Starting phenix.real_space_refine on Sat Aug 23 13:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glu_40218/08_2025/8glu_40218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glu_40218/08_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_40218/08_2025/8glu_40218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glu_40218/08_2025/8glu_40218.map" model { file = "/net/cci-nas-00/data/ceres_data/8glu_40218/08_2025/8glu_40218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glu_40218/08_2025/8glu_40218.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.85, per 1000 atoms: 0.23 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: 0.93 Conformation dependent library (CDL) restraints added in 365.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 1.51 Time building geometry restraints manager: 1.17 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: 3.100 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- 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 : 7.56 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (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 ARG 0.006 0.000 ARG G 357 TYR 0.013 0.001 TYR X 14 PHE 0.013 0.001 PHE F 187 TRP 0.017 0.001 TRP X 270 HIS 0.006 0.001 HIS X 177 Details of bonding type rmsd covalent geometry : bond 0.00265 (12579) covalent geometry : angle 0.55620 (17043) hydrogen bonds : bond 0.19143 ( 478) hydrogen bonds : angle 6.17458 ( 1362) metal coordination : bond 0.01064 ( 4) metal coordination : angle 2.15125 ( 3) *********************** 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 : 0.475 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: 0.1065 time to fit residues: 24.5053 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 : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 383 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.186359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141405 restraints weight = 16698.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141234 restraints weight = 17436.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142433 restraints weight = 17217.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143928 restraints weight = 10009.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145044 restraints weight = 8614.887| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 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 = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12583 Z= 0.163 Angle : 0.606 8.658 17046 Z= 0.300 Chirality : 0.041 0.144 1905 Planarity : 0.004 0.058 2190 Dihedral : 9.413 144.386 1788 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.99 % Allowed : 7.83 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.22), residues: 1525 helix: 0.07 (0.20), residues: 736 sheet: -0.37 (0.61), residues: 77 loop : -1.33 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 11 TYR 0.018 0.001 TYR G 375 PHE 0.011 0.002 PHE X 161 TRP 0.010 0.001 TRP G 316 HIS 0.007 0.001 HIS X 51 Details of bonding type rmsd covalent geometry : bond 0.00391 (12579) covalent geometry : angle 0.60454 (17043) hydrogen bonds : bond 0.04454 ( 478) hydrogen bonds : angle 4.65607 ( 1362) metal coordination : bond 0.01253 ( 4) metal coordination : angle 2.78185 ( 3) *********************** 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 145 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8395 (tttt) cc_final: 0.8071 (mtpp) REVERT: G 198 ASN cc_start: 0.7681 (p0) cc_final: 0.7403 (p0) REVERT: X 35 GLU cc_start: 0.6567 (tp30) cc_final: 0.6341 (mm-30) REVERT: X 99 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7664 (mm-40) REVERT: F 385 MET cc_start: 0.7274 (mpp) cc_final: 0.4570 (tpt) REVERT: E 86 MET cc_start: 0.7428 (mtp) cc_final: 0.7000 (ttm) REVERT: E 276 GLU cc_start: 0.6354 (mp0) cc_final: 0.5437 (tp30) REVERT: E 300 GLN cc_start: 0.5306 (tp40) cc_final: 0.4951 (mm-40) outliers start: 13 outliers final: 7 residues processed: 138 average time/residue: 0.1180 time to fit residues: 23.0384 Evaluate side-chains 126 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 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 105 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 20 optimal weight: 0.0040 chunk 23 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 105 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.187797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141719 restraints weight = 16786.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141658 restraints weight = 15368.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142512 restraints weight = 16099.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144521 restraints weight = 9248.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145318 restraints weight = 7615.102| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 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 = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12583 Z= 0.114 Angle : 0.546 9.757 17046 Z= 0.268 Chirality : 0.039 0.135 1905 Planarity : 0.004 0.059 2190 Dihedral : 9.065 141.693 1788 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.61 % Allowed : 10.80 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1525 helix: 0.22 (0.20), residues: 749 sheet: -0.37 (0.61), residues: 77 loop : -1.21 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 64 TYR 0.014 0.001 TYR X 284 PHE 0.009 0.001 PHE X 161 TRP 0.010 0.001 TRP X 270 HIS 0.006 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00264 (12579) covalent geometry : angle 0.54499 (17043) hydrogen bonds : bond 0.03432 ( 478) hydrogen bonds : angle 4.35761 ( 1362) metal coordination : bond 0.01027 ( 4) metal coordination : angle 2.13416 ( 3) *********************** 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 138 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8378 (tttt) cc_final: 0.8065 (mtpp) REVERT: G 198 ASN cc_start: 0.7744 (p0) cc_final: 0.7434 (p0) REVERT: G 344 MET cc_start: 0.7423 (mmt) cc_final: 0.6879 (mmt) REVERT: X 35 GLU cc_start: 0.6375 (tp30) cc_final: 0.6151 (mm-30) REVERT: X 99 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7542 (mm-40) REVERT: F 385 MET cc_start: 0.7238 (mpp) cc_final: 0.4422 (tpt) REVERT: E 86 MET cc_start: 0.7381 (mtp) cc_final: 0.6994 (ttm) REVERT: E 276 GLU cc_start: 0.6221 (mp0) cc_final: 0.5352 (tp30) outliers start: 8 outliers final: 5 residues processed: 136 average time/residue: 0.1201 time to fit residues: 23.3756 Evaluate side-chains 118 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 139 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140570 restraints weight = 16721.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140391 restraints weight = 16525.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141381 restraints weight = 16827.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143064 restraints weight = 9591.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144110 restraints weight = 8095.543| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1554 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= 0.125 Angle : 0.548 12.223 17046 Z= 0.268 Chirality : 0.039 0.135 1905 Planarity : 0.004 0.061 2190 Dihedral : 8.815 136.328 1788 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.37 % Allowed : 12.17 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.22), residues: 1525 helix: 0.35 (0.21), residues: 741 sheet: -0.39 (0.61), residues: 77 loop : -1.23 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 276 TYR 0.015 0.001 TYR G 375 PHE 0.010 0.001 PHE X 161 TRP 0.011 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00297 (12579) covalent geometry : angle 0.54694 (17043) hydrogen bonds : bond 0.03295 ( 478) hydrogen bonds : angle 4.26572 ( 1362) metal coordination : bond 0.01099 ( 4) metal coordination : angle 2.57359 ( 3) *********************** 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 139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8413 (tttt) cc_final: 0.8099 (mtpp) REVERT: G 198 ASN cc_start: 0.7774 (p0) cc_final: 0.7438 (p0) REVERT: G 344 MET cc_start: 0.7498 (mmt) cc_final: 0.7007 (mmt) REVERT: X 99 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7525 (mm-40) REVERT: F 248 MET cc_start: 0.5576 (mpp) cc_final: 0.5338 (mpp) REVERT: E 86 MET cc_start: 0.7392 (mtp) cc_final: 0.7065 (ttm) REVERT: E 191 LEU cc_start: 0.8586 (pp) cc_final: 0.8369 (tp) REVERT: E 276 GLU cc_start: 0.6291 (mp0) cc_final: 0.5485 (tp30) outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 0.1066 time to fit residues: 20.9409 Evaluate side-chains 126 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 190 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.189182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142864 restraints weight = 16911.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138656 restraints weight = 17680.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140593 restraints weight = 18203.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142564 restraints weight = 11408.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142965 restraints weight = 10208.321| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- 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: 0.7380 moved from start: 0.1667 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= 0.111 Angle : 0.539 9.150 17046 Z= 0.263 Chirality : 0.039 0.132 1905 Planarity : 0.004 0.061 2190 Dihedral : 8.577 131.644 1788 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.60 % Allowed : 12.93 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1525 helix: 0.37 (0.21), residues: 744 sheet: -0.56 (0.61), residues: 79 loop : -1.21 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 276 TYR 0.014 0.001 TYR X 284 PHE 0.009 0.001 PHE X 161 TRP 0.012 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00261 (12579) covalent geometry : angle 0.53783 (17043) hydrogen bonds : bond 0.03070 ( 478) hydrogen bonds : angle 4.15655 ( 1362) metal coordination : bond 0.01123 ( 4) metal coordination : angle 2.29196 ( 3) *********************** 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 145 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8447 (tttt) cc_final: 0.8182 (mtpp) REVERT: G 198 ASN cc_start: 0.7736 (p0) cc_final: 0.7374 (p0) REVERT: G 207 ARG cc_start: 0.7128 (mpt180) cc_final: 0.6807 (mpt180) REVERT: G 344 MET cc_start: 0.7280 (mmt) cc_final: 0.6858 (mmt) REVERT: X 99 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7544 (mm-40) REVERT: F 385 MET cc_start: 0.7125 (mpp) cc_final: 0.4420 (tpt) REVERT: E 86 MET cc_start: 0.7360 (mtp) cc_final: 0.7035 (ttm) REVERT: E 229 LEU cc_start: 0.7776 (tp) cc_final: 0.6944 (mm) REVERT: E 276 GLU cc_start: 0.6265 (mp0) cc_final: 0.5475 (tp30) REVERT: E 308 TRP cc_start: 0.6893 (t60) cc_final: 0.6537 (t60) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.1014 time to fit residues: 20.3073 Evaluate side-chains 131 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 190 SER 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 249 LEU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 15 VAL 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 97 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 88 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 51 HIS ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS F 222 ASN E 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.187576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144709 restraints weight = 17137.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143728 restraints weight = 23951.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145261 restraints weight = 21186.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146367 restraints weight = 12513.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147632 restraints weight = 10657.364| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12583 Z= 0.153 Angle : 0.574 10.916 17046 Z= 0.282 Chirality : 0.040 0.151 1905 Planarity : 0.004 0.061 2190 Dihedral : 8.390 125.665 1788 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.60 % Allowed : 14.07 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1525 helix: 0.32 (0.20), residues: 744 sheet: -0.57 (0.63), residues: 79 loop : -1.28 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 276 TYR 0.016 0.001 TYR G 375 PHE 0.013 0.001 PHE X 161 TRP 0.011 0.001 TRP X 270 HIS 0.005 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00372 (12579) covalent geometry : angle 0.57275 (17043) hydrogen bonds : bond 0.03416 ( 478) hydrogen bonds : angle 4.19231 ( 1362) metal coordination : bond 0.01368 ( 4) metal coordination : angle 3.39897 ( 3) *********************** 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 143 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8479 (tttt) cc_final: 0.8254 (mtpp) REVERT: G 198 ASN cc_start: 0.7692 (p0) cc_final: 0.7321 (p0) REVERT: G 344 MET cc_start: 0.7446 (mmt) cc_final: 0.6962 (mmt) REVERT: X 99 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7364 (mm-40) REVERT: E 86 MET cc_start: 0.7391 (mtp) cc_final: 0.7078 (ttm) REVERT: E 385 MET cc_start: 0.4674 (mtm) cc_final: 0.4255 (mtm) outliers start: 21 outliers final: 17 residues processed: 137 average time/residue: 0.1017 time to fit residues: 20.2642 Evaluate side-chains 132 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 VAL 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 232 THR Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 24 ILE 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 E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 96 optimal weight: 0.0040 chunk 103 optimal weight: 9.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 222 ASN E 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.193603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.150712 restraints weight = 16551.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149570 restraints weight = 20311.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150726 restraints weight = 20847.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152122 restraints weight = 11805.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153128 restraints weight = 10116.103| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1967 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= 0.119 Angle : 0.544 9.634 17046 Z= 0.268 Chirality : 0.039 0.151 1905 Planarity : 0.004 0.061 2190 Dihedral : 8.140 120.874 1788 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.90 % Allowed : 14.22 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.22), residues: 1525 helix: 0.37 (0.20), residues: 745 sheet: -0.54 (0.63), residues: 79 loop : -1.25 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 241 TYR 0.021 0.001 TYR E 337 PHE 0.010 0.001 PHE X 161 TRP 0.013 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00283 (12579) covalent geometry : angle 0.54310 (17043) hydrogen bonds : bond 0.03055 ( 478) hydrogen bonds : angle 4.14075 ( 1362) metal coordination : bond 0.01251 ( 4) metal coordination : angle 2.70975 ( 3) *********************** 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 147 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7588 (p0) cc_final: 0.7248 (p0) REVERT: G 344 MET cc_start: 0.7314 (mmt) cc_final: 0.6913 (mmt) REVERT: X 99 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7331 (mm-40) REVERT: F 373 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 375 TYR cc_start: 0.6710 (t80) cc_final: 0.6380 (t80) REVERT: F 385 MET cc_start: 0.7272 (mpp) cc_final: 0.4552 (tpt) REVERT: E 86 MET cc_start: 0.7299 (mtp) cc_final: 0.7051 (ttm) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.1058 time to fit residues: 21.4652 Evaluate side-chains 133 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 106 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 258 LEU Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 191 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 73 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 23 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 F 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.193371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149181 restraints weight = 16561.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.144983 restraints weight = 19354.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147532 restraints weight = 19509.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147656 restraints weight = 12557.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148831 restraints weight = 11122.601| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12583 Z= 0.118 Angle : 0.541 9.251 17046 Z= 0.267 Chirality : 0.039 0.142 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.891 115.793 1788 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.52 % Allowed : 14.90 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.22), residues: 1525 helix: 0.39 (0.21), residues: 744 sheet: -0.56 (0.62), residues: 79 loop : -1.23 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 399 TYR 0.016 0.001 TYR G 375 PHE 0.010 0.001 PHE X 161 TRP 0.014 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00280 (12579) covalent geometry : angle 0.53961 (17043) hydrogen bonds : bond 0.03010 ( 478) hydrogen bonds : angle 4.12908 ( 1362) metal coordination : bond 0.01317 ( 4) metal coordination : angle 2.66456 ( 3) *********************** 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 139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7611 (p0) cc_final: 0.7292 (p0) REVERT: G 344 MET cc_start: 0.7318 (mmt) cc_final: 0.7015 (mmt) REVERT: X 99 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7368 (mm-40) REVERT: F 373 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7563 (tm-30) REVERT: F 385 MET cc_start: 0.7243 (mpp) cc_final: 0.4433 (tpt) REVERT: E 86 MET cc_start: 0.7298 (mtp) cc_final: 0.7017 (ttm) outliers start: 20 outliers final: 19 residues processed: 135 average time/residue: 0.1047 time to fit residues: 21.0497 Evaluate side-chains 131 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP 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 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 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 73 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 126 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.189491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145365 restraints weight = 16896.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142974 restraints weight = 19582.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144601 restraints weight = 20362.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145771 restraints weight = 11719.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147730 restraints weight = 10140.093| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12583 Z= 0.111 Angle : 0.549 13.659 17046 Z= 0.268 Chirality : 0.039 0.137 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.694 112.674 1788 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 15.44 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1525 helix: 0.46 (0.21), residues: 739 sheet: -0.51 (0.62), residues: 79 loop : -1.19 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 11 TYR 0.013 0.001 TYR G 375 PHE 0.009 0.001 PHE X 161 TRP 0.022 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00262 (12579) covalent geometry : angle 0.54751 (17043) hydrogen bonds : bond 0.02886 ( 478) hydrogen bonds : angle 4.06502 ( 1362) metal coordination : bond 0.01303 ( 4) metal coordination : angle 2.60271 ( 3) *********************** 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 137 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7615 (p0) cc_final: 0.7341 (p0) REVERT: G 344 MET cc_start: 0.7271 (mmt) cc_final: 0.6978 (mmt) REVERT: X 99 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7401 (mm-40) REVERT: F 373 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7569 (tm-30) REVERT: F 385 MET cc_start: 0.7220 (mpp) cc_final: 0.4453 (tpt) REVERT: E 86 MET cc_start: 0.7332 (mtp) cc_final: 0.7055 (ttm) REVERT: E 301 ARG cc_start: 0.5581 (mmt180) cc_final: 0.5313 (mpt90) REVERT: E 308 TRP cc_start: 0.5988 (t60) cc_final: 0.5759 (t60) outliers start: 19 outliers final: 18 residues processed: 133 average time/residue: 0.1091 time to fit residues: 21.3156 Evaluate side-chains 131 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP 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 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 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 73 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 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 76 optimal weight: 0.0040 chunk 146 optimal weight: 20.0000 chunk 6 optimal weight: 0.0570 chunk 98 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- 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** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.190027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145868 restraints weight = 17021.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144040 restraints weight = 21375.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.146010 restraints weight = 19905.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146750 restraints weight = 11683.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148569 restraints weight = 10263.691| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12583 Z= 0.105 Angle : 0.547 12.643 17046 Z= 0.267 Chirality : 0.039 0.139 1905 Planarity : 0.004 0.060 2190 Dihedral : 7.535 111.586 1788 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.52 % Allowed : 15.59 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.22), residues: 1525 helix: 0.50 (0.21), residues: 740 sheet: -0.46 (0.62), residues: 79 loop : -1.17 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 301 TYR 0.017 0.001 TYR E 337 PHE 0.009 0.001 PHE F 187 TRP 0.017 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00245 (12579) covalent geometry : angle 0.54662 (17043) hydrogen bonds : bond 0.02779 ( 478) hydrogen bonds : angle 4.00184 ( 1362) metal coordination : bond 0.01253 ( 4) metal coordination : angle 2.22941 ( 3) ********************** 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 141 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7557 (p0) cc_final: 0.7350 (p0) REVERT: G 344 MET cc_start: 0.7194 (mmt) cc_final: 0.6945 (mmt) REVERT: X 99 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7402 (mm-40) REVERT: F 373 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7212 (tm-30) REVERT: E 86 MET cc_start: 0.7336 (mtp) cc_final: 0.7076 (ttm) REVERT: E 301 ARG cc_start: 0.5527 (mmt180) cc_final: 0.5286 (mpt90) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.1094 time to fit residues: 21.7844 Evaluate side-chains 134 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain X residue 229 LEU Chi-restraints excluded: chain X residue 232 THR 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 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 73 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 131 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.187351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142582 restraints weight = 16853.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140088 restraints weight = 20300.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141898 restraints weight = 20601.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142686 restraints weight = 11846.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145121 restraints weight = 10302.384| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 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 = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12583 Z= 0.162 Angle : 0.598 12.507 17046 Z= 0.293 Chirality : 0.041 0.157 1905 Planarity : 0.004 0.062 2190 Dihedral : 7.567 110.873 1788 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 1.29 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.22), residues: 1525 helix: 0.39 (0.20), residues: 736 sheet: -0.36 (0.64), residues: 79 loop : -1.26 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 189 TYR 0.020 0.002 TYR F 375 PHE 0.012 0.001 PHE X 161 TRP 0.014 0.001 TRP E 308 HIS 0.004 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00395 (12579) covalent geometry : angle 0.59545 (17043) hydrogen bonds : bond 0.03499 ( 478) hydrogen bonds : angle 4.14460 ( 1362) metal coordination : bond 0.01490 ( 4) metal coordination : angle 3.79407 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.33 seconds wall clock time: 35 minutes 24.10 seconds (2124.10 seconds total)