Starting phenix.real_space_refine on Thu Aug 6 02:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr8_36592/08_2026/8jr8_36592.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 38 5.16 5 C 8247 2.51 5 N 2202 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13127 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 11, 'RNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 11, 'RNA': 7} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3674 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 22, 'TRANS': 432} Chain breaks: 1 Chain: "C" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3674 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 22, 'TRANS': 432} Chain breaks: 1 Chain: "D" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2128 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 243} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2128 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 243} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.01, per 1000 atoms: 0.23 Number of scatterers: 13127 At special positions: 0 Unit cell: (160.65, 92.4, 88.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 75 15.00 O 2565 8.00 N 2202 7.00 C 8247 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: 1.06 Conformation dependent library (CDL) restraints added in 630.7 milliseconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 17 sheets defined 34.5% alpha, 17.2% beta 21 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.887A pdb=" N LYS A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 109 through 131 removed outlier: 3.867A pdb=" N LYS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 4.140A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.602A pdb=" N ARG A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 removed outlier: 3.546A pdb=" N ALA A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.988A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.650A pdb=" N ASP A 371 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 465 removed outlier: 3.929A pdb=" N SER A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.820A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 23 through 30 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.697A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 97 through 104 removed outlier: 3.797A pdb=" N ILE C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 131 removed outlier: 3.623A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 removed outlier: 4.180A pdb=" N TYR C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 3.619A pdb=" N LEU C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 264 removed outlier: 3.941A pdb=" N TRP C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR C 255 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 removed outlier: 3.792A pdb=" N LYS C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.743A pdb=" N ALA C 372 " --> pdb=" O GLN C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 3.658A pdb=" N LYS C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 491 removed outlier: 4.077A pdb=" N ALA C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.628A pdb=" N TYR C 505 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 227 through 233 removed outlier: 3.904A pdb=" N THR D 232 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 233 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 257 through 280 removed outlier: 3.654A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 369 through 385 Processing helix chain 'B' and resid 219 through 226 removed outlier: 4.149A pdb=" N TYR B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS B 226 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.773A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 5.838A pdb=" N LYS A 2 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.873A pdb=" N ILE A 443 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.823A pdb=" N GLY A 45 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 46 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 141 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.526A pdb=" N THR A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.383A pdb=" N LYS C 2 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 171 " --> pdb=" O PHE D 410 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 172 " --> pdb=" O TYR C 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6 removed outlier: 5.441A pdb=" N ILE C 443 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER C 389 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE C 445 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 387 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 357 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 386 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE C 359 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE C 388 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 361 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS C 279 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS C 360 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 281 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 284 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 300 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 286 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.946A pdb=" N CYS C 20 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 12 " --> pdb=" O CYS C 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 95 removed outlier: 6.880A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 141 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.558A pdb=" N VAL D 334 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.670A pdb=" N VAL D 208 " --> pdb=" O CYS D 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AB3, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AB4, first strand: chain 'D' and resid 391 through 393 Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.618A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 291 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY B 325 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.618A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 291 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY B 325 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B 318 " --> pdb=" O THR B 344 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER B 177 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 402 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 208 through 210 Processing sheet with id=AB8, first strand: chain 'B' and resid 304 through 305 416 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3820 1.34 - 1.46: 3500 1.46 - 1.58: 6093 1.58 - 1.70: 146 1.70 - 1.82: 58 Bond restraints: 13617 Sorted by residual: bond pdb=" C3' DA F 11 " pdb=" C2' DA F 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT F 21 " pdb=" C2' DT F 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG F 17 " pdb=" C2' DG F 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 bond pdb=" C3' DA F 16 " pdb=" C2' DA F 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG F 15 " pdb=" C2' DG F 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 ... (remaining 13612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18215 1.92 - 3.85: 426 3.85 - 5.77: 54 5.77 - 7.69: 13 7.69 - 9.62: 4 Bond angle restraints: 18712 Sorted by residual: angle pdb=" O5' U E 15 " pdb=" C5' U E 15 " pdb=" C4' U E 15 " ideal model delta sigma weight residual 109.40 115.57 -6.17 8.00e-01 1.56e+00 5.95e+01 angle pdb=" C5' U E 15 " pdb=" C4' U E 15 " pdb=" O4' U E 15 " ideal model delta sigma weight residual 109.80 104.24 5.56 9.00e-01 1.23e+00 3.81e+01 angle pdb=" O4' U G 17 " pdb=" C1' U G 17 " pdb=" N1 U G 17 " ideal model delta sigma weight residual 108.50 112.81 -4.31 7.00e-01 2.04e+00 3.80e+01 angle pdb=" O5' U E 17 " pdb=" C5' U E 17 " pdb=" C4' U E 17 " ideal model delta sigma weight residual 109.40 113.87 -4.47 8.00e-01 1.56e+00 3.12e+01 angle pdb=" C LYS B 211 " pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 117.23 109.93 7.30 1.36e+00 5.41e-01 2.88e+01 ... (remaining 18707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 7537 35.29 - 70.57: 438 70.57 - 105.86: 13 105.86 - 141.14: 3 141.14 - 176.43: 7 Dihedral angle restraints: 7998 sinusoidal: 3838 harmonic: 4160 Sorted by residual: dihedral pdb=" CA ILE D 170 " pdb=" C ILE D 170 " pdb=" N TYR D 171 " pdb=" CA TYR D 171 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLY C 318 " pdb=" C GLY C 318 " pdb=" N PRO C 319 " pdb=" CA PRO C 319 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DA H 16 " pdb=" C3' DA H 16 " pdb=" O3' DA H 16 " pdb=" P DG H 17 " ideal model delta sinusoidal sigma weight residual -140.00 36.43 -176.43 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1587 0.053 - 0.106: 353 0.106 - 0.159: 59 0.159 - 0.212: 5 0.212 - 0.266: 4 Chirality restraints: 2008 Sorted by residual: chirality pdb=" C1' U G 1 " pdb=" O4' U G 1 " pdb=" C2' U G 1 " pdb=" N1 U G 1 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1' U G 18 " pdb=" O4' U G 18 " pdb=" C2' U G 18 " pdb=" N1 U G 18 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2005 not shown) Planarity restraints: 2105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 392 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 393 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 319 " -0.012 2.00e-02 2.50e+03 1.27e-02 4.01e+00 pdb=" CG TRP D 319 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 319 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 319 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 319 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 319 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 319 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 319 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 319 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 319 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 181 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO D 182 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " 0.028 5.00e-02 4.00e+02 ... (remaining 2102 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 458 2.68 - 3.24: 13211 3.24 - 3.79: 22837 3.79 - 4.35: 29665 4.35 - 4.90: 45198 Nonbonded interactions: 111369 Sorted by model distance: nonbonded pdb=" OG SER A 417 " pdb=" OH TYR B 330 " model vdw 2.125 3.040 nonbonded pdb=" OH TYR D 233 " pdb=" O LYS D 237 " model vdw 2.184 3.040 nonbonded pdb=" OG SER C 417 " pdb=" OH TYR D 330 " model vdw 2.216 3.040 nonbonded pdb=" O TRP C 254 " pdb=" OG1 THR C 258 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR D 204 " pdb=" OH TYR D 225 " model vdw 2.236 3.040 ... (remaining 111364 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 1 through 17) } ncs_group { reference = chain 'F' selection = chain 'H' } 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=0.87 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: 0.960 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.330 Find NCS groups from input model: 0.180 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.040 13617 Z= 0.263 Angle : 0.700 9.618 18712 Z= 0.467 Chirality : 0.047 0.266 2008 Planarity : 0.004 0.055 2105 Dihedral : 20.309 176.431 5318 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.40 % Allowed : 32.86 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1402 helix: -0.35 (0.25), residues: 421 sheet: -1.60 (0.33), residues: 261 loop : -1.39 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 407 TYR 0.014 0.001 TYR D 383 PHE 0.028 0.001 PHE D 380 TRP 0.034 0.002 TRP D 319 HIS 0.023 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.26 (13617) covalent geometry : angle 0.69960 / 0.47 (18712) hydrogen bonds : bond 0.28488 / 30.76 ( 456) hydrogen bonds : angle 9.44629 / 12.72 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8824 (t0) cc_final: 0.8514 (t0) REVERT: C 85 LYS cc_start: 0.8224 (tppt) cc_final: 0.8015 (tppt) REVERT: C 267 LYS cc_start: 0.7388 (tptt) cc_final: 0.6664 (tptp) REVERT: C 403 TYR cc_start: 0.7283 (p90) cc_final: 0.6624 (p90) REVERT: D 183 GLU cc_start: 0.9071 (tp30) cc_final: 0.8828 (tp30) REVERT: B 234 HIS cc_start: 0.8616 (t70) cc_final: 0.8101 (m-70) outliers start: 5 outliers final: 4 residues processed: 129 average time/residue: 0.1091 time to fit residues: 20.3394 Evaluate side-chains 121 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS A 205 GLN A 217 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 468 ASN C 349 GLN C 446 ASN D 358 HIS ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.105358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082399 restraints weight = 40532.172| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.24 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13617 Z= 0.208 Angle : 0.695 8.378 18712 Z= 0.382 Chirality : 0.048 0.237 2008 Planarity : 0.005 0.059 2105 Dihedral : 19.680 179.894 2446 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.52 % Allowed : 29.37 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.22), residues: 1402 helix: -0.17 (0.24), residues: 430 sheet: -1.53 (0.33), residues: 255 loop : -1.41 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 407 TYR 0.014 0.001 TYR D 330 PHE 0.015 0.002 PHE D 342 TRP 0.025 0.002 TRP D 319 HIS 0.012 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (13617) covalent geometry : angle 0.69537 / 0.38 (18712) hydrogen bonds : bond 0.06976 / 7.42 ( 456) hydrogen bonds : angle 6.46068 / 8.95 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 134 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8755 (t0) cc_final: 0.8402 (t0) REVERT: A 95 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: A 464 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7560 (tppt) REVERT: C 85 LYS cc_start: 0.8406 (tppt) cc_final: 0.8106 (tppt) REVERT: D 231 GLU cc_start: 0.8690 (pm20) cc_final: 0.8470 (pm20) REVERT: D 283 GLN cc_start: 0.7805 (mp10) cc_final: 0.7473 (mp10) REVERT: D 376 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9138 (mttp) REVERT: D 394 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: B 179 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 193 MET cc_start: 0.4072 (ppp) cc_final: 0.3698 (ppp) REVERT: B 234 HIS cc_start: 0.8542 (t70) cc_final: 0.8046 (m-70) REVERT: B 235 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8299 (tppt) REVERT: B 294 TRP cc_start: 0.8252 (p-90) cc_final: 0.7482 (p-90) outliers start: 57 outliers final: 32 residues processed: 177 average time/residue: 0.0944 time to fit residues: 24.6202 Evaluate side-chains 159 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 0.0670 chunk 60 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS B 314 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.105791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.083250 restraints weight = 40270.107| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.16 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13617 Z= 0.174 Angle : 0.651 9.339 18712 Z= 0.355 Chirality : 0.046 0.221 2008 Planarity : 0.005 0.052 2105 Dihedral : 19.608 178.701 2443 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.71 % Allowed : 28.65 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1402 helix: -0.15 (0.24), residues: 434 sheet: -1.55 (0.33), residues: 261 loop : -1.34 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 374 TYR 0.021 0.001 TYR D 171 PHE 0.013 0.001 PHE D 343 TRP 0.022 0.001 TRP D 319 HIS 0.013 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (13617) covalent geometry : angle 0.65134 / 0.36 (18712) hydrogen bonds : bond 0.05914 / 6.38 ( 456) hydrogen bonds : angle 5.97467 / 8.27 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8813 (t0) cc_final: 0.8422 (t0) REVERT: A 79 GLU cc_start: 0.8045 (tp30) cc_final: 0.7641 (tp30) REVERT: A 95 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 464 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7588 (tppt) REVERT: C 4 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8440 (mt) REVERT: C 72 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6530 (ptt-90) REVERT: C 85 LYS cc_start: 0.8554 (tppt) cc_final: 0.8218 (tppt) REVERT: C 267 LYS cc_start: 0.7404 (tptt) cc_final: 0.6788 (tptp) REVERT: C 504 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8875 (ptmm) REVERT: D 231 GLU cc_start: 0.8605 (pm20) cc_final: 0.8376 (pm20) REVERT: D 350 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (mp) REVERT: D 376 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9077 (mttp) REVERT: B 229 LYS cc_start: 0.5718 (pptt) cc_final: 0.4854 (tptt) REVERT: B 234 HIS cc_start: 0.8502 (t70) cc_final: 0.8021 (m-70) REVERT: B 235 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: B 284 GLU cc_start: 0.7897 (mp0) cc_final: 0.7451 (mp0) REVERT: B 294 TRP cc_start: 0.8158 (p-90) cc_final: 0.7507 (p-90) REVERT: B 332 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8210 (p90) outliers start: 72 outliers final: 44 residues processed: 190 average time/residue: 0.1106 time to fit residues: 30.5546 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 32 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.105136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082436 restraints weight = 40409.755| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.16 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13617 Z= 0.197 Angle : 0.654 9.644 18712 Z= 0.356 Chirality : 0.046 0.238 2008 Planarity : 0.005 0.049 2105 Dihedral : 19.611 178.612 2442 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.11 % Allowed : 28.33 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.23), residues: 1402 helix: -0.05 (0.25), residues: 428 sheet: -1.59 (0.32), residues: 261 loop : -1.30 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 201 TYR 0.017 0.001 TYR D 171 PHE 0.011 0.001 PHE D 205 TRP 0.021 0.001 TRP D 319 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (13617) covalent geometry : angle 0.65367 / 0.36 (18712) hydrogen bonds : bond 0.05468 / 5.84 ( 456) hydrogen bonds : angle 5.77395 / 7.99 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 129 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8869 (t0) cc_final: 0.8532 (t0) REVERT: A 79 GLU cc_start: 0.8065 (tp30) cc_final: 0.7743 (tp30) REVERT: A 95 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: A 464 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7597 (tppt) REVERT: C 4 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 72 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6588 (ptt-90) REVERT: C 85 LYS cc_start: 0.8606 (tppt) cc_final: 0.8343 (tppt) REVERT: C 504 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8854 (ptmm) REVERT: D 167 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7111 (ptpt) REVERT: D 179 LEU cc_start: 0.9114 (pt) cc_final: 0.8902 (pt) REVERT: D 231 GLU cc_start: 0.8587 (pm20) cc_final: 0.8369 (pm20) REVERT: D 350 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8040 (mp) REVERT: D 376 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9068 (mttp) REVERT: B 179 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 229 LYS cc_start: 0.5840 (pptt) cc_final: 0.4666 (tptt) REVERT: B 234 HIS cc_start: 0.8579 (t70) cc_final: 0.8302 (t70) REVERT: B 284 GLU cc_start: 0.7831 (mp0) cc_final: 0.7402 (mp0) REVERT: B 294 TRP cc_start: 0.8116 (p-90) cc_final: 0.7540 (p-90) REVERT: B 332 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8240 (p90) outliers start: 77 outliers final: 52 residues processed: 186 average time/residue: 0.1045 time to fit residues: 28.3813 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.104449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.081652 restraints weight = 40666.534| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.19 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13617 Z= 0.218 Angle : 0.665 10.233 18712 Z= 0.360 Chirality : 0.047 0.284 2008 Planarity : 0.005 0.052 2105 Dihedral : 19.640 179.368 2442 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.83 % Allowed : 28.10 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.23), residues: 1402 helix: -0.01 (0.25), residues: 428 sheet: -1.61 (0.32), residues: 257 loop : -1.34 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 363 TYR 0.022 0.002 TYR D 171 PHE 0.012 0.001 PHE D 205 TRP 0.024 0.002 TRP D 319 HIS 0.014 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (13617) covalent geometry : angle 0.66491 / 0.36 (18712) hydrogen bonds : bond 0.05307 / 5.65 ( 456) hydrogen bonds : angle 5.67853 / 7.86 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 125 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8113 (tp30) cc_final: 0.7795 (tp30) REVERT: A 95 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 303 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.5590 (ttm) REVERT: A 464 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7686 (tppt) REVERT: C 4 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (mt) REVERT: C 72 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6592 (ptt-90) REVERT: C 85 LYS cc_start: 0.8636 (tppt) cc_final: 0.8406 (tppt) REVERT: C 267 LYS cc_start: 0.7371 (tptt) cc_final: 0.6873 (tptp) REVERT: C 504 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8858 (ptmm) REVERT: D 167 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7248 (ptpt) REVERT: D 231 GLU cc_start: 0.8550 (pm20) cc_final: 0.8339 (pm20) REVERT: D 350 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8099 (mp) REVERT: D 376 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9085 (mttp) REVERT: B 179 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 234 HIS cc_start: 0.8622 (t70) cc_final: 0.8309 (t70) REVERT: B 284 GLU cc_start: 0.7927 (mp0) cc_final: 0.7506 (mp0) REVERT: B 294 TRP cc_start: 0.8165 (p-90) cc_final: 0.7615 (p-90) REVERT: B 332 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8291 (p90) outliers start: 86 outliers final: 62 residues processed: 189 average time/residue: 0.0964 time to fit residues: 27.0696 Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 118 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 434 SER Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 133 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 0.0570 chunk 111 optimal weight: 10.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 468 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.107070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084697 restraints weight = 39816.653| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.20 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13617 Z= 0.137 Angle : 0.628 9.366 18712 Z= 0.337 Chirality : 0.046 0.223 2008 Planarity : 0.004 0.053 2105 Dihedral : 19.603 177.845 2442 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.16 % Allowed : 29.44 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 1402 helix: 0.17 (0.25), residues: 426 sheet: -1.49 (0.33), residues: 262 loop : -1.25 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 54 TYR 0.017 0.001 TYR D 171 PHE 0.013 0.001 PHE D 343 TRP 0.026 0.001 TRP D 319 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (13617) covalent geometry : angle 0.62763 / 0.34 (18712) hydrogen bonds : bond 0.04838 / 5.12 ( 456) hydrogen bonds : angle 5.41148 / 7.48 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8876 (t0) cc_final: 0.8583 (t0) REVERT: A 79 GLU cc_start: 0.8060 (tp30) cc_final: 0.7746 (tp30) REVERT: A 95 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: A 219 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8431 (tp) REVERT: A 435 MET cc_start: 0.7079 (ttt) cc_final: 0.5991 (ptm) REVERT: A 464 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7596 (tppt) REVERT: C 4 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8458 (mt) REVERT: C 267 LYS cc_start: 0.7235 (tptt) cc_final: 0.6665 (tptp) REVERT: C 504 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8884 (ptmm) REVERT: D 167 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7151 (ptpt) REVERT: D 231 GLU cc_start: 0.8516 (pm20) cc_final: 0.8300 (pm20) REVERT: D 277 MET cc_start: 0.7610 (mmp) cc_final: 0.7383 (mmp) REVERT: D 376 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9010 (mttp) REVERT: B 229 LYS cc_start: 0.5340 (pptt) cc_final: 0.4620 (tptt) REVERT: B 234 HIS cc_start: 0.8656 (t70) cc_final: 0.8322 (t70) REVERT: B 284 GLU cc_start: 0.7974 (mp0) cc_final: 0.7643 (mp0) REVERT: B 294 TRP cc_start: 0.8134 (p-90) cc_final: 0.7550 (p-90) REVERT: B 332 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8291 (p90) REVERT: B 367 ASN cc_start: 0.8131 (p0) cc_final: 0.7905 (p0) outliers start: 65 outliers final: 44 residues processed: 194 average time/residue: 0.1053 time to fit residues: 30.2602 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.106394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.083944 restraints weight = 40044.911| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.20 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13617 Z= 0.153 Angle : 0.646 9.696 18712 Z= 0.345 Chirality : 0.046 0.218 2008 Planarity : 0.004 0.053 2105 Dihedral : 19.573 177.830 2442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.24 % Allowed : 29.68 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.23), residues: 1402 helix: 0.18 (0.25), residues: 427 sheet: -1.41 (0.34), residues: 252 loop : -1.21 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.022 0.001 TYR D 210 PHE 0.012 0.001 PHE B 380 TRP 0.026 0.001 TRP D 319 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (13617) covalent geometry : angle 0.64592 / 0.34 (18712) hydrogen bonds : bond 0.04750 / 5.05 ( 456) hydrogen bonds : angle 5.33788 / 7.35 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8849 (t0) cc_final: 0.8537 (t0) REVERT: A 79 GLU cc_start: 0.8012 (tp30) cc_final: 0.7717 (tp30) REVERT: A 303 MET cc_start: 0.6353 (ttm) cc_final: 0.6049 (ttm) REVERT: A 435 MET cc_start: 0.7281 (ttt) cc_final: 0.6342 (ptm) REVERT: A 464 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7602 (tppt) REVERT: C 4 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8370 (mt) REVERT: C 72 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6538 (ptt-90) REVERT: C 267 LYS cc_start: 0.7257 (tptt) cc_final: 0.6708 (tptp) REVERT: C 504 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (ptmm) REVERT: D 167 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7259 (ptpt) REVERT: D 231 GLU cc_start: 0.8550 (pm20) cc_final: 0.8342 (pm20) REVERT: D 376 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9006 (mttp) REVERT: B 179 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8529 (mm) REVERT: B 234 HIS cc_start: 0.8643 (t70) cc_final: 0.8294 (t70) REVERT: B 284 GLU cc_start: 0.7974 (mp0) cc_final: 0.7693 (mp0) REVERT: B 294 TRP cc_start: 0.8098 (p-90) cc_final: 0.7585 (p-90) REVERT: B 332 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8342 (p90) REVERT: B 366 LYS cc_start: 0.8616 (ptmt) cc_final: 0.7646 (ptmt) REVERT: B 367 ASN cc_start: 0.8149 (p0) cc_final: 0.7928 (p0) outliers start: 66 outliers final: 48 residues processed: 187 average time/residue: 0.0985 time to fit residues: 27.5030 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN D 358 HIS ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.107382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.085080 restraints weight = 39696.040| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.20 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13617 Z= 0.136 Angle : 0.643 9.421 18712 Z= 0.342 Chirality : 0.046 0.218 2008 Planarity : 0.004 0.056 2105 Dihedral : 19.543 177.468 2442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.00 % Allowed : 29.76 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1402 helix: 0.25 (0.25), residues: 427 sheet: -1.24 (0.34), residues: 245 loop : -1.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.020 0.001 TYR D 210 PHE 0.019 0.001 PHE B 380 TRP 0.039 0.002 TRP D 219 HIS 0.015 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (13617) covalent geometry : angle 0.64343 / 0.34 (18712) hydrogen bonds : bond 0.04559 / 4.82 ( 456) hydrogen bonds : angle 5.24148 / 7.21 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8842 (t0) cc_final: 0.8534 (t0) REVERT: A 79 GLU cc_start: 0.8121 (tp30) cc_final: 0.7883 (tp30) REVERT: A 435 MET cc_start: 0.7229 (ttt) cc_final: 0.6336 (ptm) REVERT: A 464 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7553 (tppt) REVERT: C 243 ARG cc_start: 0.5928 (pmt170) cc_final: 0.5648 (pmt170) REVERT: C 504 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8796 (ptmm) REVERT: D 167 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7227 (ptpt) REVERT: D 231 GLU cc_start: 0.8526 (pm20) cc_final: 0.8315 (pm20) REVERT: D 277 MET cc_start: 0.7548 (mmp) cc_final: 0.7173 (mmp) REVERT: D 350 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8039 (mt) REVERT: D 376 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8769 (mttp) REVERT: B 179 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 234 HIS cc_start: 0.8640 (t70) cc_final: 0.8291 (t70) REVERT: B 284 GLU cc_start: 0.7954 (mp0) cc_final: 0.7662 (mp0) REVERT: B 294 TRP cc_start: 0.8041 (p-90) cc_final: 0.7517 (p-90) REVERT: B 332 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8363 (p90) REVERT: B 367 ASN cc_start: 0.8128 (p0) cc_final: 0.7922 (p0) outliers start: 63 outliers final: 46 residues processed: 187 average time/residue: 0.1021 time to fit residues: 28.0006 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.105129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082592 restraints weight = 40302.955| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.18 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13617 Z= 0.212 Angle : 0.680 9.061 18712 Z= 0.361 Chirality : 0.047 0.278 2008 Planarity : 0.005 0.052 2105 Dihedral : 19.543 177.805 2442 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 5.00 % Allowed : 29.60 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1402 helix: 0.20 (0.25), residues: 429 sheet: -1.30 (0.34), residues: 244 loop : -1.28 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 363 TYR 0.017 0.001 TYR D 210 PHE 0.016 0.001 PHE B 380 TRP 0.042 0.002 TRP D 219 HIS 0.037 0.002 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (13617) covalent geometry : angle 0.67953 / 0.36 (18712) hydrogen bonds : bond 0.04830 / 5.16 ( 456) hydrogen bonds : angle 5.32243 / 7.32 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8095 (tp30) cc_final: 0.7857 (tp30) REVERT: A 303 MET cc_start: 0.6638 (ttm) cc_final: 0.6377 (mtp) REVERT: A 435 MET cc_start: 0.7327 (ttt) cc_final: 0.6423 (ptm) REVERT: C 72 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6594 (ptt-90) REVERT: C 267 LYS cc_start: 0.7253 (tptt) cc_final: 0.6748 (tptp) REVERT: C 344 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: C 504 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8846 (ptmm) REVERT: D 167 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7276 (ptpt) REVERT: D 231 GLU cc_start: 0.8581 (pm20) cc_final: 0.8373 (pm20) REVERT: D 277 MET cc_start: 0.7626 (mmp) cc_final: 0.7252 (mmp) REVERT: D 350 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8102 (mp) REVERT: D 376 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8812 (mttp) REVERT: B 179 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 234 HIS cc_start: 0.8691 (t70) cc_final: 0.8350 (t70) REVERT: B 294 TRP cc_start: 0.8076 (p-90) cc_final: 0.7535 (p-90) REVERT: B 332 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8385 (p90) outliers start: 63 outliers final: 48 residues processed: 175 average time/residue: 0.0920 time to fit residues: 24.0148 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 133 optimal weight: 0.0060 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.106776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.084346 restraints weight = 39942.113| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.27 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13617 Z= 0.137 Angle : 0.658 8.395 18712 Z= 0.348 Chirality : 0.046 0.233 2008 Planarity : 0.004 0.056 2105 Dihedral : 19.526 177.771 2442 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.29 % Allowed : 30.56 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1402 helix: 0.28 (0.25), residues: 429 sheet: -1.14 (0.35), residues: 237 loop : -1.25 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 363 TYR 0.018 0.001 TYR D 210 PHE 0.012 0.001 PHE B 380 TRP 0.041 0.002 TRP D 219 HIS 0.006 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (13617) covalent geometry : angle 0.65776 / 0.35 (18712) hydrogen bonds : bond 0.04479 / 4.78 ( 456) hydrogen bonds : angle 5.19880 / 7.14 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8117 (tp30) cc_final: 0.7848 (tp30) REVERT: A 435 MET cc_start: 0.7302 (ttt) cc_final: 0.6552 (ptm) REVERT: A 464 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7565 (tppt) REVERT: C 72 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6359 (ptt-90) REVERT: C 243 ARG cc_start: 0.5828 (pmt170) cc_final: 0.5628 (pmt170) REVERT: C 267 LYS cc_start: 0.7186 (tptt) cc_final: 0.6629 (tptp) REVERT: C 344 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: C 504 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8803 (ptmm) REVERT: D 167 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7310 (ptpt) REVERT: D 231 GLU cc_start: 0.8587 (pm20) cc_final: 0.8379 (pm20) REVERT: D 277 MET cc_start: 0.7573 (mmp) cc_final: 0.7205 (mmp) REVERT: D 350 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (mt) REVERT: D 376 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8768 (mttp) REVERT: B 179 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8527 (mm) REVERT: B 187 PHE cc_start: 0.8350 (m-80) cc_final: 0.7447 (m-80) REVERT: B 234 HIS cc_start: 0.8736 (t70) cc_final: 0.8392 (t70) REVERT: B 284 GLU cc_start: 0.7690 (mp0) cc_final: 0.7107 (mp0) REVERT: B 294 TRP cc_start: 0.8096 (p-90) cc_final: 0.7470 (p-90) REVERT: B 332 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8477 (p90) outliers start: 54 outliers final: 40 residues processed: 178 average time/residue: 0.1135 time to fit residues: 29.7976 Evaluate side-chains 177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.104058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.081375 restraints weight = 40443.168| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.19 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13617 Z= 0.255 Angle : 0.715 9.795 18712 Z= 0.381 Chirality : 0.048 0.261 2008 Planarity : 0.005 0.050 2105 Dihedral : 19.551 178.655 2442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 4.37 % Allowed : 30.87 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 1402 helix: 0.12 (0.25), residues: 430 sheet: -1.42 (0.33), residues: 244 loop : -1.29 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 363 TYR 0.016 0.002 TYR D 210 PHE 0.017 0.002 PHE D 342 TRP 0.035 0.002 TRP D 219 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (13617) covalent geometry : angle 0.71542 / 0.38 (18712) hydrogen bonds : bond 0.04955 / 5.32 ( 456) hydrogen bonds : angle 5.39209 / 7.39 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.62 seconds wall clock time: 34 minutes 52.64 seconds (2092.64 seconds total)