 53 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" NE ARG K 250 " pdb=" HE ARG K 250 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 12219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 17412 3.07 - 6.14: 1272 6.14 - 9.21: 214 9.21 - 12.28: 16 12.28 - 15.35: 7 Bond angle restraints: 18921 Sorted by residual: angle pdb=" C LYS K 139 " pdb=" N VAL K 140 " pdb=" CA VAL K 140 " ideal model delta sigma weight residual 122.48 113.89 8.59 1.25e+00 6.40e-01 4.73e+01 angle pdb=" C SER K 322 " pdb=" N PRO K 323 " pdb=" CA PRO K 323 " ideal model delta sigma weight residual 119.87 126.75 -6.88 1.04e+00 9.25e-01 4.38e+01 angle pdb=" N PRO K 169 " pdb=" CA PRO K 169 " pdb=" C PRO K 169 " ideal model delta sigma weight residual 111.03 100.88 10.15 1.54e+00 4.22e-01 4.35e+01 angle pdb=" C ASN K 157 " pdb=" N PRO K 158 " pdb=" CA PRO K 158 " ideal model delta sigma weight residual 119.82 126.15 -6.33 9.80e-01 1.04e+00 4.18e+01 angle pdb=" N ILE K 152 " pdb=" CA ILE K 152 " pdb=" C ILE K 152 " ideal model delta sigma weight residual 107.80 117.06 -9.26 1.45e+00 4.76e-01 4.08e+01 ... (remaining 18916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.61: 6461 33.61 - 67.21: 146 67.21 - 100.82: 15 100.82 - 134.42: 0 134.42 - 168.03: 3 Dihedral angle restraints: 6625 sinusoidal: 3038 harmonic: 3587 Sorted by residual: dihedral pdb=" CD2 HIS K 332 " pdb=" CG HIS K 332 " pdb=" ND1 HIS K 332 " pdb=" HD1 HIS K 332 " ideal model delta harmonic sigma weight residual -180.00 -136.43 -43.57 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.70 -168.03 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.73 156.33 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 6622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 997 0.079 - 0.158: 337 0.158 - 0.237: 96 0.237 - 0.316: 21 0.316 - 0.395: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA HIS A 197 " pdb=" N HIS A 197 " pdb=" C HIS A 197 " pdb=" CB HIS A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA THR H 109 " pdb=" N THR H 109 " pdb=" C THR H 109 " pdb=" CB THR H 109 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' G2P H 501 " pdb=" C2' G2P H 501 " pdb=" C4' G2P H 501 " pdb=" O3' G2P H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.38 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1451 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 332 " 0.154 2.00e-02 2.50e+03 1.62e-01 5.92e+02 pdb=" CG HIS K 332 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS K 332 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 HIS K 332 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 HIS K 332 " 0.082 2.00e-02 2.50e+03 pdb=" NE2 HIS K 332 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 HIS K 332 " -0.382 2.00e-02 2.50e+03 pdb=" HD2 HIS K 332 " -0.123 2.00e-02 2.50e+03 pdb=" HE1 HIS K 332 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 4 " -0.072 2.00e-02 2.50e+03 2.82e-02 2.38e+01 pdb=" CG TYR K 4 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR K 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR K 4 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR K 4 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR K 4 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR K 4 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 4 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR K 4 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR K 4 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR K 4 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR K 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 75 " 0.070 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" CG TYR K 75 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR K 75 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 75 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR K 75 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR K 75 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR K 75 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR K 75 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR K 75 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR K 75 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR K 75 " -0.011 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 21 1.60 - 2.35: 1340 2.35 - 3.10: 21805 3.10 - 3.85: 37266 3.85 - 4.60: 58508 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118940 Sorted by model distance: nonbonded pdb="HG11 VAL K 48 " pdb=" OD1 ASP A 431 " model vdw 0.853 2.620 nonbonded pdb="HD21 ASN K 52 " pdb=" CE LYS A 430 " model vdw 0.973 2.750 nonbonded pdb=" OE1 GLU K 32 " pdb=" HZ3 LYS K 34 " model vdw 1.023 2.450 nonbonded pdb=" HZ1 LYS K 336 " pdb=" OG SER A 419 " model vdw 1.089 1.960 nonbonded pdb="HH12 ARG K 297 " pdb=" CB GLU H 431 " model vdw 1.109 2.200 ... (remaining 118935 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.070 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 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 : 0.012 0.256 9674 Z= 0.767 Angle : 1.591 14.075 13107 Z= 1.078 Chirality : 0.088 0.395 1454 Planarity : 0.008 0.074 1705 Dihedral : 14.559 168.027 3578 Min Nonbonded Distance : 1.386 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.02 % Favored : 96.81 % Rotamer: Outliers : 0.48 % Allowed : 5.02 % Favored : 94.49 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.04 (0.23), residues: 1193 helix: 0.63 (0.20), residues: 518 sheet: -0.25 (0.36), residues: 209 loop : -0.52 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 243 TYR 0.063 0.006 TYR K 4 PHE 0.033 0.004 PHE K 179 TRP 0.018 0.003 TRP A 21 HIS 0.015 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01179 / 0.71 ( 9670) covalent geometry : angle 1.59052 / 1.08 (13107) hydrogen bonds : bond 0.18762 / 12.27 ( 481) hydrogen bonds : angle 7.57135 / 5.38 ( 1464) Misc. bond : bond 0.14270 / 6.86 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 349 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4372 (mm-30) REVERT: K 215 HIS cc_start: 0.5474 (m-70) cc_final: 0.5006 (m90) REVERT: K 332 HIS cc_start: 0.6504 (t70) cc_final: 0.5207 (t70) REVERT: A 16 ILE cc_start: 0.7561 (mt) cc_final: 0.7023 (mt) REVERT: A 317 LEU cc_start: 0.8297 (mm) cc_final: 0.8052 (mp) REVERT: A 346 TRP cc_start: 0.5289 (p-90) cc_final: 0.2738 (t60) REVERT: H 19 LYS cc_start: 0.7754 (tptt) cc_final: 0.7503 (tppt) REVERT: H 384 ILE cc_start: 0.8279 (mm) cc_final: 0.7750 (mt) outliers start: 5 outliers final: 1 residues processed: 354 average time/residue: 0.1426 time to fit residues: 66.9777 Evaluate side-chains 207 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 133 GLN ** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 226 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 139 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.091321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068075 restraints weight = 56483.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071081 restraints weight = 28802.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073076 restraints weight = 18589.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074359 restraints weight = 13795.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075180 restraints weight = 11283.791| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9674 Z= 0.186 Angle : 0.648 11.519 13107 Z= 0.360 Chirality : 0.043 0.203 1454 Planarity : 0.010 0.346 1705 Dihedral : 10.363 173.709 1323 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1193 helix: 1.37 (0.22), residues: 532 sheet: 0.04 (0.34), residues: 218 loop : -0.59 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG K 297 TYR 0.021 0.002 TYR H 432 PHE 0.018 0.002 PHE H 262 TRP 0.011 0.002 TRP A 407 HIS 0.007 0.001 HIS K 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 ( 9670) covalent geometry : angle 0.64786 / 0.36 (13107) hydrogen bonds : bond 0.05919 / 3.93 ( 481) hydrogen bonds : angle 5.60511 / 3.91 ( 1464) Misc. bond : bond 0.00531 / 0.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7253 (mm-30) REVERT: K 190 MET cc_start: 0.9477 (ttp) cc_final: 0.9059 (tmm) REVERT: K 255 ASN cc_start: 0.6611 (m110) cc_final: 0.6212 (m110) REVERT: K 266 ASN cc_start: 0.9408 (m-40) cc_final: 0.9147 (m110) REVERT: A 36 MET cc_start: 0.6544 (tmm) cc_final: 0.6302 (tmm) REVERT: A 101 ASN cc_start: 0.9131 (m-40) cc_final: 0.8880 (m110) REVERT: A 313 MET cc_start: 0.8331 (mtp) cc_final: 0.8088 (mtp) REVERT: H 102 ASN cc_start: 0.8095 (t0) cc_final: 0.7175 (t0) REVERT: H 105 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8330 (mtpt) REVERT: H 110 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8383 (tp30) REVERT: H 116 ASP cc_start: 0.9262 (m-30) cc_final: 0.9021 (m-30) REVERT: H 267 PHE cc_start: 0.9039 (m-80) cc_final: 0.8690 (m-80) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1156 time to fit residues: 38.7568 Evaluate side-chains 179 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 93 optimal weight: 0.0570 chunk 95 optimal weight: 0.0270 chunk 86 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 overall best weight: 5.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 202 GLN K 343 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 59 ASN H 101 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.089672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067006 restraints weight = 56737.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069882 restraints weight = 29220.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071785 restraints weight = 18839.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073008 restraints weight = 13966.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073724 restraints weight = 11443.909| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9674 Z= 0.170 Angle : 0.583 12.435 13107 Z= 0.319 Chirality : 0.041 0.168 1454 Planarity : 0.010 0.367 1705 Dihedral : 9.892 174.652 1323 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 0.19 % Allowed : 2.71 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.60 (0.24), residues: 1193 helix: 1.39 (0.22), residues: 528 sheet: 0.01 (0.35), residues: 223 loop : -0.51 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG K 297 TYR 0.027 0.002 TYR H 432 PHE 0.015 0.002 PHE A 87 TRP 0.008 0.001 TRP A 21 HIS 0.009 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 9670) covalent geometry : angle 0.58338 / 0.32 (13107) hydrogen bonds : bond 0.04716 / 3.13 ( 481) hydrogen bonds : angle 5.23334 / 3.61 ( 1464) Misc. bond : bond 0.00207 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7120 (mm-30) REVERT: K 215 HIS cc_start: 0.8425 (m-70) cc_final: 0.7662 (m-70) REVERT: K 266 ASN cc_start: 0.9414 (m-40) cc_final: 0.9102 (m-40) REVERT: K 278 ILE cc_start: 0.9584 (mt) cc_final: 0.9298 (tt) REVERT: A 36 MET cc_start: 0.6897 (tmm) cc_final: 0.6451 (tmm) REVERT: A 101 ASN cc_start: 0.9247 (m-40) cc_final: 0.8976 (m-40) REVERT: A 169 PHE cc_start: 0.7901 (m-10) cc_final: 0.7534 (m-10) REVERT: A 194 THR cc_start: 0.8836 (m) cc_final: 0.8368 (t) REVERT: A 252 LEU cc_start: 0.8872 (mp) cc_final: 0.8528 (mp) REVERT: A 357 TYR cc_start: 0.8381 (m-80) cc_final: 0.8163 (m-80) REVERT: A 368 LEU cc_start: 0.8300 (mm) cc_final: 0.8092 (mm) REVERT: H 102 ASN cc_start: 0.8189 (t0) cc_final: 0.7337 (t0) REVERT: H 105 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8387 (mtpt) REVERT: H 110 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8452 (mm-30) REVERT: H 116 ASP cc_start: 0.9097 (m-30) cc_final: 0.8880 (m-30) REVERT: H 267 PHE cc_start: 0.9040 (m-80) cc_final: 0.8495 (m-10) REVERT: H 373 MET cc_start: 0.8642 (mtp) cc_final: 0.8394 (mtm) REVERT: H 416 MET cc_start: 0.8964 (tpp) cc_final: 0.8733 (tpp) REVERT: H 418 PHE cc_start: 0.8618 (m-10) cc_final: 0.8324 (m-10) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1129 time to fit residues: 33.2436 Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 5 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** 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 = 0.3679 r_free = 0.3679 target = 0.089200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066525 restraints weight = 57522.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.069465 restraints weight = 29573.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071451 restraints weight = 19066.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072712 restraints weight = 14052.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073544 restraints weight = 11435.921| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9674 Z= 0.147 Angle : 0.576 14.382 13107 Z= 0.313 Chirality : 0.041 0.172 1454 Planarity : 0.005 0.104 1705 Dihedral : 8.920 171.383 1323 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 36.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 0.10 % Allowed : 1.45 % Favored : 98.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.58 (0.24), residues: 1193 helix: 1.47 (0.22), residues: 526 sheet: -0.18 (0.34), residues: 227 loop : -0.54 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG K 297 TYR 0.021 0.001 TYR H 432 PHE 0.020 0.001 PHE A 418 TRP 0.007 0.001 TRP A 21 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 9670) covalent geometry : angle 0.57639 / 0.31 (13107) hydrogen bonds : bond 0.04661 / 3.03 ( 481) hydrogen bonds : angle 5.10948 / 3.53 ( 1464) Misc. bond : bond 0.00636 / 0.32 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7494 (mm-30) REVERT: K 190 MET cc_start: 0.9518 (ttp) cc_final: 0.9088 (tmm) REVERT: K 255 ASN cc_start: 0.7008 (m110) cc_final: 0.6577 (m110) REVERT: K 259 MET cc_start: 0.8943 (mmm) cc_final: 0.8328 (tpp) REVERT: K 278 ILE cc_start: 0.9557 (mt) cc_final: 0.9299 (tt) REVERT: A 35 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 36 MET cc_start: 0.6990 (tmm) cc_final: 0.6696 (tmm) REVERT: A 169 PHE cc_start: 0.7897 (m-10) cc_final: 0.7668 (m-10) REVERT: A 194 THR cc_start: 0.8849 (m) cc_final: 0.7991 (t) REVERT: A 198 SER cc_start: 0.7924 (t) cc_final: 0.7407 (p) REVERT: A 357 TYR cc_start: 0.8452 (m-80) cc_final: 0.8183 (m-10) REVERT: A 368 LEU cc_start: 0.8540 (mm) cc_final: 0.8335 (mm) REVERT: H 102 ASN cc_start: 0.8108 (t0) cc_final: 0.7358 (t0) REVERT: H 110 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8462 (mm-30) REVERT: H 247 GLN cc_start: 0.8899 (mm110) cc_final: 0.8037 (mp10) REVERT: H 267 PHE cc_start: 0.9047 (m-80) cc_final: 0.8757 (m-80) REVERT: H 416 MET cc_start: 0.8898 (tpp) cc_final: 0.8686 (tpp) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.1285 time to fit residues: 36.7852 Evaluate side-chains 159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 41 optimal weight: 0.4980 chunk 99 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 69 optimal weight: 0.0070 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 overall best weight: 4.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.089354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066440 restraints weight = 56384.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069348 restraints weight = 28713.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.071210 restraints weight = 18471.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072459 restraints weight = 13716.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073189 restraints weight = 11199.194| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9674 Z= 0.146 Angle : 0.554 10.665 13107 Z= 0.298 Chirality : 0.042 0.368 1454 Planarity : 0.012 0.452 1705 Dihedral : 9.113 169.922 1323 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 37.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.19 % Allowed : 1.55 % Favored : 98.26 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1193 helix: 1.57 (0.22), residues: 532 sheet: -0.16 (0.34), residues: 219 loop : -0.57 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 264 TYR 0.025 0.001 TYR H 432 PHE 0.011 0.001 PHE K 293 TRP 0.007 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 9670) covalent geometry : angle 0.55444 / 0.30 (13107) hydrogen bonds : bond 0.04259 / 2.82 ( 481) hydrogen bonds : angle 5.01369 / 3.45 ( 1464) Misc. bond : bond 0.00610 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7468 (mm-30) REVERT: K 190 MET cc_start: 0.9536 (ttp) cc_final: 0.9120 (tmm) REVERT: K 255 ASN cc_start: 0.7082 (m110) cc_final: 0.6668 (m110) REVERT: K 259 MET cc_start: 0.8919 (mmm) cc_final: 0.8352 (tpp) REVERT: K 278 ILE cc_start: 0.9545 (mt) cc_final: 0.9291 (tt) REVERT: A 35 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7646 (tm-30) REVERT: A 36 MET cc_start: 0.7091 (tmm) cc_final: 0.6867 (tmm) REVERT: A 101 ASN cc_start: 0.9216 (m-40) cc_final: 0.8935 (m-40) REVERT: A 183 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 194 THR cc_start: 0.8873 (m) cc_final: 0.8527 (m) REVERT: A 198 SER cc_start: 0.7867 (t) cc_final: 0.7435 (p) REVERT: A 357 TYR cc_start: 0.8502 (m-80) cc_final: 0.8212 (m-10) REVERT: H 102 ASN cc_start: 0.8152 (t0) cc_final: 0.7582 (t0) REVERT: H 110 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 416 MET cc_start: 0.8907 (tpp) cc_final: 0.8648 (tpp) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.1292 time to fit residues: 35.9912 Evaluate side-chains 153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 104 optimal weight: 0.0270 chunk 4 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065373 restraints weight = 56586.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068245 restraints weight = 29500.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.070138 restraints weight = 19128.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071370 restraints weight = 14199.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072210 restraints weight = 11616.331| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9674 Z= 0.169 Angle : 0.534 8.721 13107 Z= 0.291 Chirality : 0.041 0.154 1454 Planarity : 0.004 0.064 1705 Dihedral : 8.468 168.789 1323 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 40.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1193 helix: 1.48 (0.22), residues: 532 sheet: -0.17 (0.35), residues: 219 loop : -0.72 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 53 TYR 0.016 0.001 TYR K 75 PHE 0.027 0.002 PHE K 126 TRP 0.007 0.001 TRP A 21 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 9670) covalent geometry : angle 0.53435 / 0.29 (13107) hydrogen bonds : bond 0.04384 / 2.84 ( 481) hydrogen bonds : angle 5.06386 / 3.48 ( 1464) Misc. bond : bond 0.00711 / 0.36 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7283 (mm-30) REVERT: K 190 MET cc_start: 0.9542 (ttp) cc_final: 0.9097 (tmm) REVERT: K 255 ASN cc_start: 0.7068 (m110) cc_final: 0.6697 (m110) REVERT: K 259 MET cc_start: 0.8898 (mmm) cc_final: 0.8358 (tpp) REVERT: K 266 ASN cc_start: 0.9450 (m-40) cc_final: 0.9230 (t0) REVERT: K 278 ILE cc_start: 0.9542 (mt) cc_final: 0.9294 (tt) REVERT: A 35 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 101 ASN cc_start: 0.9246 (m-40) cc_final: 0.8950 (m-40) REVERT: A 183 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 194 THR cc_start: 0.8897 (m) cc_final: 0.8100 (t) REVERT: A 198 SER cc_start: 0.7869 (t) cc_final: 0.7390 (p) REVERT: A 202 PHE cc_start: 0.8659 (m-10) cc_final: 0.8381 (m-10) REVERT: A 357 TYR cc_start: 0.8505 (m-80) cc_final: 0.8189 (m-10) REVERT: A 431 ASP cc_start: 0.8695 (m-30) cc_final: 0.8495 (m-30) REVERT: H 102 ASN cc_start: 0.8127 (t0) cc_final: 0.7574 (t0) REVERT: H 110 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8404 (mm-30) REVERT: H 416 MET cc_start: 0.8961 (tpp) cc_final: 0.8688 (tpp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1302 time to fit residues: 35.5743 Evaluate side-chains 147 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.0270 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 overall best weight: 3.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.099148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075425 restraints weight = 54274.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078366 restraints weight = 28743.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080412 restraints weight = 18811.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081826 restraints weight = 14020.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082783 restraints weight = 11367.166| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9674 Z= 0.127 Angle : 0.503 13.193 13107 Z= 0.270 Chirality : 0.040 0.150 1454 Planarity : 0.011 0.429 1705 Dihedral : 8.710 167.632 1323 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 38.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 0.10 % Allowed : 0.77 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1193 helix: 1.62 (0.23), residues: 532 sheet: -0.27 (0.34), residues: 227 loop : -0.61 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG K 297 TYR 0.017 0.001 TYR K 97 PHE 0.023 0.001 PHE K 293 TRP 0.007 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 9670) covalent geometry : angle 0.50331 / 0.27 (13107) hydrogen bonds : bond 0.04044 / 2.66 ( 481) hydrogen bonds : angle 4.90381 / 3.38 ( 1464) Misc. bond : bond 0.00281 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7230 (mm-30) REVERT: K 255 ASN cc_start: 0.7099 (m110) cc_final: 0.6714 (m110) REVERT: K 259 MET cc_start: 0.8869 (mmm) cc_final: 0.8212 (tpp) REVERT: K 278 ILE cc_start: 0.9540 (mt) cc_final: 0.9277 (tt) REVERT: A 35 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 82 THR cc_start: 0.9105 (p) cc_final: 0.8886 (t) REVERT: A 101 ASN cc_start: 0.9251 (m-40) cc_final: 0.8947 (m-40) REVERT: A 183 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8175 (mm-30) REVERT: A 194 THR cc_start: 0.8905 (m) cc_final: 0.8149 (t) REVERT: A 198 SER cc_start: 0.7820 (t) cc_final: 0.7276 (p) REVERT: A 202 PHE cc_start: 0.8546 (m-10) cc_final: 0.8300 (m-10) REVERT: A 357 TYR cc_start: 0.8491 (m-80) cc_final: 0.8159 (m-10) REVERT: A 431 ASP cc_start: 0.8564 (m-30) cc_final: 0.8352 (m-30) REVERT: H 102 ASN cc_start: 0.8096 (t0) cc_final: 0.7506 (t0) REVERT: H 110 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8359 (mm-30) REVERT: H 398 MET cc_start: 0.7918 (mmp) cc_final: 0.6909 (mtt) REVERT: H 416 MET cc_start: 0.8973 (tpp) cc_final: 0.8659 (tpp) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1176 time to fit residues: 33.6093 Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 0.0570 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 149 ASN K 199 ASN K 266 ASN A 15 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.098893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075358 restraints weight = 53876.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078329 restraints weight = 28585.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080406 restraints weight = 18666.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081709 restraints weight = 13832.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.082686 restraints weight = 11269.639| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9674 Z= 0.122 Angle : 0.527 17.794 13107 Z= 0.281 Chirality : 0.040 0.192 1454 Planarity : 0.004 0.065 1705 Dihedral : 9.423 171.665 1323 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1193 helix: 1.67 (0.22), residues: 532 sheet: -0.19 (0.35), residues: 224 loop : -0.56 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 297 TYR 0.015 0.001 TYR K 97 PHE 0.027 0.001 PHE K 293 TRP 0.006 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9670) covalent geometry : angle 0.52738 / 0.28 (13107) hydrogen bonds : bond 0.03901 / 2.58 ( 481) hydrogen bonds : angle 4.87487 / 3.36 ( 1464) Misc. bond : bond 0.00295 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 150 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7682 (pm20) REVERT: K 190 MET cc_start: 0.9567 (ttp) cc_final: 0.9057 (tmm) REVERT: K 255 ASN cc_start: 0.7147 (m110) cc_final: 0.6754 (m110) REVERT: K 259 MET cc_start: 0.8903 (mmm) cc_final: 0.8317 (tpp) REVERT: K 278 ILE cc_start: 0.9539 (mt) cc_final: 0.9294 (tt) REVERT: K 300 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8797 (mmmm) REVERT: A 35 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 101 ASN cc_start: 0.9245 (m-40) cc_final: 0.8920 (m-40) REVERT: A 154 MET cc_start: 0.9056 (tpt) cc_final: 0.8642 (tpp) REVERT: A 183 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8115 (mm-30) REVERT: A 194 THR cc_start: 0.8877 (m) cc_final: 0.8085 (t) REVERT: A 198 SER cc_start: 0.7755 (t) cc_final: 0.7399 (p) REVERT: A 357 TYR cc_start: 0.8503 (m-80) cc_final: 0.8176 (m-10) REVERT: A 431 ASP cc_start: 0.8529 (m-30) cc_final: 0.8316 (m-30) REVERT: H 102 ASN cc_start: 0.8221 (t0) cc_final: 0.7366 (t0) REVERT: H 110 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8382 (mm-30) REVERT: H 296 PHE cc_start: 0.8085 (m-80) cc_final: 0.7809 (m-80) REVERT: H 398 MET cc_start: 0.7884 (mmp) cc_final: 0.6885 (mtt) REVERT: H 416 MET cc_start: 0.8967 (tpp) cc_final: 0.8592 (tpp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1174 time to fit residues: 32.8431 Evaluate side-chains 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 51 GLN K 266 ASN ** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.085214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062347 restraints weight = 57100.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065086 restraints weight = 29914.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066954 restraints weight = 19602.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068147 restraints weight = 14652.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068946 restraints weight = 12041.805| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9674 Z= 0.222 Angle : 0.610 10.468 13107 Z= 0.329 Chirality : 0.042 0.162 1454 Planarity : 0.004 0.036 1705 Dihedral : 9.717 177.343 1323 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 46.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.03 (0.25), residues: 1193 helix: 1.01 (0.22), residues: 532 sheet: -0.49 (0.36), residues: 217 loop : -0.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 297 TYR 0.029 0.002 TYR A 432 PHE 0.018 0.002 PHE A 267 TRP 0.008 0.002 TRP H 103 HIS 0.012 0.002 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 ( 9670) covalent geometry : angle 0.60968 / 0.33 (13107) hydrogen bonds : bond 0.04473 / 2.97 ( 481) hydrogen bonds : angle 5.29951 / 3.67 ( 1464) Misc. bond : bond 0.00600 / 0.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 PHE cc_start: 0.8510 (m-80) cc_final: 0.8173 (m-80) REVERT: K 150 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7771 (pm20) REVERT: K 190 MET cc_start: 0.9591 (ttp) cc_final: 0.9038 (tmm) REVERT: K 215 HIS cc_start: 0.8629 (m-70) cc_final: 0.7778 (m90) REVERT: K 255 ASN cc_start: 0.7279 (m110) cc_final: 0.6901 (m110) REVERT: K 259 MET cc_start: 0.8957 (mmm) cc_final: 0.8385 (tpp) REVERT: K 278 ILE cc_start: 0.9571 (mt) cc_final: 0.9332 (tp) REVERT: A 101 ASN cc_start: 0.9288 (m-40) cc_final: 0.8918 (m-40) REVERT: A 154 MET cc_start: 0.8996 (tpt) cc_final: 0.8754 (tpp) REVERT: A 251 ASP cc_start: 0.8534 (t0) cc_final: 0.8243 (m-30) REVERT: A 413 MET cc_start: 0.8530 (mmp) cc_final: 0.8167 (mmp) REVERT: A 425 MET cc_start: 0.9196 (mmp) cc_final: 0.8914 (mmp) REVERT: A 431 ASP cc_start: 0.8505 (m-30) cc_final: 0.8277 (m-30) REVERT: H 75 MET cc_start: 0.8694 (mmm) cc_final: 0.8469 (mpp) REVERT: H 102 ASN cc_start: 0.7833 (t0) cc_final: 0.7358 (t0) REVERT: H 127 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8894 (mt-10) REVERT: H 398 MET cc_start: 0.7937 (mmp) cc_final: 0.6990 (mtt) REVERT: H 416 MET cc_start: 0.9017 (tpp) cc_final: 0.8702 (tpp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1211 time to fit residues: 31.5778 Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 51 GLN K 266 ASN ** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN H 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.086171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.063006 restraints weight = 56624.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.065873 restraints weight = 28824.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067768 restraints weight = 18618.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.069001 restraints weight = 13817.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069786 restraints weight = 11317.227| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 9674 Z= 0.156 Angle : 0.564 19.242 13107 Z= 0.300 Chirality : 0.041 0.228 1454 Planarity : 0.011 0.433 1705 Dihedral : 8.573 168.174 1323 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 43.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.19 (0.25), residues: 1193 helix: 1.21 (0.22), residues: 534 sheet: -0.49 (0.36), residues: 217 loop : -0.81 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG K 297 TYR 0.017 0.001 TYR H 432 PHE 0.021 0.002 PHE K 293 TRP 0.011 0.001 TRP A 346 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9670) covalent geometry : angle 0.56447 / 0.30 (13107) hydrogen bonds : bond 0.04103 / 2.70 ( 481) hydrogen bonds : angle 5.08646 / 3.52 ( 1464) Misc. bond : bond 0.00836 / 0.42 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue MET 131 is missing expected H atoms. Skipping. Residue ILE 134 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 283 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 95 PHE cc_start: 0.8557 (m-80) cc_final: 0.8194 (m-80) REVERT: K 119 MET cc_start: 0.8872 (tpt) cc_final: 0.8562 (tpt) REVERT: K 150 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7787 (pm20) REVERT: K 215 HIS cc_start: 0.8652 (m-70) cc_final: 0.7805 (m90) REVERT: K 255 ASN cc_start: 0.7288 (m110) cc_final: 0.6904 (m110) REVERT: K 259 MET cc_start: 0.8980 (mmm) cc_final: 0.8441 (tpp) REVERT: K 278 ILE cc_start: 0.9556 (mt) cc_final: 0.9318 (tp) REVERT: A 35 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 101 ASN cc_start: 0.9273 (m-40) cc_final: 0.8909 (m-40) REVERT: A 154 MET cc_start: 0.9012 (tpt) cc_final: 0.8781 (tpp) REVERT: A 251 ASP cc_start: 0.8545 (t0) cc_final: 0.8256 (m-30) REVERT: A 313 MET cc_start: 0.8301 (mtt) cc_final: 0.8028 (mtp) REVERT: A 346 TRP cc_start: 0.6214 (p-90) cc_final: 0.4113 (t60) REVERT: A 413 MET cc_start: 0.8439 (mmp) cc_final: 0.8055 (mmp) REVERT: A 431 ASP cc_start: 0.8542 (m-30) cc_final: 0.8245 (m-30) REVERT: H 102 ASN cc_start: 0.8111 (t0) cc_final: 0.7475 (t0) REVERT: H 127 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8916 (mt-10) REVERT: H 398 MET cc_start: 0.7905 (mmp) cc_final: 0.6972 (mtt) REVERT: H 416 MET cc_start: 0.8898 (tpp) cc_final: 0.8545 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1221 time to fit residues: 31.8326 Evaluate side-chains 149 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 51 GLN K 266 ASN K 343 ASN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.085809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062460 restraints weight = 56440.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065312 restraints weight = 28844.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067176 restraints weight = 18681.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068407 restraints weight = 13951.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.069236 restraints weight = 11447.932| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9674 Z= 0.181 Angle : 0.564 10.229 13107 Z= 0.301 Chirality : 0.041 0.177 1454 Planarity : 0.008 0.281 1705 Dihedral : 8.372 169.579 1323 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 45.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.10 (0.25), residues: 1193 helix: 1.23 (0.22), residues: 534 sheet: -0.68 (0.36), residues: 222 loop : -0.90 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG K 297 TYR 0.024 0.001 TYR H 432 PHE 0.016 0.002 PHE A 267 TRP 0.031 0.002 TRP A 346 HIS 0.014 0.002 HIS K 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 9670) covalent geometry : angle 0.56419 / 0.30 (13107) hydrogen bonds : bond 0.04102 / 2.67 ( 481) hydrogen bonds : angle 5.00868 / 3.45 ( 1464) Misc. bond : bond 0.00626 / 0.31 ( 4) =============================================================================== Job complete usr+sys time: 2019.22 seconds wall clock time: 35 minutes 47.16 seconds (2147.16 seconds total)