Starting phenix.real_space_refine on Wed May 14 22:15:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.map" model { file = "/net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glu_40218/05_2025/8glu_40218.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Zn 1 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 43 5.16 5 C 7795 2.51 5 N 2227 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3193 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "E" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3326 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 15, 'TRANS': 402} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4188 SG CYS X 124 53.942 61.985 38.668 1.00 45.24 S ATOM 4209 SG CYS X 127 50.862 64.091 39.821 1.00 45.34 S ATOM 4427 SG CYS X 152 50.421 61.433 37.072 1.00 60.05 S Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ASP G 278 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP G 278 " occ=0.00 residue: pdb=" N LEU G 279 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 279 " occ=0.00 residue: pdb=" N ARG G 280 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 280 " occ=0.00 residue: pdb=" N SER G 281 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 281 " occ=0.00 residue: pdb=" N ALA G 282 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 282 " occ=0.00 residue: pdb=" N ARG G 283 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 283 " occ=0.00 residue: pdb=" N ARG G 284 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 284 " occ=0.00 residue: pdb=" N GLY G 285 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 285 " occ=0.00 residue: pdb=" N ALA G 286 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 286 " occ=0.00 residue: pdb=" N GLY G 287 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 287 " occ=0.00 residue: pdb=" N PHE G 288 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE G 288 " occ=0.00 Time building chain proxies: 8.55, per 1000 atoms: 0.69 Number of scatterers: 12338 At special positions: 0 Unit cell: (88.065, 120.555, 172.71, 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) Zn 1 29.99 S 43 16.00 P 8 15.00 Mg 3 11.99 O 2261 8.00 N 2227 7.00 C 7795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " Number of angles added : 3 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 8 sheets defined 54.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 34 through 38 removed outlier: 3.850A pdb=" N ALA G 37 " --> pdb=" O VAL G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.149A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS G 53 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.506A pdb=" N HIS G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N CYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.541A pdb=" N HIS G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 150 removed outlier: 3.609A pdb=" N LEU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.575A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.550A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 Processing helix chain 'G' and resid 243 through 256 removed outlier: 4.303A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 305 through 316 removed outlier: 3.695A pdb=" N ASN G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 339 Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.565A pdb=" N VAL G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 382 through 392 removed outlier: 3.586A pdb=" N LEU G 386 " --> pdb=" O VAL G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 399 removed outlier: 4.101A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 24 removed outlier: 3.662A pdb=" N GLN X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 85 removed outlier: 3.826A pdb=" N TYR X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Proline residue: X 82 - end of helix removed outlier: 4.250A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 97 removed outlier: 4.231A pdb=" N GLU X 97 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 3.781A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.704A pdb=" N VAL X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 168 Processing helix chain 'X' and resid 189 through 200 removed outlier: 4.124A pdb=" N THR X 193 " --> pdb=" O LEU X 189 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA X 194 " --> pdb=" O SER X 190 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU X 195 " --> pdb=" O GLN X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 205 through 211 removed outlier: 3.557A pdb=" N GLU X 210 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU X 211 " --> pdb=" O ALA X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 removed outlier: 3.517A pdb=" N VAL X 246 " --> pdb=" O VAL X 242 " (cutoff:3.500A) Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.687A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL X 290 " --> pdb=" O GLN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.944A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.715A pdb=" N ALA F 37 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 63 removed outlier: 3.834A pdb=" N ILE F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 removed outlier: 4.018A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 3.604A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 179 through 195 removed outlier: 3.556A pdb=" N ILE F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 187 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 removed outlier: 3.544A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 246 through 259 removed outlier: 3.526A pdb=" N PHE F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 254 " --> pdb=" O ASN F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.925A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 3.928A pdb=" N ARG F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.536A pdb=" N ILE F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 344 through 362 removed outlier: 3.944A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 399 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 21 through 27 removed outlier: 3.633A pdb=" N LEU E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.587A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 100 through 113 removed outlier: 3.920A pdb=" N HIS E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'E' and resid 181 through 195 removed outlier: 4.001A pdb=" N LEU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 224 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 271 through 276 removed outlier: 3.811A pdb=" N PHE E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 285 Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 361 removed outlier: 4.289A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 removed outlier: 3.945A pdb=" N LEU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 393 through 400 removed outlier: 3.506A pdb=" N ILE E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 421 removed outlier: 3.596A pdb=" N ARG E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.375A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.222A pdb=" N LEU G 170 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP G 232 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE G 172 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'F' and resid 171 through 173 removed outlier: 6.976A pdb=" N ILE F 172 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.679A pdb=" N TYR E 158 " --> pdb=" O ILE E 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.239A pdb=" N LEU E 229 " --> pdb=" O MET E 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 135 through 136 removed outlier: 7.094A pdb=" N ILE E 135 " --> pdb=" O TRP E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 478 hydrogen bonds defined for protein. 1362 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: 3.22 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3895 1.34 - 1.45: 1613 1.45 - 1.57: 6987 1.57 - 1.69: 14 1.69 - 1.81: 70 Bond restraints: 12579 Sorted by residual: bond pdb=" CA ASN G 198 " pdb=" CB ASN G 198 " ideal model delta sigma weight residual 1.527 1.604 -0.077 2.48e-02 1.63e+03 9.55e+00 bond pdb=" CA ASN G 198 " pdb=" C ASN G 198 " ideal model delta sigma weight residual 1.526 1.543 -0.017 1.35e-02 5.49e+03 1.53e+00 bond pdb=" CA ASP F 20 " pdb=" CB ASP F 20 " ideal model delta sigma weight residual 1.528 1.558 -0.030 2.61e-02 1.47e+03 1.30e+00 bond pdb=" CB ASN G 198 " pdb=" CG ASN G 198 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" CA ILE E 65 " pdb=" CB ILE E 65 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 9.60e-01 ... (remaining 12574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16792 1.81 - 3.63: 192 3.63 - 5.44: 46 5.44 - 7.25: 11 7.25 - 9.07: 2 Bond angle restraints: 17043 Sorted by residual: angle pdb=" OG1 THR X 45 " pdb=" CB THR X 45 " pdb=" CG2 THR X 45 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.97e+00 angle pdb=" CA ASN G 198 " pdb=" CB ASN G 198 " pdb=" CG ASN G 198 " ideal model delta sigma weight residual 112.60 115.55 -2.95 1.00e+00 1.00e+00 8.70e+00 angle pdb=" N GLN E 414 " pdb=" CA GLN E 414 " pdb=" CB GLN E 414 " ideal model delta sigma weight residual 110.28 114.84 -4.56 1.55e+00 4.16e-01 8.66e+00 angle pdb=" C ASN G 198 " pdb=" CA ASN G 198 " pdb=" CB ASN G 198 " ideal model delta sigma weight residual 111.77 116.16 -4.39 1.52e+00 4.33e-01 8.34e+00 angle pdb=" C ARG X 238 " pdb=" N HIS X 239 " pdb=" CA HIS X 239 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 ... (remaining 17038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 7245 28.07 - 56.15: 355 56.15 - 84.22: 37 84.22 - 112.29: 4 112.29 - 140.37: 3 Dihedral angle restraints: 7644 sinusoidal: 3190 harmonic: 4454 Sorted by residual: dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 80.37 -140.37 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" C5' ADP E 601 " pdb=" O5' ADP E 601 " pdb=" PA ADP E 601 " pdb=" O2A ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.29 -139.28 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PB ADP E 601 " pdb=" PA ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 74.71 -134.72 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 7641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1220 0.033 - 0.066: 513 0.066 - 0.099: 107 0.099 - 0.132: 62 0.132 - 0.164: 3 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CB THR X 45 " pdb=" CA THR X 45 " pdb=" OG1 THR X 45 " pdb=" CG2 THR X 45 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE E 393 " pdb=" CA ILE E 393 " pdb=" CG1 ILE E 393 " pdb=" CG2 ILE E 393 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA GLN E 414 " pdb=" N GLN E 414 " pdb=" C GLN E 414 " pdb=" CB GLN E 414 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1902 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 268 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO F 269 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 268 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO G 269 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 146 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO X 147 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO X 147 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO X 147 " 0.027 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 125 2.62 - 3.19: 10638 3.19 - 3.76: 18069 3.76 - 4.33: 24406 4.33 - 4.90: 40583 Nonbonded interactions: 93821 Sorted by model distance: nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 2.053 2.170 nonbonded pdb=" O3B ATP F 601 " pdb="MG MG F 602 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR E 143 " pdb="MG MG E 602 " model vdw 2.077 2.170 nonbonded pdb=" O3G ATP F 601 " pdb="MG MG F 602 " model vdw 2.081 2.170 nonbonded pdb=" O3G ATP G 601 " pdb="MG MG G 602 " model vdw 2.111 2.170 ... (remaining 93816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 4 through 403 or resid 602)) selection = (chain 'F' and (resid 4 through 403 or resid 602)) selection = (chain 'G' and (resid 4 through 403 or resid 602)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.510 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12583 Z= 0.120 Angle : 0.557 9.065 17046 Z= 0.278 Chirality : 0.040 0.164 1905 Planarity : 0.004 0.051 2190 Dihedral : 15.701 140.366 4774 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1525 helix: 0.02 (0.20), residues: 726 sheet: -0.00 (0.68), residues: 69 loop : -1.24 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 270 HIS 0.006 0.001 HIS X 177 PHE 0.013 0.001 PHE F 187 TYR 0.013 0.001 TYR X 14 ARG 0.006 0.000 ARG G 357 Details of bonding type rmsd hydrogen bonds : bond 0.19143 ( 478) hydrogen bonds : angle 6.17458 ( 1362) metal coordination : bond 0.01064 ( 4) metal coordination : angle 2.15125 ( 3) covalent geometry : bond 0.00265 (12579) covalent geometry : angle 0.55620 (17043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8424 (tttt) cc_final: 0.8211 (mtpp) REVERT: X 107 MET cc_start: 0.6728 (tmm) cc_final: 0.6513 (tmm) REVERT: F 375 TYR cc_start: 0.6798 (t80) cc_final: 0.6493 (t80) REVERT: E 276 GLU cc_start: 0.6368 (mp0) cc_final: 0.5542 (tp30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2581 time to fit residues: 58.5681 Evaluate side-chains 119 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.0270 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138624 restraints weight = 16664.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137953 restraints weight = 18279.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.139250 restraints weight = 18322.063| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12583 Z= 0.213 Angle : 0.656 8.436 17046 Z= 0.326 Chirality : 0.043 0.146 1905 Planarity : 0.005 0.058 2190 Dihedral : 9.473 143.944 1788 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.99 % Allowed : 8.59 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1525 helix: -0.05 (0.20), residues: 742 sheet: -0.52 (0.61), residues: 77 loop : -1.42 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 316 HIS 0.006 0.001 HIS X 287 PHE 0.015 0.002 PHE X 161 TYR 0.022 0.002 TYR G 375 ARG 0.006 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 478) hydrogen bonds : angle 4.71790 ( 1362) metal coordination : bond 0.01403 ( 4) metal coordination : angle 3.61560 ( 3) covalent geometry : bond 0.00518 (12579) covalent geometry : angle 0.65451 (17043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7758 (p0) cc_final: 0.7485 (p0) REVERT: X 35 GLU cc_start: 0.6743 (tp30) cc_final: 0.6534 (mm-30) REVERT: X 99 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7700 (mm-40) REVERT: F 385 MET cc_start: 0.7243 (mpp) cc_final: 0.4556 (tpt) REVERT: E 86 MET cc_start: 0.7475 (mtp) cc_final: 0.7022 (ttm) REVERT: E 276 GLU cc_start: 0.6226 (mp0) cc_final: 0.5387 (tp30) REVERT: E 300 GLN cc_start: 0.5263 (tp40) cc_final: 0.4907 (mm-40) outliers start: 13 outliers final: 8 residues processed: 133 average time/residue: 0.2585 time to fit residues: 49.2498 Evaluate side-chains 121 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 219 THR Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 142 optimal weight: 0.0670 chunk 110 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 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 = 0.4256 r_free = 0.4256 target = 0.185758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139792 restraints weight = 16726.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137461 restraints weight = 16544.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139550 restraints weight = 18286.368| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12583 Z= 0.135 Angle : 0.568 9.714 17046 Z= 0.280 Chirality : 0.040 0.140 1905 Planarity : 0.004 0.060 2190 Dihedral : 9.118 141.280 1788 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.06 % Allowed : 11.48 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1525 helix: 0.14 (0.20), residues: 742 sheet: -0.61 (0.61), residues: 79 loop : -1.34 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 270 HIS 0.006 0.001 HIS G 383 PHE 0.011 0.001 PHE X 161 TYR 0.015 0.001 TYR X 284 ARG 0.002 0.000 ARG E 399 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 478) hydrogen bonds : angle 4.45676 ( 1362) metal coordination : bond 0.01180 ( 4) metal coordination : angle 2.81498 ( 3) covalent geometry : bond 0.00321 (12579) covalent geometry : angle 0.56713 (17043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8393 (tttt) cc_final: 0.8033 (mtpp) REVERT: G 198 ASN cc_start: 0.7765 (p0) cc_final: 0.7462 (p0) REVERT: G 344 MET cc_start: 0.7542 (mmt) cc_final: 0.7127 (mmt) REVERT: X 35 GLU cc_start: 0.6520 (tp30) cc_final: 0.6269 (mm-30) REVERT: X 99 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7648 (mm-40) REVERT: F 385 MET cc_start: 0.7336 (mpp) cc_final: 0.4457 (tpt) REVERT: E 86 MET cc_start: 0.7427 (mtp) cc_final: 0.7036 (ttm) REVERT: E 276 GLU cc_start: 0.6221 (mp0) cc_final: 0.5420 (tp30) outliers start: 14 outliers final: 8 residues processed: 134 average time/residue: 0.2579 time to fit residues: 49.4379 Evaluate side-chains 126 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137421 restraints weight = 16786.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138023 restraints weight = 20223.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138748 restraints weight = 18965.818| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12583 Z= 0.222 Angle : 0.642 9.692 17046 Z= 0.318 Chirality : 0.042 0.147 1905 Planarity : 0.005 0.062 2190 Dihedral : 9.029 134.281 1788 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.90 % Allowed : 13.38 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1525 helix: -0.05 (0.20), residues: 749 sheet: -0.74 (0.61), residues: 79 loop : -1.51 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 316 HIS 0.007 0.001 HIS X 287 PHE 0.018 0.002 PHE X 161 TYR 0.022 0.002 TYR G 375 ARG 0.003 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 478) hydrogen bonds : angle 4.56394 ( 1362) metal coordination : bond 0.01497 ( 4) metal coordination : angle 4.37209 ( 3) covalent geometry : bond 0.00546 (12579) covalent geometry : angle 0.63956 (17043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7811 (p0) cc_final: 0.7448 (p0) REVERT: X 99 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7715 (mm-40) REVERT: X 107 MET cc_start: 0.7006 (tmm) cc_final: 0.6804 (tmm) REVERT: X 276 ARG cc_start: 0.6372 (ptp-110) cc_final: 0.6044 (ttm110) REVERT: F 255 MET cc_start: 0.8187 (tmm) cc_final: 0.7977 (tpp) REVERT: F 264 MET cc_start: 0.8297 (ttt) cc_final: 0.8084 (ttt) REVERT: E 86 MET cc_start: 0.7475 (mtp) cc_final: 0.6975 (ttm) REVERT: E 191 LEU cc_start: 0.8591 (pp) cc_final: 0.8286 (tp) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.2483 time to fit residues: 51.9184 Evaluate side-chains 137 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141127 restraints weight = 17017.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139858 restraints weight = 21817.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141396 restraints weight = 21254.029| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12583 Z= 0.183 Angle : 0.611 8.761 17046 Z= 0.302 Chirality : 0.041 0.147 1905 Planarity : 0.004 0.064 2190 Dihedral : 8.797 129.675 1788 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.51 % Allowed : 14.30 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1525 helix: -0.03 (0.20), residues: 755 sheet: -0.64 (0.61), residues: 79 loop : -1.55 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 316 HIS 0.006 0.001 HIS G 76 PHE 0.033 0.002 PHE E 187 TYR 0.020 0.002 TYR E 337 ARG 0.002 0.000 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 478) hydrogen bonds : angle 4.42413 ( 1362) metal coordination : bond 0.01548 ( 4) metal coordination : angle 3.87492 ( 3) covalent geometry : bond 0.00447 (12579) covalent geometry : angle 0.60926 (17043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8569 (tttt) cc_final: 0.8150 (mtpp) REVERT: G 198 ASN cc_start: 0.7693 (p0) cc_final: 0.7310 (p0) REVERT: G 344 MET cc_start: 0.7517 (mmt) cc_final: 0.7162 (mmt) REVERT: X 99 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7620 (mm-40) REVERT: F 264 MET cc_start: 0.8311 (ttt) cc_final: 0.8096 (ttt) REVERT: F 385 MET cc_start: 0.7346 (mpp) cc_final: 0.4603 (tpt) REVERT: E 86 MET cc_start: 0.7278 (mtp) cc_final: 0.6956 (ttm) REVERT: E 229 LEU cc_start: 0.7747 (tp) cc_final: 0.6914 (mm) outliers start: 33 outliers final: 23 residues processed: 148 average time/residue: 0.2425 time to fit residues: 51.9066 Evaluate side-chains 138 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 219 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 259 ASP Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 141 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN F 322 GLN E 102 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.185209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.140644 restraints weight = 16943.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141139 restraints weight = 19271.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141989 restraints weight = 18808.647| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12583 Z= 0.118 Angle : 0.553 8.887 17046 Z= 0.275 Chirality : 0.039 0.197 1905 Planarity : 0.004 0.063 2190 Dihedral : 8.455 125.022 1788 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.60 % Allowed : 15.89 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1525 helix: 0.18 (0.20), residues: 743 sheet: -0.53 (0.63), residues: 79 loop : -1.43 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 270 HIS 0.006 0.001 HIS G 383 PHE 0.017 0.001 PHE E 187 TYR 0.015 0.001 TYR X 284 ARG 0.005 0.000 ARG X 276 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 478) hydrogen bonds : angle 4.24734 ( 1362) metal coordination : bond 0.01384 ( 4) metal coordination : angle 2.51877 ( 3) covalent geometry : bond 0.00274 (12579) covalent geometry : angle 0.55239 (17043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8416 (tttt) cc_final: 0.8030 (mtpp) REVERT: G 198 ASN cc_start: 0.7716 (p0) cc_final: 0.7388 (p0) REVERT: G 344 MET cc_start: 0.7418 (mmt) cc_final: 0.7183 (mmt) REVERT: X 50 SER cc_start: 0.7322 (m) cc_final: 0.6989 (p) REVERT: X 99 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7729 (mm-40) REVERT: F 264 MET cc_start: 0.8324 (ttt) cc_final: 0.8095 (ttt) REVERT: E 86 MET cc_start: 0.7279 (mtp) cc_final: 0.6985 (ttm) REVERT: E 87 ILE cc_start: 0.7643 (mt) cc_final: 0.7438 (mt) REVERT: E 229 LEU cc_start: 0.7779 (tp) cc_final: 0.6944 (mm) REVERT: E 385 MET cc_start: 0.4873 (mtm) cc_final: 0.4498 (mtm) outliers start: 21 outliers final: 17 residues processed: 140 average time/residue: 0.2310 time to fit residues: 47.6152 Evaluate side-chains 131 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 232 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139933 restraints weight = 16741.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137594 restraints weight = 16759.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139620 restraints weight = 16855.226| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12583 Z= 0.107 Angle : 0.549 11.994 17046 Z= 0.270 Chirality : 0.039 0.181 1905 Planarity : 0.004 0.064 2190 Dihedral : 8.138 119.920 1788 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.67 % Allowed : 16.05 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1525 helix: 0.28 (0.20), residues: 744 sheet: -0.56 (0.62), residues: 79 loop : -1.35 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 PHE 0.016 0.001 PHE E 187 TYR 0.011 0.001 TYR X 123 ARG 0.005 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 478) hydrogen bonds : angle 4.12593 ( 1362) metal coordination : bond 0.01304 ( 4) metal coordination : angle 2.24319 ( 3) covalent geometry : bond 0.00248 (12579) covalent geometry : angle 0.54831 (17043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8430 (tttt) cc_final: 0.8045 (mtpp) REVERT: G 198 ASN cc_start: 0.7705 (p0) cc_final: 0.7425 (p0) REVERT: X 99 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7732 (mm-40) REVERT: X 244 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: F 264 MET cc_start: 0.8305 (ttt) cc_final: 0.8091 (ttt) REVERT: F 373 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 86 MET cc_start: 0.7247 (mtp) cc_final: 0.6980 (ttm) REVERT: E 308 TRP cc_start: 0.6608 (t60) cc_final: 0.6271 (t60) outliers start: 22 outliers final: 20 residues processed: 146 average time/residue: 0.2224 time to fit residues: 48.6024 Evaluate side-chains 137 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 232 THR Chi-restraints excluded: chain X residue 244 GLU Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 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 = 0.4240 r_free = 0.4240 target = 0.184454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140001 restraints weight = 16871.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139704 restraints weight = 19965.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141074 restraints weight = 19536.885| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12583 Z= 0.138 Angle : 0.567 9.591 17046 Z= 0.280 Chirality : 0.040 0.165 1905 Planarity : 0.004 0.062 2190 Dihedral : 7.962 115.144 1788 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.21 % Allowed : 16.81 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1525 helix: 0.25 (0.20), residues: 741 sheet: -0.59 (0.62), residues: 79 loop : -1.38 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 PHE 0.013 0.001 PHE E 187 TYR 0.019 0.001 TYR F 375 ARG 0.003 0.000 ARG X 276 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 478) hydrogen bonds : angle 4.12235 ( 1362) metal coordination : bond 0.01489 ( 4) metal coordination : angle 3.26604 ( 3) covalent geometry : bond 0.00333 (12579) covalent geometry : angle 0.56547 (17043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8420 (tttt) cc_final: 0.8090 (mtpp) REVERT: G 198 ASN cc_start: 0.7732 (p0) cc_final: 0.7464 (p0) REVERT: G 344 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6577 (mmp) REVERT: X 99 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7588 (mm-40) REVERT: F 264 MET cc_start: 0.8306 (ttt) cc_final: 0.8059 (ttt) REVERT: F 373 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7472 (tm-30) REVERT: E 86 MET cc_start: 0.7365 (mtp) cc_final: 0.7108 (ttm) REVERT: E 301 ARG cc_start: 0.5566 (mmt180) cc_final: 0.5322 (mpt90) REVERT: E 385 MET cc_start: 0.4915 (mtm) cc_final: 0.4456 (mtm) outliers start: 29 outliers final: 22 residues processed: 142 average time/residue: 0.2306 time to fit residues: 48.5552 Evaluate side-chains 138 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 232 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 3.9990 chunk 133 optimal weight: 0.0770 chunk 142 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 108 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.0010 overall best weight: 0.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 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 = 0.4273 r_free = 0.4273 target = 0.187850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142076 restraints weight = 16794.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139177 restraints weight = 16445.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141306 restraints weight = 16911.510| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12583 Z= 0.097 Angle : 0.547 12.051 17046 Z= 0.270 Chirality : 0.039 0.175 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.701 112.366 1788 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.67 % Allowed : 17.72 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1525 helix: 0.37 (0.21), residues: 744 sheet: -0.61 (0.62), residues: 79 loop : -1.20 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 PHE 0.031 0.001 PHE E 187 TYR 0.014 0.001 TYR E 337 ARG 0.003 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 478) hydrogen bonds : angle 4.08394 ( 1362) metal coordination : bond 0.01336 ( 4) metal coordination : angle 1.70979 ( 3) covalent geometry : bond 0.00215 (12579) covalent geometry : angle 0.54675 (17043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8381 (tttt) cc_final: 0.8081 (mtpp) REVERT: X 99 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7650 (mm-40) REVERT: F 248 MET cc_start: 0.5637 (mpp) cc_final: 0.5294 (mpp) REVERT: F 264 MET cc_start: 0.8209 (ttt) cc_final: 0.7977 (ttt) REVERT: F 373 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7413 (tm-30) REVERT: E 86 MET cc_start: 0.7259 (mtp) cc_final: 0.7021 (ttm) REVERT: E 301 ARG cc_start: 0.5753 (mmt180) cc_final: 0.5483 (mpt90) REVERT: E 385 MET cc_start: 0.5098 (mtm) cc_final: 0.4852 (mtm) outliers start: 22 outliers final: 19 residues processed: 144 average time/residue: 0.2557 time to fit residues: 53.2139 Evaluate side-chains 138 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 229 LEU Chi-restraints excluded: chain X residue 232 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.0050 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN G 198 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.186729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141340 restraints weight = 16585.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139111 restraints weight = 16854.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141100 restraints weight = 17804.872| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12583 Z= 0.116 Angle : 0.572 12.396 17046 Z= 0.282 Chirality : 0.039 0.150 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.582 111.625 1788 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 1.75 % Allowed : 18.17 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1525 helix: 0.39 (0.21), residues: 743 sheet: -0.60 (0.63), residues: 79 loop : -1.19 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 PHE 0.015 0.001 PHE E 187 TYR 0.012 0.001 TYR G 375 ARG 0.011 0.000 ARG F 189 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 478) hydrogen bonds : angle 4.07858 ( 1362) metal coordination : bond 0.01415 ( 4) metal coordination : angle 2.39494 ( 3) covalent geometry : bond 0.00272 (12579) covalent geometry : angle 0.57098 (17043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8398 (tttt) cc_final: 0.8101 (mtpp) REVERT: G 344 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6620 (mmp) REVERT: X 99 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7638 (mm-40) REVERT: F 248 MET cc_start: 0.5651 (mpp) cc_final: 0.5281 (mpp) REVERT: F 264 MET cc_start: 0.8222 (ttt) cc_final: 0.7981 (ttt) REVERT: F 373 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 86 MET cc_start: 0.7332 (mtp) cc_final: 0.7118 (ttm) REVERT: E 301 ARG cc_start: 0.5793 (mmt180) cc_final: 0.5502 (mpt90) REVERT: E 385 MET cc_start: 0.5158 (mtm) cc_final: 0.4862 (mtm) outliers start: 23 outliers final: 21 residues processed: 140 average time/residue: 0.2465 time to fit residues: 50.4701 Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 344 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 229 LEU Chi-restraints excluded: chain X residue 232 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 69 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN G 198 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.188742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145072 restraints weight = 16502.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143679 restraints weight = 18346.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145424 restraints weight = 18460.312| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12583 Z= 0.111 Angle : 0.573 12.842 17046 Z= 0.283 Chirality : 0.039 0.159 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.520 111.186 1788 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.48 % Rotamer: Outliers : 1.67 % Allowed : 18.40 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1525 helix: 0.43 (0.21), residues: 743 sheet: -0.60 (0.62), residues: 79 loop : -1.16 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 PHE 0.014 0.001 PHE E 187 TYR 0.022 0.001 TYR F 109 ARG 0.008 0.000 ARG F 189 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 478) hydrogen bonds : angle 4.05656 ( 1362) metal coordination : bond 0.01399 ( 4) metal coordination : angle 2.26211 ( 3) covalent geometry : bond 0.00258 (12579) covalent geometry : angle 0.57220 (17043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3850.08 seconds wall clock time: 68 minutes 15.44 seconds (4095.44 seconds total)