Starting phenix.real_space_refine on Sun Jan 19 10:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.map" model { file = "/net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utu_42550/01_2025/8utu_42550.cif" } resolution = 3.0 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= 0.001 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 87 5.16 5 C 8515 2.51 5 N 2326 2.21 5 O 2673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13615 Number of models: 1 Model: "" Number of chains: 9 Chain: "K" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3039 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATHR B 429 " occ=0.52 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.48 residue: pdb=" N AALA B 430 " occ=0.52 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.48 residue: pdb=" N AASP B 431 " occ=0.52 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.48 residue: pdb=" N AGLU B 432 " occ=0.52 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.48 Time building chain proxies: 10.73, per 1000 atoms: 0.79 Number of scatterers: 13615 At special positions: 0 Unit cell: (103.812, 113.096, 154.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 11 15.00 Mg 3 11.99 O 2673 8.00 N 2326 7.00 C 8515 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 49.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 removed outlier: 3.587A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 88 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 119 through 134 Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 262 through 295 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 353 removed outlier: 3.744A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.178A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.858A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.537A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.204A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.614A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.797A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.209A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.067A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.232A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.599A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.630A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.201A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.031A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.796A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.287A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.894A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.757A pdb=" N SER B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.630A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.770A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.632A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.618A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.652A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.281A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.874A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.764A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.323A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.251A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.715A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.852A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.650A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.268A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.804A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.613A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.672A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 338 " --> pdb=" O THR E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.185A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 417 Processing helix chain 'E' and resid 418 through 437 removed outlier: 3.638A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.601A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.601A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.680A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.936A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 12.247A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.000A pdb=" N GLU E 3 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU E 136 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N SER E 140 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N VAL E 9 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 139 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 272 684 hydrogen bonds defined for protein. 1947 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: 4.86 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2332 1.32 - 1.44: 3680 1.44 - 1.57: 7731 1.57 - 1.69: 21 1.69 - 1.82: 139 Bond restraints: 13903 Sorted by residual: bond pdb=" N TYR A 262 " pdb=" CA TYR A 262 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.14e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.608 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C4 ANP K 502 " pdb=" C5 ANP K 502 " ideal model delta sigma weight residual 1.387 1.468 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CA SER B 25 " pdb=" CB SER B 25 " ideal model delta sigma weight residual 1.530 1.464 0.065 1.63e-02 3.76e+03 1.61e+01 bond pdb=" C PRO B 61 " pdb=" O PRO B 61 " ideal model delta sigma weight residual 1.233 1.190 0.043 1.10e-02 8.26e+03 1.53e+01 ... (remaining 13898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18304 2.58 - 5.17: 501 5.17 - 7.75: 58 7.75 - 10.33: 9 10.33 - 12.92: 4 Bond angle restraints: 18876 Sorted by residual: angle pdb=" N VAL A 435 " pdb=" CA VAL A 435 " pdb=" C VAL A 435 " ideal model delta sigma weight residual 113.43 103.38 10.05 1.09e+00 8.42e-01 8.50e+01 angle pdb=" N GLU E 417 " pdb=" CA GLU E 417 " pdb=" C GLU E 417 " ideal model delta sigma weight residual 112.88 102.69 10.19 1.29e+00 6.01e-01 6.24e+01 angle pdb=" C ARG B 62 " pdb=" CA ARG B 62 " pdb=" CB ARG B 62 " ideal model delta sigma weight residual 112.12 101.75 10.37 1.50e+00 4.44e-01 4.78e+01 angle pdb=" N LEU K 122 " pdb=" CA LEU K 122 " pdb=" C LEU K 122 " ideal model delta sigma weight residual 111.07 105.33 5.74 1.07e+00 8.73e-01 2.88e+01 angle pdb=" N LYS A 336 " pdb=" CA LYS A 336 " pdb=" C LYS A 336 " ideal model delta sigma weight residual 112.89 106.44 6.45 1.24e+00 6.50e-01 2.71e+01 ... (remaining 18871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 7997 31.42 - 62.84: 366 62.84 - 94.27: 38 94.27 - 125.69: 11 125.69 - 157.11: 11 Dihedral angle restraints: 8423 sinusoidal: 3465 harmonic: 4958 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.62 -157.11 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -85.06 154.33 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -36.98 141.57 1 2.00e+01 2.50e-03 4.28e+01 ... (remaining 8420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1948 0.109 - 0.217: 121 0.217 - 0.326: 4 0.326 - 0.435: 0 0.435 - 0.543: 1 Chirality restraints: 2074 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.62 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" C02 TA1 B 502 " pdb=" C01 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" O02 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.56 2.82 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ARG B 62 " pdb=" N ARG B 62 " pdb=" C ARG B 62 " pdb=" CB ARG B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2071 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 416 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLY E 416 " -0.086 2.00e-02 2.50e+03 pdb=" O GLY E 416 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU E 417 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN K 39 " -0.078 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO K 40 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO K 40 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO K 40 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 57 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASN B 57 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN B 57 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS B 58 " -0.021 2.00e-02 2.50e+03 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 87 2.55 - 3.14: 10456 3.14 - 3.73: 19816 3.73 - 4.31: 27673 4.31 - 4.90: 47970 Nonbonded interactions: 106002 Sorted by model distance: nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.969 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.989 2.170 nonbonded pdb=" O3B GTP E 501 " pdb="MG MG E 502 " model vdw 2.013 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 2.071 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.085 2.170 ... (remaining 105997 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 'A' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.006 0.092 13903 Z= 0.380 Angle : 0.966 12.919 18876 Z= 0.554 Chirality : 0.055 0.543 2074 Planarity : 0.008 0.116 2452 Dihedral : 18.777 157.110 5243 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.70 % Favored : 96.06 % Rotamer: Outliers : 1.50 % Allowed : 19.11 % Favored : 79.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.39 % 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: -0.42 (0.20), residues: 1705 helix: 0.74 (0.20), residues: 704 sheet: -0.46 (0.29), residues: 310 loop : -1.18 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 346 HIS 0.013 0.001 HIS B 6 PHE 0.040 0.002 PHE K 52 TYR 0.035 0.002 TYR B 50 ARG 0.014 0.001 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: K 107 MET cc_start: 0.8167 (mmt) cc_final: 0.7887 (mmm) REVERT: K 179 GLU cc_start: 0.8132 (tt0) cc_final: 0.7870 (tt0) REVERT: K 192 ILE cc_start: 0.7898 (tt) cc_final: 0.7603 (pp) REVERT: K 248 ASP cc_start: 0.7111 (t0) cc_final: 0.6803 (t0) REVERT: A 24 TYR cc_start: 0.8233 (m-80) cc_final: 0.7969 (m-80) REVERT: A 302 MET cc_start: 0.7880 (mmm) cc_final: 0.6475 (mtm) REVERT: B 1 MET cc_start: 0.5365 (tpt) cc_final: 0.5128 (tpt) REVERT: B 415 MET cc_start: 0.8478 (ttm) cc_final: 0.8276 (ttp) REVERT: E 26 LEU cc_start: 0.8463 (mm) cc_final: 0.8191 (tp) REVERT: E 203 MET cc_start: 0.8550 (mtp) cc_final: 0.8277 (mtm) REVERT: E 297 GLU cc_start: 0.7814 (tp30) cc_final: 0.7438 (tp30) REVERT: E 302 MET cc_start: 0.8423 (mmm) cc_final: 0.7912 (mtm) REVERT: E 322 ASP cc_start: 0.8460 (t0) cc_final: 0.8044 (t0) outliers start: 21 outliers final: 11 residues processed: 294 average time/residue: 1.2200 time to fit residues: 393.4549 Evaluate side-chains 263 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 252 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 215 SER Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 309 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 1.9990 chunk 128 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 0.0010 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106790 restraints weight = 21533.381| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.17 r_work: 0.3359 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13903 Z= 0.159 Angle : 0.589 11.152 18876 Z= 0.298 Chirality : 0.043 0.231 2074 Planarity : 0.005 0.072 2452 Dihedral : 12.110 151.173 2063 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 3.07 % Allowed : 16.86 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.40 (0.20), residues: 1705 helix: 1.51 (0.20), residues: 718 sheet: 0.10 (0.30), residues: 296 loop : -0.97 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 388 HIS 0.004 0.001 HIS B 28 PHE 0.011 0.001 PHE A 255 TYR 0.017 0.001 TYR A 24 ARG 0.006 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.531 Fit side-chains REVERT: K 11 ARG cc_start: 0.7534 (ttt180) cc_final: 0.7269 (ttt180) REVERT: K 179 GLU cc_start: 0.8248 (tt0) cc_final: 0.8032 (tt0) REVERT: K 192 ILE cc_start: 0.7720 (tt) cc_final: 0.7339 (pp) REVERT: K 248 ASP cc_start: 0.7321 (t0) cc_final: 0.7040 (t0) REVERT: K 353 GLN cc_start: 0.7681 (mp10) cc_final: 0.7441 (mp10) REVERT: A 49 PHE cc_start: 0.7250 (m-10) cc_final: 0.6982 (m-10) REVERT: B 57 ASN cc_start: 0.7507 (t0) cc_final: 0.7022 (t0) REVERT: B 164 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7775 (ttp) REVERT: B 188 SER cc_start: 0.8536 (p) cc_final: 0.8302 (p) REVERT: B 291 GLN cc_start: 0.8236 (tt0) cc_final: 0.7983 (mt0) REVERT: B 316 ILE cc_start: 0.8604 (mm) cc_final: 0.8323 (mt) REVERT: B 415 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: E 398 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7248 (ttm) outliers start: 44 outliers final: 19 residues processed: 288 average time/residue: 1.1761 time to fit residues: 373.7610 Evaluate side-chains 273 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 398 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 298 ASN E 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099322 restraints weight = 18929.224| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.98 r_work: 0.3246 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13903 Z= 0.453 Angle : 0.675 8.106 18876 Z= 0.347 Chirality : 0.048 0.383 2074 Planarity : 0.005 0.067 2452 Dihedral : 10.393 158.534 2046 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 4.03 % Allowed : 17.47 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.22 (0.20), residues: 1705 helix: 1.40 (0.20), residues: 721 sheet: 0.10 (0.29), residues: 305 loop : -1.20 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 344 HIS 0.013 0.002 HIS E 88 PHE 0.022 0.002 PHE A 141 TYR 0.021 0.002 TYR B 222 ARG 0.011 0.001 ARG E 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 1.533 Fit side-chains REVERT: K 105 TYR cc_start: 0.7647 (t80) cc_final: 0.7212 (t80) REVERT: K 107 MET cc_start: 0.8200 (mmt) cc_final: 0.7964 (mmm) REVERT: K 192 ILE cc_start: 0.7799 (tt) cc_final: 0.7415 (pp) REVERT: K 248 ASP cc_start: 0.7330 (t0) cc_final: 0.7048 (t0) REVERT: K 276 THR cc_start: 0.8142 (m) cc_final: 0.7690 (m) REVERT: K 341 THR cc_start: 0.8799 (m) cc_final: 0.8534 (p) REVERT: K 353 GLN cc_start: 0.7769 (mp10) cc_final: 0.7530 (mp10) REVERT: B 57 ASN cc_start: 0.7932 (t0) cc_final: 0.7400 (t0) REVERT: B 164 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7766 (ttt) REVERT: B 282 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8072 (mtm180) REVERT: E 26 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8428 (tp) REVERT: E 322 ASP cc_start: 0.8663 (t0) cc_final: 0.8379 (t0) REVERT: E 392 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7992 (t0) outliers start: 58 outliers final: 25 residues processed: 312 average time/residue: 1.1705 time to fit residues: 402.4923 Evaluate side-chains 299 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 GLN A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.133840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103224 restraints weight = 18648.253| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.97 r_work: 0.3297 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13903 Z= 0.192 Angle : 0.555 7.993 18876 Z= 0.284 Chirality : 0.043 0.293 2074 Planarity : 0.004 0.063 2452 Dihedral : 9.939 158.606 2046 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 2.94 % Allowed : 20.14 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.48 (0.20), residues: 1705 helix: 1.70 (0.20), residues: 719 sheet: 0.29 (0.29), residues: 301 loop : -1.18 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS B 6 PHE 0.014 0.001 PHE B 367 TYR 0.012 0.001 TYR E 108 ARG 0.008 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 1.512 Fit side-chains REVERT: K 7 LYS cc_start: 0.8140 (mptt) cc_final: 0.7736 (tmtp) REVERT: K 19 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7814 (tt0) REVERT: K 105 TYR cc_start: 0.7524 (t80) cc_final: 0.7027 (t80) REVERT: K 116 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.6054 (mm-40) REVERT: K 192 ILE cc_start: 0.7817 (tt) cc_final: 0.7407 (pp) REVERT: K 248 ASP cc_start: 0.7366 (t0) cc_final: 0.7100 (t0) REVERT: K 276 THR cc_start: 0.8061 (m) cc_final: 0.7639 (m) REVERT: K 341 THR cc_start: 0.8837 (m) cc_final: 0.8617 (p) REVERT: K 345 LEU cc_start: 0.8940 (mp) cc_final: 0.8707 (mm) REVERT: K 353 GLN cc_start: 0.7759 (mp10) cc_final: 0.7475 (mp10) REVERT: A 332 ILE cc_start: 0.8426 (mm) cc_final: 0.8219 (mt) REVERT: B 57 ASN cc_start: 0.7809 (t0) cc_final: 0.7300 (t0) REVERT: B 164 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (ttt) REVERT: B 316 ILE cc_start: 0.8551 (mm) cc_final: 0.8283 (mt) REVERT: E 26 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8406 (tp) outliers start: 42 outliers final: 24 residues processed: 306 average time/residue: 1.1940 time to fit residues: 401.7680 Evaluate side-chains 299 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 116 GLN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 121 optimal weight: 0.0470 chunk 157 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 GLN A 11 GLN B 8 GLN B 165 ASN B 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100531 restraints weight = 18931.552| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.01 r_work: 0.3269 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13903 Z= 0.289 Angle : 0.584 8.240 18876 Z= 0.298 Chirality : 0.045 0.254 2074 Planarity : 0.005 0.061 2452 Dihedral : 9.847 160.443 2046 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 3.82 % Allowed : 19.73 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.53 (0.20), residues: 1705 helix: 1.80 (0.20), residues: 713 sheet: 0.40 (0.29), residues: 300 loop : -1.25 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.007 0.001 HIS E 88 PHE 0.017 0.002 PHE B 367 TYR 0.014 0.001 TYR E 108 ARG 0.006 0.001 ARG E 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.505 Fit side-chains REVERT: K 7 LYS cc_start: 0.8121 (mptt) cc_final: 0.7669 (tmmt) REVERT: K 19 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7741 (tt0) REVERT: K 105 TYR cc_start: 0.7475 (t80) cc_final: 0.7039 (t80) REVERT: K 136 ASP cc_start: 0.5787 (m-30) cc_final: 0.5465 (t0) REVERT: K 192 ILE cc_start: 0.7848 (tt) cc_final: 0.7419 (pp) REVERT: K 248 ASP cc_start: 0.7420 (t0) cc_final: 0.7146 (t0) REVERT: K 276 THR cc_start: 0.8081 (m) cc_final: 0.7672 (m) REVERT: K 327 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6622 (tpp) REVERT: K 341 THR cc_start: 0.8806 (m) cc_final: 0.8589 (p) REVERT: K 342 LEU cc_start: 0.8877 (tt) cc_final: 0.8584 (tm) REVERT: K 353 GLN cc_start: 0.7820 (mp10) cc_final: 0.7437 (mp10) REVERT: A 3 GLU cc_start: 0.8058 (mp0) cc_final: 0.7850 (mp0) REVERT: A 254 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 320 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8309 (mtp180) REVERT: B 57 ASN cc_start: 0.7889 (t0) cc_final: 0.7381 (t0) REVERT: B 67 ASP cc_start: 0.8319 (t0) cc_final: 0.8027 (t0) REVERT: B 164 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7770 (ttt) REVERT: B 179 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8306 (t) REVERT: B 316 ILE cc_start: 0.8575 (mm) cc_final: 0.8289 (mt) REVERT: E 26 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (tp) REVERT: E 69 ASP cc_start: 0.8304 (t0) cc_final: 0.8096 (t0) REVERT: E 108 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6334 (p90) REVERT: E 181 VAL cc_start: 0.8703 (p) cc_final: 0.8391 (t) REVERT: E 265 ILE cc_start: 0.8213 (pt) cc_final: 0.7737 (mt) REVERT: E 302 MET cc_start: 0.8435 (mmm) cc_final: 0.7957 (mtm) outliers start: 55 outliers final: 32 residues processed: 311 average time/residue: 1.2008 time to fit residues: 410.2379 Evaluate side-chains 315 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 165 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 337 ASN A 11 GLN B 165 ASN B 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102546 restraints weight = 21194.601| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.14 r_work: 0.3292 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13903 Z= 0.203 Angle : 0.563 9.064 18876 Z= 0.286 Chirality : 0.043 0.228 2074 Planarity : 0.004 0.059 2452 Dihedral : 9.642 159.544 2046 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.34 % Allowed : 20.41 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.63 (0.20), residues: 1705 helix: 1.90 (0.20), residues: 715 sheet: 0.44 (0.30), residues: 299 loop : -1.22 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS B 6 PHE 0.015 0.001 PHE A 49 TYR 0.011 0.001 TYR B 310 ARG 0.006 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 1.512 Fit side-chains REVERT: K 7 LYS cc_start: 0.8066 (mptt) cc_final: 0.7605 (tmmt) REVERT: K 19 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7700 (mt-10) REVERT: K 105 TYR cc_start: 0.7394 (t80) cc_final: 0.6942 (t80) REVERT: K 124 GLU cc_start: 0.7093 (tt0) cc_final: 0.6842 (tp30) REVERT: K 136 ASP cc_start: 0.5760 (m-30) cc_final: 0.5444 (t0) REVERT: K 192 ILE cc_start: 0.7865 (tt) cc_final: 0.7418 (pp) REVERT: K 246 LEU cc_start: 0.7940 (mt) cc_final: 0.7635 (mt) REVERT: K 248 ASP cc_start: 0.7501 (t0) cc_final: 0.7234 (t0) REVERT: K 276 THR cc_start: 0.8038 (m) cc_final: 0.7615 (m) REVERT: K 342 LEU cc_start: 0.8831 (tt) cc_final: 0.8487 (tm) REVERT: K 353 GLN cc_start: 0.7833 (mp10) cc_final: 0.7423 (mp10) REVERT: A 3 GLU cc_start: 0.8089 (mp0) cc_final: 0.7886 (mp0) REVERT: A 254 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: A 437 VAL cc_start: 0.9050 (p) cc_final: 0.8681 (m) REVERT: B 57 ASN cc_start: 0.7845 (t0) cc_final: 0.7369 (t0) REVERT: B 123 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: B 164 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7779 (ttt) REVERT: B 282 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8145 (mtp85) REVERT: B 291 GLN cc_start: 0.8282 (tt0) cc_final: 0.8020 (tt0) REVERT: B 316 ILE cc_start: 0.8572 (mm) cc_final: 0.8279 (mt) REVERT: E 26 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8409 (tp) REVERT: E 181 VAL cc_start: 0.8678 (p) cc_final: 0.8377 (t) REVERT: E 449 GLU cc_start: -0.1596 (OUTLIER) cc_final: -0.1869 (pm20) outliers start: 48 outliers final: 31 residues processed: 298 average time/residue: 1.2446 time to fit residues: 407.3347 Evaluate side-chains 298 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 449 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN B 137 HIS B 165 ASN B 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097909 restraints weight = 21319.369| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.15 r_work: 0.3220 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13903 Z= 0.435 Angle : 0.654 9.145 18876 Z= 0.335 Chirality : 0.047 0.256 2074 Planarity : 0.005 0.058 2452 Dihedral : 9.917 162.762 2046 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.10 % Allowed : 20.48 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.40 (0.20), residues: 1705 helix: 1.68 (0.20), residues: 709 sheet: 0.40 (0.30), residues: 300 loop : -1.33 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 344 HIS 0.011 0.002 HIS A 88 PHE 0.018 0.002 PHE B 367 TYR 0.019 0.002 TYR A 319 ARG 0.006 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.538 Fit side-chains REVERT: K 7 LYS cc_start: 0.8103 (mptt) cc_final: 0.7619 (tmmt) REVERT: K 19 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7808 (tt0) REVERT: K 105 TYR cc_start: 0.7407 (t80) cc_final: 0.6921 (t80) REVERT: K 136 ASP cc_start: 0.5854 (m-30) cc_final: 0.5543 (t0) REVERT: K 248 ASP cc_start: 0.7436 (t0) cc_final: 0.7164 (t0) REVERT: K 253 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7883 (mm-30) REVERT: K 342 LEU cc_start: 0.8850 (tp) cc_final: 0.8518 (tm) REVERT: K 353 GLN cc_start: 0.7851 (mp10) cc_final: 0.7459 (mp10) REVERT: A 187 SER cc_start: 0.8889 (t) cc_final: 0.8561 (p) REVERT: A 254 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: A 320 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8374 (mtp180) REVERT: A 437 VAL cc_start: 0.9077 (p) cc_final: 0.8748 (m) REVERT: B 57 ASN cc_start: 0.7935 (t0) cc_final: 0.7459 (t0) REVERT: B 67 ASP cc_start: 0.8372 (t0) cc_final: 0.8079 (t0) REVERT: B 131 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8283 (tp40) REVERT: B 164 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7775 (ttt) REVERT: B 193 VAL cc_start: 0.8641 (p) cc_final: 0.8393 (t) REVERT: B 282 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8151 (mtp85) REVERT: B 291 GLN cc_start: 0.8310 (tt0) cc_final: 0.8053 (tt0) REVERT: B 316 ILE cc_start: 0.8642 (mm) cc_final: 0.8383 (mt) REVERT: E 26 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8488 (tp) REVERT: E 108 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6373 (p90) REVERT: E 265 ILE cc_start: 0.8348 (pt) cc_final: 0.7917 (mt) REVERT: E 302 MET cc_start: 0.8489 (mmm) cc_final: 0.8006 (mtm) REVERT: E 449 GLU cc_start: -0.1570 (OUTLIER) cc_final: -0.1831 (pm20) outliers start: 59 outliers final: 37 residues processed: 300 average time/residue: 1.2020 time to fit residues: 395.6359 Evaluate side-chains 306 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 337 ASN Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 108 TYR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 337 ASN A 11 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101480 restraints weight = 21279.311| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.15 r_work: 0.3281 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13903 Z= 0.211 Angle : 0.570 9.925 18876 Z= 0.291 Chirality : 0.044 0.216 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.639 162.024 2046 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.21 % Allowed : 21.50 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.53 (0.20), residues: 1705 helix: 1.82 (0.20), residues: 712 sheet: 0.37 (0.30), residues: 307 loop : -1.26 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.006 0.001 HIS B 137 PHE 0.015 0.001 PHE B 367 TYR 0.015 0.001 TYR K 96 ARG 0.007 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: K 7 LYS cc_start: 0.8105 (mptt) cc_final: 0.7622 (ttpt) REVERT: K 19 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7754 (tt0) REVERT: K 105 TYR cc_start: 0.7423 (t80) cc_final: 0.6919 (t80) REVERT: K 112 GLU cc_start: 0.6909 (mp0) cc_final: 0.6492 (pp20) REVERT: K 124 GLU cc_start: 0.7011 (tt0) cc_final: 0.6739 (mt-10) REVERT: K 136 ASP cc_start: 0.5768 (m-30) cc_final: 0.5492 (t0) REVERT: K 248 ASP cc_start: 0.7447 (t0) cc_final: 0.7189 (t0) REVERT: K 253 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7809 (mm-30) REVERT: K 342 LEU cc_start: 0.8796 (tp) cc_final: 0.8470 (tm) REVERT: K 353 GLN cc_start: 0.7821 (mp10) cc_final: 0.7417 (mp10) REVERT: K 354 ILE cc_start: 0.8270 (mt) cc_final: 0.7733 (mm) REVERT: A 187 SER cc_start: 0.8859 (t) cc_final: 0.8571 (p) REVERT: A 254 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: A 437 VAL cc_start: 0.9072 (p) cc_final: 0.8758 (m) REVERT: B 57 ASN cc_start: 0.7841 (t0) cc_final: 0.7375 (t0) REVERT: B 67 ASP cc_start: 0.8326 (t0) cc_final: 0.8029 (t0) REVERT: B 131 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8193 (tp40) REVERT: B 164 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7760 (ttt) REVERT: B 179 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 193 VAL cc_start: 0.8610 (p) cc_final: 0.8369 (t) REVERT: B 213 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8122 (mtm-85) REVERT: B 282 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8157 (mtp85) REVERT: B 291 GLN cc_start: 0.8250 (tt0) cc_final: 0.7996 (tt0) REVERT: B 316 ILE cc_start: 0.8580 (mm) cc_final: 0.8301 (mt) REVERT: E 26 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8415 (tp) REVERT: E 181 VAL cc_start: 0.8675 (p) cc_final: 0.8361 (t) REVERT: E 449 GLU cc_start: -0.1591 (OUTLIER) cc_final: -0.1838 (pm20) outliers start: 46 outliers final: 29 residues processed: 300 average time/residue: 1.2524 time to fit residues: 411.6896 Evaluate side-chains 308 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 449 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.933 > 50: distance: 64 - 82: 16.607 distance: 68 - 91: 34.039 distance: 72 - 99: 22.597 distance: 78 - 82: 14.440 distance: 82 - 83: 26.106 distance: 83 - 84: 30.780 distance: 83 - 86: 3.024 distance: 84 - 85: 44.633 distance: 84 - 91: 31.304 distance: 86 - 87: 18.981 distance: 89 - 90: 40.457 distance: 92 - 93: 35.296 distance: 93 - 94: 30.117 distance: 93 - 99: 36.636 distance: 94 - 129: 35.571 distance: 95 - 96: 11.665 distance: 96 - 97: 28.713 distance: 96 - 98: 3.542 distance: 99 - 100: 40.736 distance: 100 - 101: 50.361 distance: 100 - 103: 52.589 distance: 101 - 102: 29.222 distance: 101 - 111: 36.664 distance: 103 - 104: 17.718 distance: 104 - 105: 14.264 distance: 104 - 106: 20.714 distance: 105 - 107: 19.702 distance: 106 - 108: 18.428 distance: 107 - 109: 11.605 distance: 108 - 109: 18.034 distance: 109 - 110: 10.455 distance: 111 - 112: 28.149 distance: 112 - 113: 33.361 distance: 112 - 115: 10.292 distance: 113 - 114: 13.356 distance: 113 - 120: 15.251 distance: 115 - 116: 14.333 distance: 116 - 117: 8.916 distance: 117 - 119: 6.032 distance: 120 - 121: 30.893 distance: 121 - 122: 48.243 distance: 121 - 124: 26.980 distance: 122 - 123: 39.048 distance: 122 - 129: 38.509 distance: 124 - 125: 46.029 distance: 125 - 126: 29.277 distance: 126 - 127: 22.511 distance: 126 - 128: 40.298 distance: 129 - 130: 39.274 distance: 130 - 131: 55.188 distance: 130 - 133: 42.403 distance: 131 - 132: 39.873 distance: 133 - 134: 34.359 distance: 133 - 135: 32.108 distance: 137 - 138: 39.603 distance: 138 - 139: 40.229 distance: 138 - 140: 38.949 distance: 140 - 141: 20.158 distance: 141 - 142: 4.329 distance: 141 - 144: 45.482 distance: 142 - 143: 22.011 distance: 142 - 147: 12.108 distance: 144 - 145: 15.771 distance: 144 - 146: 39.171 distance: 147 - 148: 4.057 distance: 148 - 151: 56.915 distance: 151 - 152: 38.792 distance: 152 - 154: 40.733 distance: 155 - 156: 45.642 distance: 156 - 157: 28.017 distance: 156 - 159: 13.935 distance: 157 - 161: 34.167 distance: 159 - 160: 4.346