Starting phenix.real_space_refine on Sat Nov 16 23:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_40218.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_40218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_40218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_40218.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glu_40218/11_2024/8glu_40218.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 8 5.49 5 Mg 3 5.21 5 S 43 5.16 5 C 7795 2.51 5 N 2227 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3193 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "E" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3326 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 15, 'TRANS': 402} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4188 SG CYS X 124 53.942 61.985 38.668 1.00 45.24 S ATOM 4209 SG CYS X 127 50.862 64.091 39.821 1.00 45.34 S ATOM 4427 SG CYS X 152 50.421 61.433 37.072 1.00 60.05 S Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ASP G 278 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP G 278 " occ=0.00 residue: pdb=" N LEU G 279 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 279 " occ=0.00 residue: pdb=" N ARG G 280 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 280 " occ=0.00 residue: pdb=" N SER G 281 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 281 " occ=0.00 residue: pdb=" N ALA G 282 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 282 " occ=0.00 residue: pdb=" N ARG G 283 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 283 " occ=0.00 residue: pdb=" N ARG G 284 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG G 284 " occ=0.00 residue: pdb=" N GLY G 285 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 285 " occ=0.00 residue: pdb=" N ALA G 286 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 286 " occ=0.00 residue: pdb=" N GLY G 287 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 287 " occ=0.00 residue: pdb=" N PHE G 288 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE G 288 " occ=0.00 Time building chain proxies: 7.87, per 1000 atoms: 0.64 Number of scatterers: 12338 At special positions: 0 Unit cell: (88.065, 120.555, 172.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 43 16.00 P 8 15.00 Mg 3 11.99 O 2261 8.00 N 2227 7.00 C 7795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " Number of angles added : 3 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 8 sheets defined 54.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 34 through 38 removed outlier: 3.850A pdb=" N ALA G 37 " --> pdb=" O VAL G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.149A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS G 53 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.506A pdb=" N HIS G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N CYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.541A pdb=" N HIS G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 150 removed outlier: 3.609A pdb=" N LEU G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.575A pdb=" N PHE G 188 " --> pdb=" O CYS G 184 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.550A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 Processing helix chain 'G' and resid 243 through 256 removed outlier: 4.303A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 305 through 316 removed outlier: 3.695A pdb=" N ASN G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 339 Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.565A pdb=" N VAL G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 Processing helix chain 'G' and resid 382 through 392 removed outlier: 3.586A pdb=" N LEU G 386 " --> pdb=" O VAL G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 399 removed outlier: 4.101A pdb=" N ARG G 399 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 24 removed outlier: 3.662A pdb=" N GLN X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 85 removed outlier: 3.826A pdb=" N TYR X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Proline residue: X 82 - end of helix removed outlier: 4.250A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 97 removed outlier: 4.231A pdb=" N GLU X 97 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 3.781A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU X 108 " --> pdb=" O VAL X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.704A pdb=" N VAL X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 168 Processing helix chain 'X' and resid 189 through 200 removed outlier: 4.124A pdb=" N THR X 193 " --> pdb=" O LEU X 189 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA X 194 " --> pdb=" O SER X 190 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU X 195 " --> pdb=" O GLN X 191 " (cutoff:3.500A) Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 205 through 211 removed outlier: 3.557A pdb=" N GLU X 210 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU X 211 " --> pdb=" O ALA X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 removed outlier: 3.517A pdb=" N VAL X 246 " --> pdb=" O VAL X 242 " (cutoff:3.500A) Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.687A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL X 290 " --> pdb=" O GLN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.944A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.715A pdb=" N ALA F 37 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 63 removed outlier: 3.834A pdb=" N ILE F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 removed outlier: 4.018A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 3.604A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 Processing helix chain 'F' and resid 179 through 195 removed outlier: 3.556A pdb=" N ILE F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 187 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 removed outlier: 3.544A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 246 through 259 removed outlier: 3.526A pdb=" N PHE F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 254 " --> pdb=" O ASN F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.925A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 3.928A pdb=" N ARG F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.536A pdb=" N ILE F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 344 through 362 removed outlier: 3.944A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 399 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 21 through 27 removed outlier: 3.633A pdb=" N LEU E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.587A pdb=" N LEU E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 75 through 90 Processing helix chain 'E' and resid 100 through 113 removed outlier: 3.920A pdb=" N HIS E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'E' and resid 181 through 195 removed outlier: 4.001A pdb=" N LEU E 185 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 224 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 271 through 276 removed outlier: 3.811A pdb=" N PHE E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 285 Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 361 removed outlier: 4.289A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 removed outlier: 3.945A pdb=" N LEU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 393 through 400 removed outlier: 3.506A pdb=" N ILE E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 421 removed outlier: 3.596A pdb=" N ARG E 411 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.375A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.222A pdb=" N LEU G 170 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP G 232 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE G 172 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'F' and resid 171 through 173 removed outlier: 6.976A pdb=" N ILE F 172 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.679A pdb=" N TYR E 158 " --> pdb=" O ILE E 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.239A pdb=" N LEU E 229 " --> pdb=" O MET E 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 135 through 136 removed outlier: 7.094A pdb=" N ILE E 135 " --> pdb=" O TRP E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 478 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.69 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: 2.870 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.620 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- 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 12579 Z= 0.169 Angle : 0.556 9.065 17043 Z= 0.278 Chirality : 0.040 0.164 1905 Planarity : 0.004 0.051 2190 Dihedral : 15.701 140.366 4774 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1525 helix: 0.02 (0.20), residues: 726 sheet: -0.00 (0.68), residues: 69 loop : -1.24 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 270 HIS 0.006 0.001 HIS X 177 PHE 0.013 0.001 PHE F 187 TYR 0.013 0.001 TYR X 14 ARG 0.006 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.175 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: 0.2738 time to fit residues: 62.2828 Evaluate side-chains 119 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.0270 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12579 Z= 0.342 Angle : 0.655 8.436 17043 Z= 0.326 Chirality : 0.043 0.146 1905 Planarity : 0.005 0.058 2190 Dihedral : 9.473 143.944 1788 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.99 % Allowed : 8.59 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1525 helix: -0.05 (0.20), residues: 742 sheet: -0.52 (0.61), residues: 77 loop : -1.42 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 316 HIS 0.006 0.001 HIS X 287 PHE 0.015 0.002 PHE X 161 TYR 0.022 0.002 TYR G 375 ARG 0.006 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7659 (p0) cc_final: 0.7374 (p0) REVERT: X 35 GLU cc_start: 0.6698 (tp30) cc_final: 0.6483 (mm-30) REVERT: X 99 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7673 (mm-40) REVERT: F 385 MET cc_start: 0.7287 (mpp) cc_final: 0.4609 (tpt) REVERT: E 86 MET cc_start: 0.7468 (mtp) cc_final: 0.7014 (ttm) REVERT: E 276 GLU cc_start: 0.6201 (mp0) cc_final: 0.5361 (tp30) REVERT: E 300 GLN cc_start: 0.5242 (tp40) cc_final: 0.4882 (mm-40) outliers start: 13 outliers final: 8 residues processed: 133 average time/residue: 0.2684 time to fit residues: 51.2269 Evaluate side-chains 121 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 219 THR Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12579 Z= 0.335 Angle : 0.633 9.501 17043 Z= 0.314 Chirality : 0.042 0.149 1905 Planarity : 0.005 0.060 2190 Dihedral : 9.177 139.113 1788 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.67 % Allowed : 12.62 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1525 helix: -0.05 (0.20), residues: 747 sheet: -0.78 (0.60), residues: 79 loop : -1.49 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 316 HIS 0.007 0.001 HIS X 287 PHE 0.017 0.002 PHE X 161 TYR 0.021 0.002 TYR G 375 ARG 0.003 0.000 ARG F 148 *********************** 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 144 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7677 (p0) cc_final: 0.7325 (p0) REVERT: X 35 GLU cc_start: 0.6649 (tp30) cc_final: 0.6445 (mm-30) REVERT: X 99 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7687 (mm-40) REVERT: F 385 MET cc_start: 0.7452 (mpp) cc_final: 0.4582 (tpt) REVERT: E 86 MET cc_start: 0.7453 (mtp) cc_final: 0.7073 (ttm) outliers start: 22 outliers final: 16 residues processed: 134 average time/residue: 0.2563 time to fit residues: 50.0989 Evaluate side-chains 132 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 219 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 259 ASP Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12579 Z= 0.333 Angle : 0.636 13.247 17043 Z= 0.314 Chirality : 0.042 0.148 1905 Planarity : 0.005 0.064 2190 Dihedral : 8.943 132.447 1788 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.59 % Allowed : 13.61 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1525 helix: -0.10 (0.20), residues: 749 sheet: -0.66 (0.63), residues: 73 loop : -1.62 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 316 HIS 0.006 0.001 HIS X 287 PHE 0.018 0.002 PHE X 161 TYR 0.021 0.002 TYR G 375 ARG 0.003 0.000 ARG F 148 *********************** 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 160 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 198 ASN cc_start: 0.7761 (p0) cc_final: 0.7369 (p0) REVERT: G 344 MET cc_start: 0.7576 (mmt) cc_final: 0.7182 (mmt) REVERT: X 99 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7690 (mm-40) REVERT: E 86 MET cc_start: 0.7421 (mtp) cc_final: 0.6944 (ttm) REVERT: E 191 LEU cc_start: 0.8602 (pp) cc_final: 0.8174 (tp) outliers start: 34 outliers final: 23 residues processed: 149 average time/residue: 0.2708 time to fit residues: 58.6484 Evaluate side-chains 139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 363 ASN Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 219 THR Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 259 ASP Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 383 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN E 102 GLN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12579 Z= 0.158 Angle : 0.557 9.830 17043 Z= 0.274 Chirality : 0.039 0.178 1905 Planarity : 0.004 0.063 2190 Dihedral : 8.512 128.136 1788 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.60 % Allowed : 15.89 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1525 helix: 0.22 (0.20), residues: 744 sheet: -0.61 (0.62), residues: 79 loop : -1.44 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 270 HIS 0.006 0.001 HIS G 383 PHE 0.037 0.001 PHE E 187 TYR 0.027 0.001 TYR E 109 ARG 0.002 0.000 ARG G 189 *********************** 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 151 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8437 (tttt) cc_final: 0.8174 (mtpp) REVERT: G 198 ASN cc_start: 0.7643 (p0) cc_final: 0.7320 (p0) REVERT: G 344 MET cc_start: 0.7251 (mmt) cc_final: 0.6999 (mmt) REVERT: X 99 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7625 (mm-40) REVERT: E 86 MET cc_start: 0.7186 (mtp) cc_final: 0.6936 (ttm) REVERT: E 191 LEU cc_start: 0.8578 (pp) cc_final: 0.8364 (tp) REVERT: E 308 TRP cc_start: 0.6398 (t60) cc_final: 0.6140 (t60) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.2547 time to fit residues: 54.3930 Evaluate side-chains 132 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.1980 chunk 68 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12579 Z= 0.166 Angle : 0.553 10.084 17043 Z= 0.271 Chirality : 0.039 0.156 1905 Planarity : 0.004 0.060 2190 Dihedral : 8.222 123.512 1788 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.83 % Allowed : 16.43 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1525 helix: 0.30 (0.21), residues: 744 sheet: -0.54 (0.62), residues: 79 loop : -1.35 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 270 HIS 0.005 0.001 HIS G 383 PHE 0.030 0.001 PHE E 187 TYR 0.020 0.001 TYR E 109 ARG 0.003 0.000 ARG X 276 *********************** 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 150 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8421 (tttt) cc_final: 0.8195 (mtpp) REVERT: G 198 ASN cc_start: 0.7651 (p0) cc_final: 0.7345 (p0) REVERT: G 344 MET cc_start: 0.7258 (mmt) cc_final: 0.7048 (mmt) REVERT: X 99 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7652 (mm-40) REVERT: X 276 ARG cc_start: 0.6041 (ptp-110) cc_final: 0.5832 (ttm110) REVERT: F 248 MET cc_start: 0.5620 (mpp) cc_final: 0.5289 (mpp) REVERT: F 373 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7453 (tm-30) REVERT: E 86 MET cc_start: 0.7305 (mtp) cc_final: 0.7060 (ttm) REVERT: E 191 LEU cc_start: 0.8566 (pp) cc_final: 0.8348 (tp) REVERT: E 385 MET cc_start: 0.4684 (mtm) cc_final: 0.4293 (mtm) outliers start: 24 outliers final: 20 residues processed: 144 average time/residue: 0.2530 time to fit residues: 53.1783 Evaluate side-chains 135 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 170 HIS Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 91 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12579 Z= 0.149 Angle : 0.539 10.822 17043 Z= 0.264 Chirality : 0.039 0.151 1905 Planarity : 0.004 0.060 2190 Dihedral : 7.936 118.825 1788 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.75 % Allowed : 16.81 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1525 helix: 0.38 (0.21), residues: 744 sheet: -0.62 (0.62), residues: 79 loop : -1.25 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 308 HIS 0.005 0.001 HIS G 383 PHE 0.030 0.001 PHE E 187 TYR 0.019 0.001 TYR E 109 ARG 0.003 0.000 ARG G 189 *********************** 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 151 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8450 (tttt) cc_final: 0.8235 (mtpp) REVERT: G 198 ASN cc_start: 0.7591 (p0) cc_final: 0.7338 (p0) REVERT: G 357 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7474 (ttt90) REVERT: X 99 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7557 (mm-40) REVERT: X 276 ARG cc_start: 0.5970 (ptp-110) cc_final: 0.5715 (ttm110) REVERT: F 248 MET cc_start: 0.5626 (mpp) cc_final: 0.5359 (mpp) REVERT: F 373 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7483 (tm-30) REVERT: E 86 MET cc_start: 0.7289 (mtp) cc_final: 0.7061 (ttm) REVERT: E 191 LEU cc_start: 0.8554 (pp) cc_final: 0.8331 (tp) REVERT: E 308 TRP cc_start: 0.6236 (t60) cc_final: 0.5972 (t60) outliers start: 23 outliers final: 20 residues processed: 145 average time/residue: 0.2581 time to fit residues: 54.2567 Evaluate side-chains 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 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 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12579 Z= 0.194 Angle : 0.560 11.042 17043 Z= 0.275 Chirality : 0.039 0.155 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.782 114.680 1788 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.13 % Allowed : 17.03 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1525 helix: 0.37 (0.21), residues: 737 sheet: -0.56 (0.63), residues: 79 loop : -1.25 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 308 HIS 0.004 0.001 HIS G 383 PHE 0.029 0.001 PHE E 187 TYR 0.020 0.001 TYR E 109 ARG 0.003 0.000 ARG G 323 *********************** 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 148 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8480 (tttt) cc_final: 0.8254 (mtpp) REVERT: G 198 ASN cc_start: 0.7666 (p0) cc_final: 0.7406 (p0) REVERT: X 99 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7532 (mm-40) REVERT: X 276 ARG cc_start: 0.6009 (ptp-110) cc_final: 0.5735 (ttm110) REVERT: F 248 MET cc_start: 0.5709 (mpp) cc_final: 0.5445 (mpp) REVERT: F 373 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 86 MET cc_start: 0.7301 (mtp) cc_final: 0.7052 (ttm) REVERT: E 191 LEU cc_start: 0.8609 (pp) cc_final: 0.8384 (tp) REVERT: E 308 TRP cc_start: 0.6181 (t60) cc_final: 0.5911 (t60) REVERT: E 337 TYR cc_start: 0.5808 (t80) cc_final: 0.5522 (t80) REVERT: E 385 MET cc_start: 0.4954 (mtm) cc_final: 0.4494 (mtm) outliers start: 28 outliers final: 25 residues processed: 143 average time/residue: 0.2542 time to fit residues: 52.8741 Evaluate side-chains 139 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 229 LEU Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 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 128 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12579 Z= 0.185 Angle : 0.554 10.028 17043 Z= 0.271 Chirality : 0.039 0.154 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.613 111.996 1788 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.05 % Allowed : 17.11 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1525 helix: 0.39 (0.20), residues: 737 sheet: -0.56 (0.63), residues: 79 loop : -1.23 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 270 HIS 0.004 0.001 HIS G 383 PHE 0.028 0.001 PHE E 187 TYR 0.019 0.001 TYR E 109 ARG 0.002 0.000 ARG E 58 *********************** 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 147 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8484 (tttt) cc_final: 0.8258 (mtpp) REVERT: G 207 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6900 (mpt180) REVERT: X 99 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7569 (mm-40) REVERT: F 373 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 86 MET cc_start: 0.7306 (mtp) cc_final: 0.7056 (ttm) REVERT: E 191 LEU cc_start: 0.8607 (pp) cc_final: 0.8390 (tp) REVERT: E 301 ARG cc_start: 0.5607 (mmt180) cc_final: 0.5363 (mpt90) REVERT: E 385 MET cc_start: 0.5037 (mtm) cc_final: 0.4743 (mtm) outliers start: 27 outliers final: 21 residues processed: 143 average time/residue: 0.2674 time to fit residues: 55.0336 Evaluate side-chains 135 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 106 LEU Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain X residue 229 LEU Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 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 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.0470 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 198 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12579 Z= 0.185 Angle : 0.571 14.209 17043 Z= 0.279 Chirality : 0.039 0.162 1905 Planarity : 0.004 0.061 2190 Dihedral : 7.547 111.580 1788 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.75 % Allowed : 17.87 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1525 helix: 0.41 (0.21), residues: 737 sheet: -0.55 (0.63), residues: 79 loop : -1.22 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 308 HIS 0.004 0.001 HIS G 383 PHE 0.027 0.001 PHE E 187 TYR 0.020 0.001 TYR E 337 ARG 0.010 0.000 ARG F 189 ********************** 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 140 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 181 LYS cc_start: 0.8461 (tttt) cc_final: 0.8252 (mtpp) REVERT: G 344 MET cc_start: 0.7274 (mmt) cc_final: 0.6532 (mmp) REVERT: X 99 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7573 (mm-40) REVERT: F 373 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 86 MET cc_start: 0.7323 (mtp) cc_final: 0.7069 (ttm) REVERT: E 191 LEU cc_start: 0.8609 (pp) cc_final: 0.8393 (tp) REVERT: E 301 ARG cc_start: 0.5722 (mmt180) cc_final: 0.5437 (mpt90) REVERT: E 385 MET cc_start: 0.5026 (mtm) cc_final: 0.4720 (mtm) outliers start: 23 outliers final: 22 residues processed: 134 average time/residue: 0.2491 time to fit residues: 49.5613 Evaluate side-chains 136 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 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 229 LEU Chi-restraints excluded: chain X residue 255 LEU Chi-restraints excluded: chain X residue 258 LEU Chi-restraints excluded: chain X residue 274 ILE Chi-restraints excluded: chain X residue 275 PHE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.185360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140869 restraints weight = 16964.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138345 restraints weight = 20790.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139774 restraints weight = 22233.948| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12579 Z= 0.310 Angle : 0.636 13.789 17043 Z= 0.313 Chirality : 0.042 0.214 1905 Planarity : 0.005 0.064 2190 Dihedral : 7.645 111.262 1788 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.90 % Allowed : 17.95 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1525 helix: 0.26 (0.20), residues: 735 sheet: -0.43 (0.64), residues: 77 loop : -1.37 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 308 HIS 0.006 0.001 HIS G 76 PHE 0.027 0.002 PHE E 187 TYR 0.025 0.002 TYR G 199 ARG 0.007 0.000 ARG F 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.41 seconds wall clock time: 46 minutes 18.45 seconds (2778.45 seconds total)