Starting phenix.real_space_refine on Mon Dec 30 17:29:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utu_42550/12_2024/8utu_42550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utu_42550/12_2024/8utu_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_42550/12_2024/8utu_42550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utu_42550/12_2024/8utu_42550.map" model { file = "/net/cci-nas-00/data/ceres_data/8utu_42550/12_2024/8utu_42550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utu_42550/12_2024/8utu_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-5532/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: 10.85, per 1000 atoms: 0.80 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: 3.41 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: 1.56 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: 4.35 Time building geometry restraints manager: 3.91 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: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.290 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.610 ------------------------------------------------------------------------------- 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 : 1.509 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: 1.2307 time to fit residues: 397.6486 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 : 1.706 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 1.549 Fit side-chains REVERT: K 11 ARG cc_start: 0.7528 (ttt180) cc_final: 0.7279 (ttt180) REVERT: K 98 GLN cc_start: 0.8044 (pt0) cc_final: 0.7840 (pt0) REVERT: K 192 ILE cc_start: 0.7772 (tt) cc_final: 0.7410 (pp) REVERT: K 248 ASP cc_start: 0.7374 (t0) cc_final: 0.7120 (t0) REVERT: K 287 GLU cc_start: 0.7739 (tp30) cc_final: 0.7534 (tp30) REVERT: K 353 GLN cc_start: 0.7743 (mp10) cc_final: 0.7519 (mp10) REVERT: A 24 TYR cc_start: 0.8146 (m-80) cc_final: 0.7900 (m-80) REVERT: B 57 ASN cc_start: 0.7345 (t0) cc_final: 0.6875 (t0) REVERT: B 164 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7769 (ttp) REVERT: B 188 SER cc_start: 0.8577 (p) cc_final: 0.8323 (p) REVERT: B 291 GLN cc_start: 0.7917 (tt0) cc_final: 0.7634 (mt0) REVERT: B 316 ILE cc_start: 0.8571 (mm) cc_final: 0.8314 (mt) REVERT: B 415 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8301 (ttp) REVERT: E 69 ASP cc_start: 0.8252 (t0) cc_final: 0.8028 (t70) REVERT: E 398 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7099 (ttm) outliers start: 44 outliers final: 19 residues processed: 288 average time/residue: 1.1563 time to fit residues: 367.3430 Evaluate side-chains 272 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 165 ASN B 298 ASN E 139 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13903 Z= 0.204 Angle : 0.556 7.011 18876 Z= 0.282 Chirality : 0.044 0.384 2074 Planarity : 0.004 0.067 2452 Dihedral : 9.863 152.379 2046 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 3.48 % Allowed : 17.88 % Favored : 78.63 % 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: 0.59 (0.20), residues: 1705 helix: 1.71 (0.20), residues: 724 sheet: 0.30 (0.30), residues: 296 loop : -1.01 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.005 0.001 HIS E 88 PHE 0.015 0.001 PHE B 367 TYR 0.012 0.001 TYR B 310 ARG 0.010 0.001 ARG A 79 *********************** 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 309 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: K 107 MET cc_start: 0.8111 (mmt) cc_final: 0.7883 (mmm) REVERT: K 192 ILE cc_start: 0.7779 (tt) cc_final: 0.7403 (pp) REVERT: K 248 ASP cc_start: 0.7421 (t0) cc_final: 0.7133 (t0) REVERT: K 353 GLN cc_start: 0.7769 (mp10) cc_final: 0.7500 (mp10) REVERT: A 24 TYR cc_start: 0.8222 (m-80) cc_final: 0.7882 (m-80) REVERT: A 49 PHE cc_start: 0.7247 (m-10) cc_final: 0.7012 (m-10) REVERT: B 57 ASN cc_start: 0.7549 (t0) cc_final: 0.7053 (t0) REVERT: B 94 GLN cc_start: 0.8042 (mp10) cc_final: 0.7777 (mm-40) REVERT: B 164 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7788 (ttt) REVERT: B 257 MET cc_start: 0.8074 (mmp) cc_final: 0.7670 (mmm) REVERT: B 291 GLN cc_start: 0.7932 (tt0) cc_final: 0.7610 (mt0) REVERT: B 316 ILE cc_start: 0.8559 (mm) cc_final: 0.8332 (mt) REVERT: B 415 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8337 (ttp) REVERT: E 26 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8235 (tp) REVERT: E 69 ASP cc_start: 0.8318 (t0) cc_final: 0.8108 (t70) outliers start: 50 outliers final: 17 residues processed: 281 average time/residue: 1.1719 time to fit residues: 363.7926 Evaluate side-chains 265 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 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 360 ILE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 ILE 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 B residue 415 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 334 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 115 GLN ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 GLN B 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13903 Z= 0.186 Angle : 0.543 7.708 18876 Z= 0.274 Chirality : 0.043 0.291 2074 Planarity : 0.004 0.062 2452 Dihedral : 9.593 153.246 2046 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 19.39 % Favored : 77.75 % 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: 0.69 (0.20), residues: 1705 helix: 1.87 (0.20), residues: 719 sheet: 0.39 (0.30), residues: 296 loop : -1.05 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.004 0.001 HIS E 88 PHE 0.014 0.001 PHE B 367 TYR 0.011 0.001 TYR B 310 ARG 0.005 0.000 ARG A 339 *********************** 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 312 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 1.322 Fit side-chains REVERT: K 19 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: K 42 GLN cc_start: 0.5400 (mp10) cc_final: 0.5181 (mp10) REVERT: K 105 TYR cc_start: 0.7597 (t80) cc_final: 0.7069 (t80) REVERT: K 192 ILE cc_start: 0.7837 (tt) cc_final: 0.7444 (pp) REVERT: K 248 ASP cc_start: 0.7473 (t0) cc_final: 0.7206 (t0) REVERT: K 338 TYR cc_start: 0.6369 (t80) cc_final: 0.5712 (t80) REVERT: K 353 GLN cc_start: 0.7823 (mp10) cc_final: 0.7592 (mp10) REVERT: A 49 PHE cc_start: 0.7231 (m-10) cc_final: 0.7023 (m-10) REVERT: A 332 ILE cc_start: 0.8429 (mm) cc_final: 0.8226 (mt) REVERT: B 57 ASN cc_start: 0.7610 (t0) cc_final: 0.7098 (t0) REVERT: B 94 GLN cc_start: 0.8023 (mp10) cc_final: 0.7697 (mm-40) REVERT: B 164 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7844 (ttt) REVERT: B 291 GLN cc_start: 0.7959 (tt0) cc_final: 0.7630 (mt0) REVERT: B 415 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8334 (ttp) REVERT: E 26 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (tp) outliers start: 41 outliers final: 23 residues processed: 289 average time/residue: 1.1895 time to fit residues: 377.5900 Evaluate side-chains 287 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 28 ILE 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 305 LEU Chi-restraints excluded: chain K residue 339 ASP Chi-restraints excluded: chain K residue 360 ILE 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 432 TYR 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 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 B residue 415 MET Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 198 SER 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 136 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 227 GLN B 165 ASN B 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13903 Z= 0.175 Angle : 0.537 8.200 18876 Z= 0.270 Chirality : 0.043 0.235 2074 Planarity : 0.004 0.062 2452 Dihedral : 9.407 153.536 2046 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 2.87 % Allowed : 19.66 % Favored : 77.47 % 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: 0.81 (0.20), residues: 1705 helix: 1.96 (0.20), residues: 730 sheet: 0.46 (0.30), residues: 299 loop : -1.05 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.003 0.001 HIS E 88 PHE 0.013 0.001 PHE B 367 TYR 0.019 0.001 TYR A 24 ARG 0.007 0.000 ARG E 339 *********************** 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 307 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.483 Fit side-chains REVERT: K 7 LYS cc_start: 0.8109 (mptt) cc_final: 0.7767 (tmmt) REVERT: K 19 GLU cc_start: 0.7759 (tt0) cc_final: 0.7464 (mt-10) REVERT: K 105 TYR cc_start: 0.7487 (t80) cc_final: 0.7122 (t80) REVERT: K 192 ILE cc_start: 0.7822 (tt) cc_final: 0.7409 (pp) REVERT: K 246 LEU cc_start: 0.8039 (mt) cc_final: 0.7711 (mt) REVERT: K 248 ASP cc_start: 0.7504 (t0) cc_final: 0.7252 (t0) REVERT: K 276 THR cc_start: 0.7994 (m) cc_final: 0.7555 (m) REVERT: K 353 GLN cc_start: 0.7782 (mp10) cc_final: 0.7486 (mp10) REVERT: A 24 TYR cc_start: 0.8223 (m-80) cc_final: 0.7874 (m-80) REVERT: A 49 PHE cc_start: 0.7299 (m-10) cc_final: 0.7077 (m-10) REVERT: A 332 ILE cc_start: 0.8399 (mm) cc_final: 0.8142 (mt) REVERT: B 57 ASN cc_start: 0.7611 (t0) cc_final: 0.7107 (t0) REVERT: B 94 GLN cc_start: 0.7976 (mp10) cc_final: 0.7734 (mm-40) REVERT: B 164 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7839 (ttt) REVERT: E 26 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8236 (tp) REVERT: E 302 MET cc_start: 0.8400 (mmm) cc_final: 0.7955 (mtm) outliers start: 41 outliers final: 25 residues processed: 286 average time/residue: 1.2107 time to fit residues: 380.0691 Evaluate side-chains 292 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 133 THR 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 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 259 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 164 MET 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 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 198 SER 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 55 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13903 Z= 0.361 Angle : 0.610 8.583 18876 Z= 0.311 Chirality : 0.045 0.247 2074 Planarity : 0.005 0.059 2452 Dihedral : 9.668 157.392 2046 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.23 % Allowed : 19.18 % Favored : 76.59 % 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: 0.64 (0.20), residues: 1705 helix: 1.88 (0.20), residues: 716 sheet: 0.39 (0.29), residues: 301 loop : -1.15 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 344 HIS 0.010 0.002 HIS E 88 PHE 0.017 0.002 PHE A 141 TYR 0.015 0.002 TYR A 319 ARG 0.006 0.001 ARG A 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 333 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 1.540 Fit side-chains REVERT: K 7 LYS cc_start: 0.8163 (mptt) cc_final: 0.7811 (tmtp) REVERT: K 19 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: K 42 GLN cc_start: 0.5741 (OUTLIER) cc_final: 0.4826 (mp10) REVERT: K 105 TYR cc_start: 0.7400 (t80) cc_final: 0.6966 (t80) REVERT: K 112 GLU cc_start: 0.6675 (mp0) cc_final: 0.6135 (pp20) REVERT: K 136 ASP cc_start: 0.5535 (m-30) cc_final: 0.5260 (t0) REVERT: K 143 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7440 (mt-10) REVERT: K 152 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7540 (mm-30) REVERT: K 183 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7745 (tptt) REVERT: K 192 ILE cc_start: 0.7844 (tt) cc_final: 0.7414 (pp) REVERT: K 246 LEU cc_start: 0.7967 (mt) cc_final: 0.7639 (mt) REVERT: K 248 ASP cc_start: 0.7483 (t0) cc_final: 0.7236 (t0) REVERT: K 276 THR cc_start: 0.8044 (m) cc_final: 0.7638 (m) REVERT: K 327 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7185 (ttp) REVERT: K 342 LEU cc_start: 0.8879 (tt) cc_final: 0.8522 (tm) REVERT: K 353 GLN cc_start: 0.7886 (mp10) cc_final: 0.7532 (mp10) REVERT: A 332 ILE cc_start: 0.8408 (mm) cc_final: 0.8174 (mt) REVERT: B 57 ASN cc_start: 0.7709 (t0) cc_final: 0.7225 (t0) REVERT: B 67 ASP cc_start: 0.8323 (t0) cc_final: 0.8025 (t0) REVERT: B 164 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7813 (ttt) REVERT: E 26 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8396 (tp) REVERT: E 181 VAL cc_start: 0.8805 (p) cc_final: 0.8466 (t) REVERT: E 265 ILE cc_start: 0.8203 (pt) cc_final: 0.7793 (mt) outliers start: 61 outliers final: 35 residues processed: 302 average time/residue: 1.2194 time to fit residues: 405.6753 Evaluate side-chains 300 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 42 GLN 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 157 LEU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 223 ILE 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 K residue 339 ASP Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 VAL 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 135 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 164 MET 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 316 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 26 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN B 165 ASN B 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13903 Z= 0.225 Angle : 0.563 9.031 18876 Z= 0.285 Chirality : 0.043 0.222 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.512 158.035 2046 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.07 % Allowed : 21.23 % Favored : 75.70 % 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: 0.70 (0.20), residues: 1705 helix: 1.92 (0.20), residues: 717 sheet: 0.54 (0.30), residues: 296 loop : -1.17 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS E 88 PHE 0.014 0.001 PHE B 367 TYR 0.014 0.001 TYR A 24 ARG 0.006 0.000 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 314 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 270 time to evaluate : 1.792 Fit side-chains REVERT: K 7 LYS cc_start: 0.8089 (mptt) cc_final: 0.7651 (tmmt) REVERT: K 19 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: K 42 GLN cc_start: 0.5551 (OUTLIER) cc_final: 0.4816 (mp10) REVERT: K 105 TYR cc_start: 0.7423 (t80) cc_final: 0.6937 (t80) REVERT: K 136 ASP cc_start: 0.5439 (m-30) cc_final: 0.5201 (t0) REVERT: K 143 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7083 (mt-10) REVERT: K 183 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7682 (tmtp) REVERT: K 192 ILE cc_start: 0.7921 (tt) cc_final: 0.7445 (pp) REVERT: K 224 ILE cc_start: 0.8204 (mt) cc_final: 0.7977 (pt) REVERT: K 246 LEU cc_start: 0.7883 (mt) cc_final: 0.7580 (mt) REVERT: K 248 ASP cc_start: 0.7472 (t0) cc_final: 0.7252 (t0) REVERT: K 276 THR cc_start: 0.7961 (m) cc_final: 0.7560 (m) REVERT: K 342 LEU cc_start: 0.8845 (tt) cc_final: 0.8500 (tm) REVERT: K 353 GLN cc_start: 0.7908 (mp10) cc_final: 0.7557 (mp10) REVERT: A 254 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: A 332 ILE cc_start: 0.8394 (mm) cc_final: 0.8188 (mt) REVERT: B 57 ASN cc_start: 0.7682 (t0) cc_final: 0.7231 (t0) REVERT: B 164 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7801 (ttt) REVERT: B 282 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7974 (mtp85) REVERT: E 26 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8356 (tp) REVERT: E 69 ASP cc_start: 0.8358 (t0) cc_final: 0.8115 (t70) REVERT: E 108 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6267 (p90) REVERT: E 265 ILE cc_start: 0.8050 (pt) cc_final: 0.7613 (mt) REVERT: E 302 MET cc_start: 0.8423 (mmm) cc_final: 0.7974 (mtm) outliers start: 44 outliers final: 28 residues processed: 292 average time/residue: 1.2422 time to fit residues: 399.4227 Evaluate side-chains 296 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 42 GLN 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 157 LEU Chi-restraints excluded: chain K residue 179 GLU Chi-restraints excluded: chain K residue 183 LYS 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 230 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 164 MET 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 333 VAL 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 191 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 0.0050 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13903 Z= 0.254 Angle : 0.591 10.904 18876 Z= 0.298 Chirality : 0.044 0.227 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.502 159.588 2046 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.14 % Allowed : 21.57 % 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: 0.69 (0.20), residues: 1705 helix: 1.91 (0.20), residues: 718 sheet: 0.55 (0.30), residues: 296 loop : -1.19 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.006 0.001 HIS A 88 PHE 0.015 0.001 PHE B 367 TYR 0.016 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 312 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: K 7 LYS cc_start: 0.8095 (mptt) cc_final: 0.7662 (tmmt) REVERT: K 19 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: K 42 GLN cc_start: 0.5689 (OUTLIER) cc_final: 0.4918 (mp10) REVERT: K 105 TYR cc_start: 0.7410 (t80) cc_final: 0.6871 (t80) REVERT: K 136 ASP cc_start: 0.5508 (m-30) cc_final: 0.5284 (t0) REVERT: K 143 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7168 (mt-10) REVERT: K 183 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7697 (tmtp) REVERT: K 224 ILE cc_start: 0.8221 (mt) cc_final: 0.7848 (pt) REVERT: K 248 ASP cc_start: 0.7443 (t0) cc_final: 0.7214 (t0) REVERT: K 276 THR cc_start: 0.7988 (m) cc_final: 0.7599 (m) REVERT: K 287 GLU cc_start: 0.7811 (tp30) cc_final: 0.7553 (tp30) REVERT: K 327 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6663 (tpp) REVERT: K 342 LEU cc_start: 0.8862 (tt) cc_final: 0.8535 (tm) REVERT: K 353 GLN cc_start: 0.7897 (mp10) cc_final: 0.7557 (mp10) REVERT: A 254 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: A 332 ILE cc_start: 0.8393 (mm) cc_final: 0.8138 (mt) REVERT: A 437 VAL cc_start: 0.9063 (p) cc_final: 0.8731 (m) REVERT: B 57 ASN cc_start: 0.7686 (t0) cc_final: 0.7242 (t0) REVERT: B 164 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7783 (ttt) REVERT: B 282 ARG cc_start: 0.8367 (ttm110) cc_final: 0.7943 (mtp85) REVERT: B 291 GLN cc_start: 0.7910 (tt0) cc_final: 0.7676 (tt0) REVERT: E 1 MET cc_start: 0.7860 (tpp) cc_final: 0.7381 (tpp) REVERT: E 26 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8369 (tp) REVERT: E 108 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6311 (p90) REVERT: E 181 VAL cc_start: 0.8790 (p) cc_final: 0.8460 (t) REVERT: E 265 ILE cc_start: 0.8169 (pt) cc_final: 0.7783 (mt) outliers start: 45 outliers final: 29 residues processed: 288 average time/residue: 1.1542 time to fit residues: 366.0815 Evaluate side-chains 292 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 42 GLN 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 179 GLU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain A residue 125 LEU 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 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 417 GLU 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 164 MET 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 161 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** B 195 ASN B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13903 Z= 0.229 Angle : 0.580 9.978 18876 Z= 0.294 Chirality : 0.044 0.241 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.419 159.106 2046 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.00 % Allowed : 22.32 % Favored : 74.68 % 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: 0.71 (0.20), residues: 1705 helix: 1.94 (0.20), residues: 712 sheet: 0.54 (0.30), residues: 296 loop : -1.15 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.005 0.001 HIS E 88 PHE 0.014 0.001 PHE B 367 TYR 0.020 0.001 TYR K 96 ARG 0.007 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 9 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: 43 poor density : 266 time to evaluate : 1.495 Fit side-chains REVERT: K 7 LYS cc_start: 0.8126 (mptt) cc_final: 0.7627 (tmtp) REVERT: K 42 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.4866 (mp10) REVERT: K 98 GLN cc_start: 0.8072 (pt0) cc_final: 0.7775 (tm-30) REVERT: K 105 TYR cc_start: 0.7406 (t80) cc_final: 0.6878 (t80) REVERT: K 136 ASP cc_start: 0.5475 (m-30) cc_final: 0.5246 (t0) REVERT: K 248 ASP cc_start: 0.7416 (t0) cc_final: 0.7201 (t0) REVERT: K 276 THR cc_start: 0.7936 (m) cc_final: 0.7524 (m) REVERT: K 287 GLU cc_start: 0.7791 (tp30) cc_final: 0.7510 (tp30) REVERT: K 342 LEU cc_start: 0.8831 (tt) cc_final: 0.8517 (tm) REVERT: K 345 LEU cc_start: 0.8908 (mp) cc_final: 0.8685 (mm) REVERT: K 353 GLN cc_start: 0.7889 (mp10) cc_final: 0.7563 (mp10) REVERT: A 254 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 332 ILE cc_start: 0.8384 (mm) cc_final: 0.8175 (mt) REVERT: A 413 MET cc_start: 0.9055 (ttp) cc_final: 0.8808 (ttm) REVERT: A 437 VAL cc_start: 0.9072 (p) cc_final: 0.8759 (m) REVERT: B 57 ASN cc_start: 0.7683 (t0) cc_final: 0.7241 (t0) REVERT: B 67 ASP cc_start: 0.8302 (t0) cc_final: 0.8007 (t0) REVERT: B 164 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7794 (ttt) REVERT: B 179 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 196 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (m) REVERT: B 282 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7962 (mtp85) REVERT: B 291 GLN cc_start: 0.7901 (tt0) cc_final: 0.7660 (tt0) REVERT: B 304 ASP cc_start: 0.8335 (t0) cc_final: 0.8131 (t70) REVERT: E 26 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8361 (tp) REVERT: E 69 ASP cc_start: 0.8270 (t0) cc_final: 0.7991 (t70) REVERT: E 108 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6325 (p90) REVERT: E 181 VAL cc_start: 0.8778 (p) cc_final: 0.8446 (t) REVERT: E 265 ILE cc_start: 0.8064 (pt) cc_final: 0.7656 (mt) outliers start: 43 outliers final: 27 residues processed: 288 average time/residue: 1.1730 time to fit residues: 376.9492 Evaluate side-chains 291 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 GLN 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 157 LEU 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 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 417 GLU 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 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 196 THR 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 108 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 337 ASN A 11 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13903 Z= 0.210 Angle : 0.583 11.399 18876 Z= 0.294 Chirality : 0.043 0.214 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.361 159.248 2046 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.46 % Allowed : 23.00 % Favored : 74.54 % 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: 0.74 (0.20), residues: 1705 helix: 1.96 (0.20), residues: 712 sheet: 0.53 (0.29), residues: 297 loop : -1.12 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.004 0.001 HIS A 88 PHE 0.013 0.001 PHE B 367 TYR 0.027 0.001 TYR K 177 ARG 0.007 0.000 ARG E 339 ********************** REFINEMENT MACRO_CYCLE 10 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 294 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 1.560 Fit side-chains revert: symmetry clash REVERT: K 7 LYS cc_start: 0.8138 (mptt) cc_final: 0.7651 (tmtp) REVERT: K 42 GLN cc_start: 0.5609 (OUTLIER) cc_final: 0.4861 (mp10) REVERT: K 98 GLN cc_start: 0.8018 (pt0) cc_final: 0.7756 (tm-30) REVERT: K 136 ASP cc_start: 0.5504 (m-30) cc_final: 0.5294 (t0) REVERT: K 224 ILE cc_start: 0.8204 (mt) cc_final: 0.7817 (pp) REVERT: K 248 ASP cc_start: 0.7348 (t0) cc_final: 0.7137 (t0) REVERT: K 276 THR cc_start: 0.7931 (m) cc_final: 0.7535 (m) REVERT: K 287 GLU cc_start: 0.7792 (tp30) cc_final: 0.7529 (tp30) REVERT: K 342 LEU cc_start: 0.8775 (tt) cc_final: 0.8467 (tm) REVERT: K 345 LEU cc_start: 0.8890 (mp) cc_final: 0.8673 (mm) REVERT: K 353 GLN cc_start: 0.7895 (mp10) cc_final: 0.7580 (mp10) REVERT: A 254 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: A 332 ILE cc_start: 0.8375 (mm) cc_final: 0.8161 (mt) REVERT: A 413 MET cc_start: 0.9021 (ttp) cc_final: 0.8792 (ttm) REVERT: A 437 VAL cc_start: 0.9069 (p) cc_final: 0.8766 (m) REVERT: B 57 ASN cc_start: 0.7650 (t0) cc_final: 0.7210 (t0) REVERT: B 67 ASP cc_start: 0.8301 (t0) cc_final: 0.8009 (t0) REVERT: B 164 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7786 (ttt) REVERT: B 179 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8260 (t) REVERT: B 193 VAL cc_start: 0.8572 (p) cc_final: 0.8326 (t) REVERT: B 196 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8698 (m) REVERT: B 282 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7953 (mtp85) REVERT: B 291 GLN cc_start: 0.7925 (tt0) cc_final: 0.7695 (tt0) REVERT: B 304 ASP cc_start: 0.8325 (t0) cc_final: 0.8119 (t70) REVERT: E 26 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8356 (tp) REVERT: E 69 ASP cc_start: 0.8257 (t0) cc_final: 0.7967 (t70) REVERT: E 108 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6314 (p90) REVERT: E 181 VAL cc_start: 0.8780 (p) cc_final: 0.8459 (t) REVERT: E 265 ILE cc_start: 0.8088 (pt) cc_final: 0.7681 (mt) REVERT: E 302 MET cc_start: 0.8417 (mmm) cc_final: 0.7950 (mtm) outliers start: 35 outliers final: 25 residues processed: 278 average time/residue: 1.1959 time to fit residues: 365.5988 Evaluate side-chains 284 residues out of total 1459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 GLN 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 246 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 305 LEU 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 417 GLU 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 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 196 THR 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 108 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0770 chunk 124 optimal weight: 0.0970 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105370 restraints weight = 21078.436| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.08 r_work: 0.3330 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13903 Z= 0.175 Angle : 0.557 10.691 18876 Z= 0.279 Chirality : 0.043 0.213 2074 Planarity : 0.004 0.058 2452 Dihedral : 9.135 158.119 2046 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.39 % Allowed : 23.34 % Favored : 74.27 % 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: 0.89 (0.21), residues: 1705 helix: 2.10 (0.20), residues: 713 sheet: 0.61 (0.30), residues: 296 loop : -1.07 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 388 HIS 0.003 0.001 HIS E 88 PHE 0.012 0.001 PHE B 367 TYR 0.026 0.001 TYR K 177 ARG 0.007 0.000 ARG E 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6175.14 seconds wall clock time: 111 minutes 5.32 seconds (6665.32 seconds total)