Starting phenix.real_space_refine on Sun Dec 29 04:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.map" model { file = "/net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utr_42547/12_2024/8utr_42547.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 7 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6118 2.51 5 N 1679 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9792 Number of models: 1 Model: "" Number of chains: 7 Chain: "K" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2798 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} 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: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N THR B 429 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR B 429 " occ=0.50 residue: pdb=" N ALA B 430 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA B 430 " occ=0.50 residue: pdb=" N ASP B 431 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP B 431 " occ=0.50 residue: pdb=" N GLU B 432 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 432 " occ=0.50 residue: pdb=" N GLN B 433 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN B 433 " occ=0.50 Time building chain proxies: 7.41, per 1000 atoms: 0.76 Number of scatterers: 9792 At special positions: 0 Unit cell: (108.876, 74.272, 111.408, 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 66 16.00 P 7 15.00 Mg 1 11.99 O 1921 8.00 N 1679 7.00 C 6118 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 48.0% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 103 through 108 Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.545A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.547A pdb=" N ALA K 202 " --> pdb=" O SER K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 296 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.861A pdb=" N ASP K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 309 through 315 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 349 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.216A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.633A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.935A 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 128 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.625A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.573A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.766A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.076A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.154A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.984A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.881A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.622A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.597A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.782A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.077A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.167A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.725A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 70 through 78 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: 3.711A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.541A pdb=" N GLY B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.651A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.742A 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 237 removed outlier: 3.662A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 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 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.530A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.506A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.266A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.303A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.378A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.520A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 324 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS K 92 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA K 326 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR K 238 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG K 229 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 8.520A pdb=" N TYR K 54 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 324 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS K 92 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA K 326 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR K 238 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG K 229 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS K 240 " --> pdb=" O GLN K 227 " (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: 7.242A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (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 removed outlier: 3.606A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.274A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.802A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.087A 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 53 473 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1825 1.33 - 1.45: 2572 1.45 - 1.58: 5480 1.58 - 1.70: 16 1.70 - 1.82: 107 Bond restraints: 10000 Sorted by residual: bond pdb=" N LYS K 300 " pdb=" CA LYS K 300 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 bond pdb=" N LYS K 298 " pdb=" CA LYS K 298 " ideal model delta sigma weight residual 1.462 1.489 -0.028 1.27e-02 6.20e+03 4.77e+00 bond pdb=" N LYS K 299 " pdb=" CA LYS K 299 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.30e-02 5.92e+03 4.56e+00 bond pdb=" CB ILE K 77 " pdb=" CG2 ILE K 77 " ideal model delta sigma weight residual 1.521 1.586 -0.065 3.30e-02 9.18e+02 3.84e+00 bond pdb=" CB ASN K 159 " pdb=" CG ASN K 159 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.62e+00 ... (remaining 9995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 12960 1.61 - 3.23: 447 3.23 - 4.84: 123 4.84 - 6.45: 35 6.45 - 8.06: 6 Bond angle restraints: 13571 Sorted by residual: angle pdb=" CB GLU A 411 " pdb=" CG GLU A 411 " pdb=" CD GLU A 411 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA ASN K 159 " pdb=" CB ASN K 159 " pdb=" CG ASN K 159 " ideal model delta sigma weight residual 112.60 115.99 -3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" CA TYR K 74 " pdb=" CB TYR K 74 " pdb=" CG TYR K 74 " ideal model delta sigma weight residual 113.90 119.56 -5.66 1.80e+00 3.09e-01 9.88e+00 angle pdb=" CG LYS B 122 " pdb=" CD LYS B 122 " pdb=" CE LYS B 122 " ideal model delta sigma weight residual 111.30 118.07 -6.77 2.30e+00 1.89e-01 8.68e+00 angle pdb=" CB GLU K 317 " pdb=" CG GLU K 317 " pdb=" CD GLU K 317 " ideal model delta sigma weight residual 112.60 117.46 -4.86 1.70e+00 3.46e-01 8.17e+00 ... (remaining 13566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 5751 29.60 - 59.20: 286 59.20 - 88.79: 28 88.79 - 118.39: 5 118.39 - 147.99: 10 Dihedral angle restraints: 6080 sinusoidal: 2516 harmonic: 3564 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -42.18 146.78 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP K 801 " pdb=" O3A ADP K 801 " pdb=" PA ADP K 801 " pdb=" PB ADP K 801 " ideal model delta sinusoidal sigma weight residual -60.00 65.36 -125.36 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" C2' ADP K 801 " pdb=" C1' ADP K 801 " pdb=" N9 ADP K 801 " pdb=" C4 ADP K 801 " ideal model delta sinusoidal sigma weight residual 91.55 -151.67 -116.78 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 6077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 870 0.032 - 0.064: 410 0.064 - 0.096: 113 0.096 - 0.127: 70 0.127 - 0.159: 26 Chirality restraints: 1489 Sorted by residual: chirality pdb=" CA ILE K 304 " pdb=" N ILE K 304 " pdb=" C ILE K 304 " pdb=" CB ILE K 304 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA ASP B 31 " pdb=" N ASP B 31 " pdb=" C ASP B 31 " pdb=" CB ASP B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1486 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO K 292 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 429 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C GLU A 429 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 429 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 430 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A 89 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.029 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 22 2.40 - 3.03: 5729 3.03 - 3.65: 14222 3.65 - 4.28: 21191 4.28 - 4.90: 36634 Nonbonded interactions: 77798 Sorted by model distance: nonbonded pdb=" CE LYS K 299 " pdb=" O GLN B 433 " model vdw 1.777 3.440 nonbonded pdb=" OD2 ASP A 98 " pdb="MG MG A 502 " model vdw 1.975 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 1.981 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 2.040 2.170 nonbonded pdb=" OG SER B 172 " pdb=" OD1 ASP B 203 " model vdw 2.065 3.040 ... (remaining 77793 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.004 0.065 10000 Z= 0.296 Angle : 0.784 8.065 13571 Z= 0.403 Chirality : 0.046 0.159 1489 Planarity : 0.006 0.095 1761 Dihedral : 18.166 147.991 3792 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 0.66 % Allowed : 13.34 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.03 (0.24), residues: 1224 helix: 1.24 (0.23), residues: 487 sheet: -0.11 (0.34), residues: 227 loop : -1.10 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.005 0.001 HIS A 283 PHE 0.027 0.002 PHE A 49 TYR 0.034 0.002 TYR K 150 ARG 0.006 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 246 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 125 ASP cc_start: 0.7593 (t0) cc_final: 0.7226 (t0) REVERT: K 148 GLU cc_start: 0.8020 (pt0) cc_final: 0.7624 (pp20) REVERT: K 152 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7684 (mm-30) REVERT: K 298 LYS cc_start: 0.4993 (OUTLIER) cc_final: 0.4520 (ptpt) REVERT: K 300 LYS cc_start: -0.0801 (OUTLIER) cc_final: -0.1083 (mmtp) REVERT: A 1 MET cc_start: 0.7043 (mmm) cc_final: 0.6711 (mmm) REVERT: A 24 TYR cc_start: 0.8554 (m-10) cc_final: 0.8231 (m-10) REVERT: A 154 MET cc_start: 0.8647 (mmm) cc_final: 0.8164 (mtp) REVERT: B 356 ILE cc_start: 0.8918 (mm) cc_final: 0.8709 (mm) outliers start: 7 outliers final: 2 residues processed: 252 average time/residue: 0.2302 time to fit residues: 79.5747 Evaluate side-chains 231 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 70 GLN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 204 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10000 Z= 0.216 Angle : 0.593 9.145 13571 Z= 0.291 Chirality : 0.045 0.250 1489 Planarity : 0.005 0.088 1761 Dihedral : 12.562 144.876 1497 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 2.08 % Allowed : 12.87 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1224 helix: 1.83 (0.24), residues: 495 sheet: 0.21 (0.34), residues: 240 loop : -0.95 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 PHE 0.013 0.001 PHE K 15 TYR 0.022 0.001 TYR K 177 ARG 0.003 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 86 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7307 (t80) REVERT: K 138 MET cc_start: 0.4397 (mmt) cc_final: 0.3810 (mmm) REVERT: K 152 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7868 (mm-30) REVERT: K 159 ASN cc_start: 0.8277 (t0) cc_final: 0.7968 (t0) REVERT: K 210 MET cc_start: 0.7185 (mtp) cc_final: 0.6968 (mtp) REVERT: K 347 TYR cc_start: 0.8758 (t80) cc_final: 0.8248 (t80) REVERT: A 1 MET cc_start: 0.7168 (mmm) cc_final: 0.6422 (mmm) REVERT: A 3 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7213 (pt0) REVERT: A 24 TYR cc_start: 0.8641 (m-10) cc_final: 0.8298 (m-80) REVERT: A 69 ASP cc_start: 0.8165 (t0) cc_final: 0.7911 (t0) REVERT: A 322 ASP cc_start: 0.8799 (t0) cc_final: 0.8593 (t0) REVERT: B 1 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.4683 (mmm) REVERT: B 67 ASP cc_start: 0.8137 (t0) cc_final: 0.7764 (t70) REVERT: B 74 ASP cc_start: 0.8384 (m-30) cc_final: 0.8110 (m-30) REVERT: B 388 MET cc_start: 0.8544 (mtt) cc_final: 0.8185 (mtp) REVERT: B 417 ASP cc_start: 0.8260 (m-30) cc_final: 0.7995 (m-30) outliers start: 22 outliers final: 9 residues processed: 261 average time/residue: 0.2261 time to fit residues: 83.2173 Evaluate side-chains 237 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 318 ASN A 61 HIS A 258 ASN B 190 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10000 Z= 0.380 Angle : 0.644 8.171 13571 Z= 0.317 Chirality : 0.049 0.483 1489 Planarity : 0.005 0.082 1761 Dihedral : 10.268 145.074 1485 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.99 % Allowed : 15.42 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1224 helix: 1.75 (0.24), residues: 493 sheet: 0.29 (0.35), residues: 240 loop : -1.16 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.007 0.002 HIS B 190 PHE 0.016 0.002 PHE B 367 TYR 0.018 0.002 TYR B 50 ARG 0.004 0.001 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 152 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7803 (mm-30) REVERT: K 159 ASN cc_start: 0.8280 (t0) cc_final: 0.7956 (t0) REVERT: K 210 MET cc_start: 0.7132 (mtp) cc_final: 0.6927 (mtp) REVERT: K 346 ARG cc_start: 0.8422 (mtt90) cc_final: 0.7992 (mmt90) REVERT: A 24 TYR cc_start: 0.8684 (m-10) cc_final: 0.8412 (m-10) REVERT: A 434 GLU cc_start: 0.8214 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 3 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7196 (mt-10) REVERT: B 67 ASP cc_start: 0.8256 (t0) cc_final: 0.7799 (t70) REVERT: B 74 ASP cc_start: 0.8341 (m-30) cc_final: 0.7916 (m-30) REVERT: B 143 THR cc_start: 0.8777 (p) cc_final: 0.8573 (t) REVERT: B 232 THR cc_start: 0.8721 (m) cc_final: 0.8492 (t) REVERT: B 239 CYS cc_start: 0.9141 (m) cc_final: 0.8757 (m) REVERT: B 388 MET cc_start: 0.8593 (mtt) cc_final: 0.8294 (mtp) REVERT: B 417 ASP cc_start: 0.8299 (m-30) cc_final: 0.8060 (m-30) REVERT: B 423 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 424 GLN cc_start: 0.8850 (tt0) cc_final: 0.8471 (tt0) outliers start: 21 outliers final: 16 residues processed: 251 average time/residue: 0.2342 time to fit residues: 81.8485 Evaluate side-chains 244 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.0370 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 190 HIS B 424 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10000 Z= 0.162 Angle : 0.553 6.750 13571 Z= 0.269 Chirality : 0.045 0.367 1489 Planarity : 0.004 0.079 1761 Dihedral : 9.312 145.539 1485 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 2.08 % Allowed : 15.70 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.73 (0.24), residues: 1224 helix: 1.89 (0.24), residues: 495 sheet: 0.58 (0.35), residues: 238 loop : -1.05 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 PHE 0.012 0.001 PHE K 15 TYR 0.016 0.001 TYR K 177 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 31 SER cc_start: 0.7871 (t) cc_final: 0.7513 (p) REVERT: K 42 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: K 86 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7349 (t80) REVERT: K 152 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7778 (mm-30) REVERT: K 159 ASN cc_start: 0.8333 (t0) cc_final: 0.7962 (t0) REVERT: K 327 MET cc_start: 0.8745 (ttp) cc_final: 0.8406 (ttt) REVERT: K 346 ARG cc_start: 0.8368 (mtt90) cc_final: 0.7960 (mmt90) REVERT: A 98 ASP cc_start: 0.6751 (t0) cc_final: 0.6475 (t70) REVERT: A 108 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7166 (p90) REVERT: A 434 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 3 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 67 ASP cc_start: 0.8166 (t0) cc_final: 0.7743 (t70) REVERT: B 108 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 135 LEU cc_start: 0.8708 (tp) cc_final: 0.8501 (tp) REVERT: B 194 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: B 239 CYS cc_start: 0.9108 (m) cc_final: 0.8751 (m) REVERT: B 416 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (m-40) REVERT: B 417 ASP cc_start: 0.8257 (m-30) cc_final: 0.7907 (m-30) REVERT: B 423 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 426 GLN cc_start: 0.8678 (tt0) cc_final: 0.8372 (tt0) outliers start: 22 outliers final: 11 residues processed: 245 average time/residue: 0.2232 time to fit residues: 76.3576 Evaluate side-chains 236 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN B 190 HIS B 256 ASN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10000 Z= 0.197 Angle : 0.557 6.742 13571 Z= 0.272 Chirality : 0.044 0.268 1489 Planarity : 0.004 0.076 1761 Dihedral : 9.121 144.786 1485 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 2.27 % Allowed : 16.18 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.83 (0.24), residues: 1224 helix: 2.01 (0.24), residues: 494 sheet: 0.58 (0.35), residues: 241 loop : -1.01 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 PHE 0.015 0.001 PHE A 255 TYR 0.014 0.001 TYR K 177 ARG 0.003 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 31 SER cc_start: 0.7891 (t) cc_final: 0.7494 (p) REVERT: K 42 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: K 152 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7778 (mm-30) REVERT: K 159 ASN cc_start: 0.8315 (t0) cc_final: 0.7908 (t0) REVERT: K 243 LYS cc_start: 0.8290 (mttt) cc_final: 0.8031 (mttp) REVERT: K 327 MET cc_start: 0.8707 (ttp) cc_final: 0.8413 (ttt) REVERT: K 347 TYR cc_start: 0.8766 (t80) cc_final: 0.8202 (t80) REVERT: A 62 VAL cc_start: 0.8925 (t) cc_final: 0.8575 (m) REVERT: A 108 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7665 (p90) REVERT: A 434 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 3 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7057 (mt-10) REVERT: B 67 ASP cc_start: 0.8154 (t0) cc_final: 0.7748 (t70) REVERT: B 239 CYS cc_start: 0.9088 (m) cc_final: 0.8729 (m) REVERT: B 416 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: B 417 ASP cc_start: 0.8284 (m-30) cc_final: 0.8026 (m-30) REVERT: B 423 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 426 GLN cc_start: 0.8668 (tt0) cc_final: 0.8379 (tt0) outliers start: 24 outliers final: 15 residues processed: 240 average time/residue: 0.2218 time to fit residues: 73.8207 Evaluate side-chains 230 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10000 Z= 0.294 Angle : 0.596 7.168 13571 Z= 0.291 Chirality : 0.046 0.245 1489 Planarity : 0.005 0.075 1761 Dihedral : 9.166 145.163 1485 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.74 % Allowed : 15.61 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.24), residues: 1224 helix: 1.83 (0.24), residues: 493 sheet: 0.54 (0.36), residues: 241 loop : -1.04 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 PHE 0.015 0.002 PHE B 367 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: K 152 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7770 (mm-30) REVERT: K 159 ASN cc_start: 0.8316 (t0) cc_final: 0.7896 (t0) REVERT: K 243 LYS cc_start: 0.8243 (mttt) cc_final: 0.7999 (mttp) REVERT: K 322 ASN cc_start: 0.8281 (t0) cc_final: 0.7919 (t0) REVERT: K 327 MET cc_start: 0.8721 (ttp) cc_final: 0.8436 (ttt) REVERT: K 347 TYR cc_start: 0.8761 (t80) cc_final: 0.8170 (t80) REVERT: A 24 TYR cc_start: 0.8641 (m-10) cc_final: 0.8311 (m-10) REVERT: A 62 VAL cc_start: 0.8946 (t) cc_final: 0.8619 (m) REVERT: A 98 ASP cc_start: 0.6669 (t0) cc_final: 0.6381 (t0) REVERT: A 434 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7892 (mm-30) REVERT: B 3 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 67 ASP cc_start: 0.8220 (t0) cc_final: 0.7790 (t70) REVERT: B 232 THR cc_start: 0.8635 (m) cc_final: 0.8395 (t) REVERT: B 239 CYS cc_start: 0.9133 (m) cc_final: 0.8756 (m) REVERT: B 417 ASP cc_start: 0.8280 (m-30) cc_final: 0.8033 (m-30) REVERT: B 423 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 424 GLN cc_start: 0.8846 (tt0) cc_final: 0.8426 (tt0) REVERT: B 426 GLN cc_start: 0.8690 (tt0) cc_final: 0.8404 (tt0) outliers start: 29 outliers final: 23 residues processed: 246 average time/residue: 0.2208 time to fit residues: 76.1327 Evaluate side-chains 251 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10000 Z= 0.212 Angle : 0.569 8.185 13571 Z= 0.276 Chirality : 0.045 0.214 1489 Planarity : 0.004 0.074 1761 Dihedral : 8.967 144.465 1485 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.37 % Allowed : 15.99 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.73 (0.24), residues: 1224 helix: 1.85 (0.24), residues: 493 sheet: 0.69 (0.36), residues: 233 loop : -1.03 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.007 0.001 HIS B 190 PHE 0.012 0.001 PHE B 367 TYR 0.012 0.001 TYR K 54 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 31 SER cc_start: 0.7914 (t) cc_final: 0.7563 (p) REVERT: K 42 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: K 152 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7773 (mm-30) REVERT: K 159 ASN cc_start: 0.8331 (t0) cc_final: 0.7907 (t0) REVERT: K 174 LEU cc_start: 0.9006 (mt) cc_final: 0.8802 (mt) REVERT: K 243 LYS cc_start: 0.8270 (mttt) cc_final: 0.8019 (mttp) REVERT: K 322 ASN cc_start: 0.8322 (t0) cc_final: 0.7975 (t0) REVERT: K 327 MET cc_start: 0.8688 (ttp) cc_final: 0.8432 (ttt) REVERT: K 347 TYR cc_start: 0.8743 (t80) cc_final: 0.8158 (t80) REVERT: A 3 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7285 (pt0) REVERT: A 62 VAL cc_start: 0.8940 (t) cc_final: 0.8604 (m) REVERT: A 98 ASP cc_start: 0.6659 (t0) cc_final: 0.6408 (t0) REVERT: A 108 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7525 (p90) REVERT: A 398 MET cc_start: 0.8378 (ttp) cc_final: 0.8029 (ttm) REVERT: A 434 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 3 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7096 (mt-10) REVERT: B 67 ASP cc_start: 0.8251 (t0) cc_final: 0.7812 (t70) REVERT: B 232 THR cc_start: 0.8563 (m) cc_final: 0.8295 (t) REVERT: B 239 CYS cc_start: 0.9111 (m) cc_final: 0.8771 (m) REVERT: B 282 ARG cc_start: 0.8663 (ttt90) cc_final: 0.8152 (mtp85) REVERT: B 417 ASP cc_start: 0.8237 (m-30) cc_final: 0.7964 (m-30) REVERT: B 423 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 426 GLN cc_start: 0.8662 (tt0) cc_final: 0.8371 (tt0) outliers start: 25 outliers final: 18 residues processed: 236 average time/residue: 0.2246 time to fit residues: 74.2448 Evaluate side-chains 237 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10000 Z= 0.249 Angle : 0.575 6.996 13571 Z= 0.281 Chirality : 0.045 0.211 1489 Planarity : 0.005 0.074 1761 Dihedral : 8.988 144.556 1485 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.27 % Allowed : 15.80 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.73 (0.24), residues: 1224 helix: 1.86 (0.24), residues: 494 sheet: 0.63 (0.36), residues: 232 loop : -1.01 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS B 190 PHE 0.013 0.001 PHE B 367 TYR 0.012 0.001 TYR K 54 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 31 SER cc_start: 0.7941 (t) cc_final: 0.7617 (p) REVERT: K 42 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: K 110 LYS cc_start: 0.8778 (tppt) cc_final: 0.8574 (tppt) REVERT: K 152 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7770 (mm-30) REVERT: K 159 ASN cc_start: 0.8352 (t0) cc_final: 0.7971 (t0) REVERT: K 174 LEU cc_start: 0.8999 (mt) cc_final: 0.8784 (mt) REVERT: K 243 LYS cc_start: 0.8265 (mttt) cc_final: 0.8007 (mttp) REVERT: K 322 ASN cc_start: 0.8362 (t0) cc_final: 0.8021 (t0) REVERT: K 327 MET cc_start: 0.8720 (ttp) cc_final: 0.8467 (ttt) REVERT: K 347 TYR cc_start: 0.8737 (t80) cc_final: 0.8246 (t80) REVERT: A 3 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7119 (pt0) REVERT: A 24 TYR cc_start: 0.8655 (m-10) cc_final: 0.8347 (m-10) REVERT: A 62 VAL cc_start: 0.8917 (t) cc_final: 0.8584 (m) REVERT: A 69 ASP cc_start: 0.8263 (t0) cc_final: 0.8029 (t70) REVERT: A 98 ASP cc_start: 0.6675 (t0) cc_final: 0.6405 (t0) REVERT: A 108 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7113 (p90) REVERT: A 434 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 3 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 67 ASP cc_start: 0.8292 (t0) cc_final: 0.7858 (t70) REVERT: B 232 THR cc_start: 0.8600 (m) cc_final: 0.8362 (t) REVERT: B 239 CYS cc_start: 0.9113 (m) cc_final: 0.8762 (m) REVERT: B 282 ARG cc_start: 0.8675 (ttt90) cc_final: 0.8160 (mtp85) REVERT: B 417 ASP cc_start: 0.8291 (m-30) cc_final: 0.8002 (m-30) REVERT: B 423 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 424 GLN cc_start: 0.8853 (tt0) cc_final: 0.8438 (tt0) REVERT: B 426 GLN cc_start: 0.8668 (tt0) cc_final: 0.8390 (tt0) outliers start: 24 outliers final: 19 residues processed: 240 average time/residue: 0.2275 time to fit residues: 76.4763 Evaluate side-chains 244 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.0050 chunk 115 optimal weight: 4.9990 overall best weight: 0.5452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10000 Z= 0.150 Angle : 0.547 7.208 13571 Z= 0.265 Chirality : 0.043 0.224 1489 Planarity : 0.004 0.074 1761 Dihedral : 8.737 142.634 1485 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.89 % Allowed : 16.65 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.91 (0.24), residues: 1224 helix: 1.98 (0.24), residues: 495 sheet: 0.75 (0.36), residues: 232 loop : -0.89 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.007 0.001 HIS B 190 PHE 0.014 0.001 PHE A 255 TYR 0.012 0.001 TYR K 150 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 31 SER cc_start: 0.8084 (t) cc_final: 0.7793 (p) REVERT: K 42 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: K 152 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7758 (mm-30) REVERT: K 159 ASN cc_start: 0.8342 (t0) cc_final: 0.7915 (t0) REVERT: K 174 LEU cc_start: 0.8980 (mt) cc_final: 0.8752 (mt) REVERT: K 181 LEU cc_start: 0.8545 (tp) cc_final: 0.8322 (tp) REVERT: K 243 LYS cc_start: 0.8311 (mttt) cc_final: 0.8055 (mttp) REVERT: K 322 ASN cc_start: 0.8342 (t0) cc_final: 0.7979 (t0) REVERT: K 327 MET cc_start: 0.8650 (ttp) cc_final: 0.8442 (ttt) REVERT: K 347 TYR cc_start: 0.8707 (t80) cc_final: 0.8134 (t80) REVERT: A 3 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7293 (pt0) REVERT: A 24 TYR cc_start: 0.8626 (m-10) cc_final: 0.8323 (m-10) REVERT: A 62 VAL cc_start: 0.8918 (t) cc_final: 0.8560 (m) REVERT: A 79 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7818 (mtt180) REVERT: A 103 TYR cc_start: 0.8711 (t80) cc_final: 0.8470 (t80) REVERT: A 108 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7795 (p90) REVERT: A 434 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 3 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7104 (mt-10) REVERT: B 67 ASP cc_start: 0.8263 (t0) cc_final: 0.7838 (t70) REVERT: B 239 CYS cc_start: 0.9044 (m) cc_final: 0.8756 (m) REVERT: B 282 ARG cc_start: 0.8633 (ttt90) cc_final: 0.8087 (mmm160) REVERT: B 336 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8889 (ttpp) REVERT: B 417 ASP cc_start: 0.8208 (m-30) cc_final: 0.7862 (m-30) REVERT: B 423 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 426 GLN cc_start: 0.8608 (tt0) cc_final: 0.8322 (tt0) outliers start: 20 outliers final: 13 residues processed: 238 average time/residue: 0.2177 time to fit residues: 72.1982 Evaluate side-chains 228 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.0870 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10000 Z= 0.174 Angle : 0.572 8.626 13571 Z= 0.277 Chirality : 0.044 0.218 1489 Planarity : 0.005 0.073 1761 Dihedral : 8.743 143.757 1485 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.61 % Allowed : 17.69 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.97 (0.25), residues: 1224 helix: 2.03 (0.24), residues: 498 sheet: 0.71 (0.36), residues: 232 loop : -0.86 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 190 PHE 0.013 0.001 PHE A 255 TYR 0.038 0.001 TYR K 189 ARG 0.011 0.000 ARG A 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: K 31 SER cc_start: 0.7976 (t) cc_final: 0.7704 (p) REVERT: K 42 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: K 125 ASP cc_start: 0.8038 (t0) cc_final: 0.7539 (t0) REVERT: K 152 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7762 (mm-30) REVERT: K 159 ASN cc_start: 0.8357 (t0) cc_final: 0.7922 (t0) REVERT: K 174 LEU cc_start: 0.8952 (mt) cc_final: 0.8722 (mt) REVERT: K 181 LEU cc_start: 0.8550 (tp) cc_final: 0.8330 (tp) REVERT: K 243 LYS cc_start: 0.8312 (mttt) cc_final: 0.8056 (mttp) REVERT: K 322 ASN cc_start: 0.8374 (t0) cc_final: 0.8030 (t0) REVERT: K 347 TYR cc_start: 0.8709 (t80) cc_final: 0.8151 (t80) REVERT: A 3 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7250 (pt0) REVERT: A 24 TYR cc_start: 0.8656 (m-10) cc_final: 0.8383 (m-10) REVERT: A 62 VAL cc_start: 0.8942 (t) cc_final: 0.8586 (m) REVERT: A 79 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7749 (mtt180) REVERT: A 98 ASP cc_start: 0.6663 (t0) cc_final: 0.6422 (t0) REVERT: A 108 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7787 (p90) REVERT: A 434 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 3 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 67 ASP cc_start: 0.8258 (t0) cc_final: 0.7887 (t70) REVERT: B 191 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8675 (mm-40) REVERT: B 239 CYS cc_start: 0.9016 (m) cc_final: 0.8735 (m) REVERT: B 282 ARG cc_start: 0.8624 (ttt90) cc_final: 0.8118 (mtp85) REVERT: B 336 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8895 (ttpp) REVERT: B 417 ASP cc_start: 0.8231 (m-30) cc_final: 0.7916 (m-30) REVERT: B 423 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 424 GLN cc_start: 0.8852 (tt0) cc_final: 0.8480 (tt0) REVERT: B 426 GLN cc_start: 0.8693 (tt0) cc_final: 0.8421 (tt0) outliers start: 17 outliers final: 12 residues processed: 232 average time/residue: 0.2171 time to fit residues: 70.9312 Evaluate side-chains 232 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 42 GLN Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 0.0470 chunk 5 optimal weight: 7.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 59 HIS ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098013 restraints weight = 14377.732| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.38 r_work: 0.3114 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10000 Z= 0.158 Angle : 0.561 7.553 13571 Z= 0.271 Chirality : 0.043 0.221 1489 Planarity : 0.004 0.073 1761 Dihedral : 8.575 144.492 1485 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.80 % Allowed : 17.88 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1224 helix: 2.06 (0.24), residues: 499 sheet: 0.79 (0.36), residues: 231 loop : -0.84 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.007 0.001 HIS B 190 PHE 0.013 0.001 PHE A 255 TYR 0.021 0.001 TYR K 189 ARG 0.010 0.000 ARG A 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.68 seconds wall clock time: 47 minutes 15.73 seconds (2835.73 seconds total)