Starting phenix.real_space_refine on Wed Sep 17 23:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2c_14461/09_2025/7z2c_14461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2c_14461/09_2025/7z2c_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_14461/09_2025/7z2c_14461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2c_14461/09_2025/7z2c_14461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z2c_14461/09_2025/7z2c_14461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2c_14461/09_2025/7z2c_14461.map" } 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-2.0-5805/lib/python3.9/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: 3.00, per 1000 atoms: 0.25 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: 1.30 Conformation dependent library (CDL) restraints added in 495.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.41 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: 2.67 Time building geometry restraints manager: 1.66 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: 6482 33.61 - 67.21: 151 67.21 - 100.82: 17 100.82 - 134.42: 0 134.42 - 168.03: 3 Dihedral angle restraints: 6653 sinusoidal: 3066 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 6650 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: 0.010 Normalize map: mean=0, sd=1: 0.040 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: 0.110 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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 : 14.711 168.027 3606 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 aren 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 covalent geometry : bond 0.01179 ( 9670) covalent geometry : angle 1.59052 (13107) hydrogen bonds : bond 0.18762 ( 481) hydrogen bonds : angle 7.57135 ( 1464) Misc. bond : bond 0.14270 ( 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 : 0.424 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: K 150 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4362 (mm-30) REVERT: K 215 HIS cc_start: 0.5474 (m-70) cc_final: 0.5030 (m90) REVERT: K 332 HIS cc_start: 0.6504 (t70) cc_final: 0.5203 (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: 0.2736 (t60) REVERT: H 19 LYS cc_start: 0.7754 (tptt) cc_final: 0.7501 (tppt) REVERT: H 384 ILE cc_start: 0.8279 (mm) cc_final: 0.7749 (mt) outliers start: 5 outliers final: 0 residues processed: 354 average time/residue: 0.1632 time to fit residues: 75.6862 Evaluate side-chains 206 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: K 133 GLN K 343 ASN ** 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 258 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.090972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067782 restraints weight = 56250.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070765 restraints weight = 28659.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072729 restraints weight = 18496.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074023 restraints weight = 13745.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.074881 restraints weight = 11213.974| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9674 Z= 0.185 Angle : 0.650 13.376 13107 Z= 0.358 Chirality : 0.044 0.204 1454 Planarity : 0.009 0.305 1705 Dihedral : 11.059 173.386 1351 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 29.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.49 % Rotamer: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.81 % 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 aren not related in a simple way. whole: 0.60 (0.24), residues: 1193 helix: 1.36 (0.22), residues: 532 sheet: 0.02 (0.34), residues: 222 loop : -0.50 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 297 TYR 0.020 0.002 TYR K 75 PHE 0.017 0.002 PHE H 135 TRP 0.011 0.002 TRP A 407 HIS 0.007 0.001 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9670) covalent geometry : angle 0.65022 (13107) hydrogen bonds : bond 0.05538 ( 481) hydrogen bonds : angle 5.52561 ( 1464) Misc. bond : bond 0.00630 ( 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 242 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.422 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: 0.8069 (mm-30) cc_final: 0.6957 (mm-30) REVERT: K 190 MET cc_start: 0.9454 (ttp) cc_final: 0.9048 (tmm) REVERT: K 255 ASN cc_start: 0.6533 (m110) cc_final: 0.6134 (m110) REVERT: K 266 ASN cc_start: 0.9410 (m-40) cc_final: 0.9196 (t0) REVERT: K 300 LYS cc_start: 0.9242 (mmtp) cc_final: 0.9034 (mmmm) REVERT: A 36 MET cc_start: 0.6551 (tmm) cc_final: 0.6306 (tmm) REVERT: A 70 LEU cc_start: 0.8344 (mt) cc_final: 0.8096 (mt) REVERT: A 101 ASN cc_start: 0.9168 (m-40) cc_final: 0.8913 (m110) REVERT: A 194 THR cc_start: 0.8647 (m) cc_final: 0.8150 (t) REVERT: A 313 MET cc_start: 0.8372 (mtp) cc_final: 0.8075 (mtt) REVERT: A 368 LEU cc_start: 0.8083 (mm) cc_final: 0.7879 (mm) REVERT: H 102 ASN cc_start: 0.8081 (t0) cc_final: 0.7175 (t0) REVERT: H 105 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8341 (mtpt) REVERT: H 110 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8379 (tp30) REVERT: H 116 ASP cc_start: 0.9270 (m-30) cc_final: 0.9027 (m-30) REVERT: H 267 PHE cc_start: 0.9048 (m-80) cc_final: 0.8725 (m-80) REVERT: H 418 PHE cc_start: 0.8795 (m-10) cc_final: 0.8438 (m-10) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1412 time to fit residues: 46.9142 Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 9.9990 chunk 109 optimal weight: 20.0000 chunk 93 optimal weight: 0.0870 chunk 95 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 overall best weight: 7.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 202 GLN ** 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 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 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 = 0.3673 r_free = 0.3673 target = 0.088579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065636 restraints weight = 57107.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068419 restraints weight = 29850.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070314 restraints weight = 19538.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071460 restraints weight = 14617.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072299 restraints weight = 12104.496| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9674 Z= 0.202 Angle : 0.605 11.255 13107 Z= 0.333 Chirality : 0.042 0.193 1454 Planarity : 0.006 0.203 1705 Dihedral : 10.834 174.523 1351 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 35.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 aren not related in a simple way. whole: 0.41 (0.24), residues: 1193 helix: 1.20 (0.22), residues: 528 sheet: -0.25 (0.34), residues: 230 loop : -0.47 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG K 297 TYR 0.019 0.002 TYR K 97 PHE 0.016 0.002 PHE H 87 TRP 0.008 0.001 TRP A 21 HIS 0.008 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9670) covalent geometry : angle 0.60550 (13107) hydrogen bonds : bond 0.04826 ( 481) hydrogen bonds : angle 5.34968 ( 1464) Misc. bond : bond 0.00693 ( 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 203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.424 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: K 150 GLU cc_start: 0.8069 (mm-30) cc_final: 0.6924 (mm-30) REVERT: K 278 ILE cc_start: 0.9573 (mt) cc_final: 0.9303 (tt) REVERT: A 36 MET cc_start: 0.6932 (tmm) cc_final: 0.6504 (tmm) REVERT: A 70 LEU cc_start: 0.8391 (mt) cc_final: 0.8114 (mt) REVERT: A 101 ASN cc_start: 0.9282 (m-40) cc_final: 0.9010 (m-40) REVERT: A 194 THR cc_start: 0.8877 (m) cc_final: 0.8389 (t) REVERT: A 252 LEU cc_start: 0.8911 (mp) cc_final: 0.8573 (mp) REVERT: A 368 LEU cc_start: 0.8329 (mm) cc_final: 0.8099 (mm) REVERT: H 55 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7945 (tp30) REVERT: H 102 ASN cc_start: 0.8163 (t0) cc_final: 0.7365 (t0) REVERT: H 105 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8336 (mtpt) REVERT: H 116 ASP cc_start: 0.9085 (m-30) cc_final: 0.8871 (m-30) REVERT: H 267 PHE cc_start: 0.9086 (m-80) cc_final: 0.8465 (m-10) REVERT: H 373 MET cc_start: 0.8767 (mtp) cc_final: 0.8535 (mtm) REVERT: H 416 MET cc_start: 0.8894 (tpp) cc_final: 0.8692 (tpp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1431 time to fit residues: 39.3532 Evaluate side-chains 156 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 40.0000 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 3 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 ASN K 149 ASN K 266 ASN ** 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 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 101 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.088319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.065880 restraints weight = 57315.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.068749 restraints weight = 29463.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070587 restraints weight = 19049.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071754 restraints weight = 14174.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072503 restraints weight = 11655.129| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9674 Z= 0.174 Angle : 0.564 8.439 13107 Z= 0.305 Chirality : 0.041 0.224 1454 Planarity : 0.008 0.262 1705 Dihedral : 10.451 171.569 1351 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 38.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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 aren not related in a simple way. whole: 0.44 (0.24), residues: 1193 helix: 1.38 (0.22), residues: 527 sheet: -0.35 (0.34), residues: 232 loop : -0.59 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 264 TYR 0.019 0.002 TYR H 432 PHE 0.015 0.002 PHE K 144 TRP 0.008 0.001 TRP A 21 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9670) covalent geometry : angle 0.56420 (13107) hydrogen bonds : bond 0.04550 ( 481) hydrogen bonds : angle 5.14299 ( 1464) Misc. bond : bond 0.00520 ( 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 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.423 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 190 MET cc_start: 0.9500 (ttp) cc_final: 0.9021 (tmm) REVERT: K 255 ASN cc_start: 0.7033 (m110) cc_final: 0.6659 (m110) REVERT: K 259 MET cc_start: 0.8933 (mmm) cc_final: 0.8322 (tpp) REVERT: K 278 ILE cc_start: 0.9568 (mt) cc_final: 0.9322 (tt) REVERT: A 35 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 36 MET cc_start: 0.7148 (tmm) cc_final: 0.6847 (tmm) REVERT: A 70 LEU cc_start: 0.8414 (mt) cc_final: 0.8143 (mt) REVERT: A 101 ASN cc_start: 0.9260 (m-40) cc_final: 0.8997 (m-40) REVERT: A 194 THR cc_start: 0.8941 (m) cc_final: 0.8416 (t) REVERT: H 101 ASN cc_start: 0.8486 (m-40) cc_final: 0.8166 (m-40) REVERT: H 102 ASN cc_start: 0.8130 (t0) cc_final: 0.7368 (t0) REVERT: H 105 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8348 (mtpt) REVERT: H 110 GLU cc_start: 0.8616 (tp30) cc_final: 0.8363 (tp30) REVERT: H 116 ASP cc_start: 0.9099 (m-30) cc_final: 0.8897 (m-30) REVERT: H 373 MET cc_start: 0.8856 (mtp) cc_final: 0.8645 (mtm) REVERT: H 416 MET cc_start: 0.8910 (tpp) cc_final: 0.8705 (tpp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1334 time to fit residues: 35.2936 Evaluate side-chains 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 overall best weight: 9.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 266 ASN A 31 GLN ** 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 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 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 15 GLN ** H 43 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.086129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063286 restraints weight = 58477.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066052 restraints weight = 30820.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067894 restraints weight = 20280.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069059 restraints weight = 15217.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069781 restraints weight = 12582.036| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9674 Z= 0.251 Angle : 0.665 14.820 13107 Z= 0.359 Chirality : 0.042 0.168 1454 Planarity : 0.005 0.095 1705 Dihedral : 10.686 174.240 1351 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 44.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 0.10 % Allowed : 2.80 % 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 aren not related in a simple way. whole: -0.05 (0.24), residues: 1193 helix: 0.97 (0.22), residues: 532 sheet: -0.57 (0.34), residues: 234 loop : -0.87 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG K 297 TYR 0.028 0.002 TYR H 432 PHE 0.023 0.002 PHE H 87 TRP 0.007 0.002 TRP A 21 HIS 0.010 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9670) covalent geometry : angle 0.66464 (13107) hydrogen bonds : bond 0.04831 ( 481) hydrogen bonds : angle 5.35880 ( 1464) Misc. bond : bond 0.00984 ( 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 174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.413 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 255 ASN cc_start: 0.7098 (m110) cc_final: 0.6711 (m110) REVERT: K 259 MET cc_start: 0.8866 (mmm) cc_final: 0.8364 (tpp) REVERT: K 278 ILE cc_start: 0.9600 (mt) cc_final: 0.9374 (tt) REVERT: A 70 LEU cc_start: 0.8630 (mt) cc_final: 0.8331 (mt) REVERT: A 101 ASN cc_start: 0.9270 (m-40) cc_final: 0.8946 (m-40) REVERT: A 413 MET cc_start: 0.8370 (mmp) cc_final: 0.8044 (mmp) REVERT: A 431 ASP cc_start: 0.8458 (m-30) cc_final: 0.8219 (m-30) REVERT: H 102 ASN cc_start: 0.8114 (t0) cc_final: 0.7855 (t0) REVERT: H 398 MET cc_start: 0.8001 (mmp) cc_final: 0.7058 (mtt) REVERT: H 416 MET cc_start: 0.8929 (tpp) cc_final: 0.8662 (tpp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1405 time to fit residues: 33.8247 Evaluate side-chains 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 40.0000 chunk 45 optimal weight: 10.0000 chunk 111 optimal weight: 40.0000 chunk 104 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 266 ASN ** A 35 GLN ** 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 228 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 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 = 0.3641 r_free = 0.3641 target = 0.086646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.063555 restraints weight = 57700.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066371 restraints weight = 29846.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068228 restraints weight = 19414.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.069480 restraints weight = 14507.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070212 restraints weight = 11924.263| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9674 Z= 0.178 Angle : 0.543 6.296 13107 Z= 0.299 Chirality : 0.041 0.260 1454 Planarity : 0.004 0.033 1705 Dihedral : 10.473 177.115 1351 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 43.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 1.06 % Favored : 98.84 % 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 aren not related in a simple way. whole: 0.10 (0.24), residues: 1193 helix: 1.16 (0.22), residues: 532 sheet: -0.64 (0.35), residues: 229 loop : -0.81 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 264 TYR 0.018 0.001 TYR H 432 PHE 0.017 0.002 PHE H 135 TRP 0.008 0.001 TRP A 21 HIS 0.007 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9670) covalent geometry : angle 0.54252 (13107) hydrogen bonds : bond 0.04360 ( 481) hydrogen bonds : angle 5.20858 ( 1464) Misc. bond : bond 0.00680 ( 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 174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.426 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: 0.8175 (mm-30) cc_final: 0.7695 (pm20) REVERT: K 255 ASN cc_start: 0.7151 (m110) cc_final: 0.6762 (m110) REVERT: K 259 MET cc_start: 0.8881 (mmm) cc_final: 0.8329 (tpp) REVERT: K 278 ILE cc_start: 0.9585 (mt) cc_final: 0.9360 (tt) REVERT: K 300 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8860 (mmtp) REVERT: A 35 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 70 LEU cc_start: 0.8538 (mt) cc_final: 0.8249 (mt) REVERT: A 101 ASN cc_start: 0.9280 (m-40) cc_final: 0.8977 (m-40) REVERT: A 194 THR cc_start: 0.9052 (m) cc_final: 0.8710 (t) REVERT: A 413 MET cc_start: 0.8483 (mmp) cc_final: 0.7995 (mmp) REVERT: A 431 ASP cc_start: 0.8430 (m-30) cc_final: 0.8203 (m-30) REVERT: H 102 ASN cc_start: 0.8120 (t0) cc_final: 0.7863 (t0) REVERT: H 269 MET cc_start: 0.8099 (ptm) cc_final: 0.7879 (ptm) REVERT: H 398 MET cc_start: 0.7906 (mmp) cc_final: 0.6988 (mtt) REVERT: H 416 MET cc_start: 0.8886 (tpp) cc_final: 0.8568 (tpp) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.1433 time to fit residues: 34.4312 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 266 ASN ** A 35 GLN ** 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 228 ASN ** A 258 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** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.063544 restraints weight = 57307.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066407 restraints weight = 29472.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.068298 restraints weight = 19001.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069520 restraints weight = 14078.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070324 restraints weight = 11505.867| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9674 Z= 0.164 Angle : 0.558 16.775 13107 Z= 0.302 Chirality : 0.040 0.186 1454 Planarity : 0.010 0.404 1705 Dihedral : 9.359 167.086 1351 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 43.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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 aren not related in a simple way. whole: 0.27 (0.25), residues: 1193 helix: 1.31 (0.22), residues: 531 sheet: -0.57 (0.36), residues: 217 loop : -0.71 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K 297 TYR 0.016 0.001 TYR H 432 PHE 0.028 0.002 PHE K 126 TRP 0.007 0.001 TRP A 21 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9670) covalent geometry : angle 0.55796 (13107) hydrogen bonds : bond 0.04245 ( 481) hydrogen bonds : angle 5.11069 ( 1464) Misc. bond : bond 0.00502 ( 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 174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 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: K 255 ASN cc_start: 0.7155 (m110) cc_final: 0.6775 (m110) REVERT: K 259 MET cc_start: 0.8921 (mmm) cc_final: 0.8353 (tpp) REVERT: K 278 ILE cc_start: 0.9580 (mt) cc_final: 0.9338 (tt) REVERT: A 35 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 70 LEU cc_start: 0.8498 (mt) cc_final: 0.8221 (mt) REVERT: A 101 ASN cc_start: 0.9296 (m-40) cc_final: 0.9003 (m-40) REVERT: A 154 MET cc_start: 0.9095 (tpt) cc_final: 0.8688 (tpp) REVERT: A 194 THR cc_start: 0.9037 (m) cc_final: 0.8242 (t) REVERT: A 198 SER cc_start: 0.7953 (t) cc_final: 0.7576 (p) REVERT: A 413 MET cc_start: 0.8585 (mmp) cc_final: 0.7954 (mmp) REVERT: A 431 ASP cc_start: 0.8405 (m-30) cc_final: 0.8194 (m-30) REVERT: H 102 ASN cc_start: 0.8116 (t0) cc_final: 0.7870 (t0) REVERT: H 127 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8874 (mt-10) REVERT: H 296 PHE cc_start: 0.7922 (m-80) cc_final: 0.7613 (m-80) REVERT: H 398 MET cc_start: 0.7927 (mmp) cc_final: 0.7005 (mtt) REVERT: H 416 MET cc_start: 0.8834 (tpp) cc_final: 0.8530 (tpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1344 time to fit residues: 32.5260 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 266 ASN ** 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 249 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.083831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.061437 restraints weight = 58209.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064182 restraints weight = 30243.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066030 restraints weight = 19731.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067233 restraints weight = 14685.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068028 restraints weight = 12013.093| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.7009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9674 Z= 0.286 Angle : 0.711 19.147 13107 Z= 0.386 Chirality : 0.042 0.230 1454 Planarity : 0.012 0.453 1705 Dihedral : 9.716 167.866 1351 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 51.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 aren not related in a simple way. whole: -0.43 (0.24), residues: 1193 helix: 0.70 (0.22), residues: 532 sheet: -0.81 (0.36), residues: 222 loop : -1.10 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 264 TYR 0.023 0.002 TYR A 432 PHE 0.025 0.002 PHE A 267 TRP 0.008 0.002 TRP A 407 HIS 0.009 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9670) covalent geometry : angle 0.71089 (13107) hydrogen bonds : bond 0.04763 ( 481) hydrogen bonds : angle 5.48997 ( 1464) Misc. bond : bond 0.00485 ( 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 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.413 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 255 ASN cc_start: 0.7225 (m110) cc_final: 0.6859 (m110) REVERT: K 259 MET cc_start: 0.8954 (mmm) cc_final: 0.8481 (tpp) REVERT: K 278 ILE cc_start: 0.9602 (mt) cc_final: 0.9379 (tp) REVERT: A 35 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 101 ASN cc_start: 0.9295 (m-40) cc_final: 0.8937 (m-40) REVERT: A 154 MET cc_start: 0.9087 (tpt) cc_final: 0.8787 (tpp) REVERT: A 413 MET cc_start: 0.8658 (mmp) cc_final: 0.8126 (mmp) REVERT: A 431 ASP cc_start: 0.8400 (m-30) cc_final: 0.7972 (m-30) REVERT: H 75 MET cc_start: 0.8753 (mmp) cc_final: 0.8443 (mmp) REVERT: H 127 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8895 (mt-10) REVERT: H 398 MET cc_start: 0.7986 (mmp) cc_final: 0.7046 (mtt) REVERT: H 416 MET cc_start: 0.8853 (tpp) cc_final: 0.8441 (tpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1315 time to fit residues: 30.0440 Evaluate side-chains 133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN H 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062681 restraints weight = 57169.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065496 restraints weight = 29642.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.067324 restraints weight = 19316.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.068587 restraints weight = 14503.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069348 restraints weight = 11861.133| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9674 Z= 0.159 Angle : 0.536 9.625 13107 Z= 0.292 Chirality : 0.041 0.192 1454 Planarity : 0.004 0.056 1705 Dihedral : 9.166 165.774 1351 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 43.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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 aren not related in a simple way. whole: -0.09 (0.25), residues: 1193 helix: 1.04 (0.22), residues: 532 sheet: -0.88 (0.36), residues: 220 loop : -0.87 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG K 297 TYR 0.016 0.001 TYR H 432 PHE 0.013 0.001 PHE H 395 TRP 0.013 0.001 TRP A 346 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9670) covalent geometry : angle 0.53562 (13107) hydrogen bonds : bond 0.04187 ( 481) hydrogen bonds : angle 5.19481 ( 1464) Misc. bond : bond 0.00893 ( 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 169 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.426 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 241 CYS cc_start: 0.7499 (t) cc_final: 0.7285 (t) REVERT: K 255 ASN cc_start: 0.7206 (m110) cc_final: 0.6835 (m110) REVERT: K 259 MET cc_start: 0.8942 (mmm) cc_final: 0.8359 (tpp) REVERT: K 278 ILE cc_start: 0.9590 (mt) cc_final: 0.9360 (tp) REVERT: A 35 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 101 ASN cc_start: 0.9249 (m-40) cc_final: 0.8893 (m-40) REVERT: A 154 MET cc_start: 0.9048 (tpt) cc_final: 0.8715 (tpp) REVERT: A 198 SER cc_start: 0.7996 (t) cc_final: 0.7581 (p) REVERT: A 313 MET cc_start: 0.8231 (mtt) cc_final: 0.7966 (mtp) REVERT: A 346 TRP cc_start: 0.6393 (p-90) cc_final: 0.4253 (t60) REVERT: A 413 MET cc_start: 0.8712 (mmp) cc_final: 0.8167 (mmp) REVERT: A 431 ASP cc_start: 0.8373 (m-30) cc_final: 0.8151 (m-30) REVERT: H 105 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8584 (mtpt) REVERT: H 127 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8880 (mt-10) REVERT: H 398 MET cc_start: 0.7795 (mmp) cc_final: 0.6977 (mtt) REVERT: H 416 MET cc_start: 0.8720 (tpp) cc_final: 0.8411 (tpp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1409 time to fit residues: 32.7133 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.4980 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 32 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 GLN ** K 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063517 restraints weight = 56251.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.066416 restraints weight = 29002.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068333 restraints weight = 18711.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.069579 restraints weight = 13883.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.070349 restraints weight = 11379.230| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9674 Z= 0.120 Angle : 0.547 15.686 13107 Z= 0.289 Chirality : 0.041 0.184 1454 Planarity : 0.005 0.158 1705 Dihedral : 9.995 164.835 1351 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 41.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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 aren not related in a simple way. whole: 0.22 (0.25), residues: 1193 helix: 1.32 (0.22), residues: 538 sheet: -0.85 (0.36), residues: 222 loop : -0.69 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K 297 TYR 0.018 0.001 TYR H 432 PHE 0.014 0.001 PHE K 293 TRP 0.012 0.001 TRP A 388 HIS 0.004 0.001 HIS H 266 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9670) covalent geometry : angle 0.54684 (13107) hydrogen bonds : bond 0.04160 ( 481) hydrogen bonds : angle 5.02495 ( 1464) Misc. bond : bond 0.00712 ( 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 173 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.251 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 119 MET cc_start: 0.9316 (tmm) cc_final: 0.8952 (tpt) REVERT: K 215 HIS cc_start: 0.8524 (m-70) cc_final: 0.8070 (m-70) REVERT: K 255 ASN cc_start: 0.7220 (m110) cc_final: 0.6847 (m110) REVERT: K 259 MET cc_start: 0.8925 (mmm) cc_final: 0.8321 (tpp) REVERT: K 278 ILE cc_start: 0.9575 (mt) cc_final: 0.9337 (tp) REVERT: A 35 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 101 ASN cc_start: 0.9252 (m-40) cc_final: 0.8916 (m-40) REVERT: A 154 MET cc_start: 0.9002 (tpt) cc_final: 0.8711 (tpp) REVERT: A 194 THR cc_start: 0.9066 (m) cc_final: 0.8317 (t) REVERT: A 198 SER cc_start: 0.7760 (t) cc_final: 0.7526 (p) REVERT: A 313 MET cc_start: 0.8212 (mtt) cc_final: 0.8005 (mtp) REVERT: A 346 TRP cc_start: 0.6431 (p-90) cc_final: 0.4169 (t60) REVERT: A 413 MET cc_start: 0.8594 (mmp) cc_final: 0.8176 (mmp) REVERT: A 431 ASP cc_start: 0.8375 (m-30) cc_final: 0.8133 (m-30) REVERT: H 127 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8904 (mt-10) REVERT: H 218 LYS cc_start: 0.9420 (pttt) cc_final: 0.9184 (pttp) REVERT: H 398 MET cc_start: 0.7811 (mmp) cc_final: 0.6976 (mtt) REVERT: H 416 MET cc_start: 0.8712 (tpp) cc_final: 0.8251 (tpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1261 time to fit residues: 30.9348 Evaluate side-chains 143 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 6.9990 chunk 50 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 115 optimal weight: 0.1980 chunk 4 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 51 GLN ** K 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.085481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.062500 restraints weight = 56744.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065355 restraints weight = 29190.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067230 restraints weight = 18876.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068465 restraints weight = 14038.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069277 restraints weight = 11526.312| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9674 Z= 0.154 Angle : 0.533 11.159 13107 Z= 0.286 Chirality : 0.041 0.146 1454 Planarity : 0.005 0.171 1705 Dihedral : 9.949 166.280 1351 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 44.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.18 (0.25), residues: 1193 helix: 1.32 (0.22), residues: 535 sheet: -0.82 (0.36), residues: 222 loop : -0.78 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 297 TYR 0.029 0.001 TYR H 435 PHE 0.013 0.001 PHE H 395 TRP 0.025 0.002 TRP A 346 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9670) covalent geometry : angle 0.53309 (13107) hydrogen bonds : bond 0.03894 ( 481) hydrogen bonds : angle 4.94803 ( 1464) Misc. bond : bond 0.00540 ( 4) =============================================================================== Job complete usr+sys time: 2045.53 seconds wall clock time: 36 minutes 10.29 seconds (2170.29 seconds total)