Starting phenix.real_space_refine on Thu Jul 31 04:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_36592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_36592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_36592.map" model { file = "/net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_36592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr8_36592/07_2025/8jr8_36592.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.98, per 1000 atoms: 0.61 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: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.52 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: 4.84 Time building geometry restraints manager: 3.63 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=" C GLU B 169 " pdb=" N ILE B 170 " ideal model delta sigma weight residual 1.334 1.315 0.018 1.24e-02 6.50e+03 2.17e+00 bond pdb=" CA ILE C 64 " pdb=" CB ILE C 64 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.08e+00 bond pdb=" CD LYS C 11 " pdb=" CE LYS C 11 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" C THR A 498 " pdb=" O THR A 498 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.60e+00 bond pdb=" CA MET B 193 " pdb=" CB MET B 193 " ideal model delta sigma weight residual 1.535 1.555 -0.020 1.64e-02 3.72e+03 1.45e+00 ... (remaining 13612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18283 1.92 - 3.85: 367 3.85 - 5.77: 46 5.77 - 7.69: 12 7.69 - 9.62: 4 Bond angle restraints: 18712 Sorted by residual: 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 angle pdb=" CA LYS B 211 " pdb=" C LYS B 211 " pdb=" N ASN B 212 " ideal model delta sigma weight residual 119.98 116.40 3.58 8.50e-01 1.38e+00 1.77e+01 angle pdb=" N PRO C 10 " pdb=" CD PRO C 10 " pdb=" CG PRO C 10 " ideal model delta sigma weight residual 103.20 98.20 5.00 1.50e+00 4.44e-01 1.11e+01 angle pdb=" CA MET B 193 " pdb=" CB MET B 193 " pdb=" CG MET B 193 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB MET B 193 " pdb=" CG MET B 193 " pdb=" SD MET B 193 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+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 - 0.050: 1617 0.050 - 0.100: 311 0.100 - 0.150: 70 0.150 - 0.200: 5 0.200 - 0.250: 5 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 2.46 2.21 0.25 2.00e-01 2.50e+01 1.57e+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 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+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 2.46 2.24 0.22 2.00e-01 2.50e+01 1.16e+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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13617 Z= 0.140 Angle : 0.659 9.618 18712 Z= 0.344 Chirality : 0.043 0.250 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.034 0.002 TRP D 319 HIS 0.023 0.001 HIS B 226 PHE 0.028 0.001 PHE D 380 TYR 0.014 0.001 TYR D 383 ARG 0.009 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.28488 ( 456) hydrogen bonds : angle 9.44629 ( 1242) covalent geometry : bond 0.00309 (13617) covalent geometry : angle 0.65935 (18712) *********************** 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 : 1.906 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: 0.3337 time to fit residues: 61.5675 Evaluate side-chains 120 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 123 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 205 GLN ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN A 468 ASN C 349 GLN C 360 HIS 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 = 0.3936 r_free = 0.3936 target = 0.104921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082158 restraints weight = 39788.492| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.18 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 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 = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.040 13617 Z= 0.210 Angle : 0.678 9.382 18712 Z= 0.352 Chirality : 0.048 0.342 2008 Planarity : 0.005 0.058 2105 Dihedral : 19.777 177.038 2446 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.16 % Allowed : 28.33 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1402 helix: -0.04 (0.25), residues: 434 sheet: -1.50 (0.33), residues: 263 loop : -1.38 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 319 HIS 0.010 0.001 HIS D 358 PHE 0.014 0.001 PHE D 343 TYR 0.014 0.001 TYR D 225 ARG 0.005 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.05734 ( 456) hydrogen bonds : angle 6.13960 ( 1242) covalent geometry : bond 0.00473 (13617) covalent geometry : angle 0.67820 (18712) *********************** 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 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8802 (t0) cc_final: 0.8484 (t0) REVERT: A 95 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 430 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: A 464 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7619 (tppt) REVERT: C 249 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: D 231 GLU cc_start: 0.8646 (pm20) cc_final: 0.8439 (pm20) REVERT: D 350 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 376 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9067 (mttp) REVERT: D 394 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: B 234 HIS cc_start: 0.8552 (t70) cc_final: 0.8035 (m-70) REVERT: B 235 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8307 (tppt) REVERT: B 294 TRP cc_start: 0.8203 (p-90) cc_final: 0.7367 (p-90) REVERT: B 332 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8163 (p90) outliers start: 65 outliers final: 37 residues processed: 188 average time/residue: 0.2694 time to fit residues: 73.6982 Evaluate side-chains 166 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 462 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 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 249 GLU 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 357 VAL 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 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 356 VAL Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 394 GLU 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 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 53 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085099 restraints weight = 40040.830| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.23 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13617 Z= 0.140 Angle : 0.618 9.463 18712 Z= 0.317 Chirality : 0.046 0.324 2008 Planarity : 0.004 0.057 2105 Dihedral : 19.712 178.627 2446 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.00 % Allowed : 28.97 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1402 helix: 0.13 (0.25), residues: 430 sheet: -1.35 (0.33), residues: 257 loop : -1.26 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 319 HIS 0.010 0.001 HIS D 358 PHE 0.011 0.001 PHE D 343 TYR 0.015 0.001 TYR D 210 ARG 0.004 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 456) hydrogen bonds : angle 5.46516 ( 1242) covalent geometry : bond 0.00312 (13617) covalent geometry : angle 0.61758 (18712) *********************** 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 217 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8783 (t0) cc_final: 0.8434 (t0) REVERT: A 95 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: C 54 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.7921 (mtp85) REVERT: C 72 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6446 (ptp90) REVERT: C 85 LYS cc_start: 0.8436 (tppt) cc_final: 0.8151 (tppt) REVERT: D 167 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7055 (ptpt) REVERT: D 231 GLU cc_start: 0.8544 (pm20) cc_final: 0.8344 (pm20) REVERT: D 277 MET cc_start: 0.7716 (mmp) cc_final: 0.7298 (mmp) REVERT: D 309 MET cc_start: 0.7121 (mpp) cc_final: 0.6766 (mpp) REVERT: D 376 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8993 (mttp) REVERT: B 179 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (mm) REVERT: B 234 HIS cc_start: 0.8609 (t70) cc_final: 0.8285 (t70) REVERT: B 284 GLU cc_start: 0.7787 (mp0) cc_final: 0.7311 (mp0) REVERT: B 294 TRP cc_start: 0.8053 (p-90) cc_final: 0.7255 (p-90) REVERT: B 332 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8298 (p90) outliers start: 63 outliers final: 35 residues processed: 202 average time/residue: 0.3030 time to fit residues: 88.8225 Evaluate side-chains 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 219 ILE 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 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 338 LEU Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL 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 295 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 391 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** 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 = 0.3961 r_free = 0.3961 target = 0.107281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084793 restraints weight = 39652.347| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.30 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13617 Z= 0.134 Angle : 0.613 9.883 18712 Z= 0.312 Chirality : 0.045 0.318 2008 Planarity : 0.004 0.054 2105 Dihedral : 19.618 179.281 2442 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.76 % Allowed : 29.05 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.23), residues: 1402 helix: 0.31 (0.25), residues: 428 sheet: -1.30 (0.33), residues: 262 loop : -1.20 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 319 HIS 0.012 0.001 HIS D 358 PHE 0.010 0.001 PHE D 343 TYR 0.015 0.001 TYR B 330 ARG 0.004 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 456) hydrogen bonds : angle 5.17107 ( 1242) covalent geometry : bond 0.00302 (13617) covalent geometry : angle 0.61284 (18712) *********************** 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 204 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8728 (t0) cc_final: 0.8414 (t0) REVERT: A 79 GLU cc_start: 0.8016 (tp30) cc_final: 0.7512 (tp30) REVERT: A 95 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: A 303 MET cc_start: 0.6525 (ttm) cc_final: 0.6218 (tpp) REVERT: A 435 MET cc_start: 0.7003 (ttt) cc_final: 0.5933 (ptm) REVERT: C 72 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6270 (ptp90) REVERT: C 85 LYS cc_start: 0.8529 (tppt) cc_final: 0.8234 (tppt) REVERT: D 167 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7164 (ptpt) REVERT: D 309 MET cc_start: 0.7293 (mpp) cc_final: 0.6946 (mpp) REVERT: D 376 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8993 (mttp) REVERT: D 394 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: B 179 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8447 (mm) REVERT: B 185 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8081 (pp) REVERT: B 187 PHE cc_start: 0.8336 (m-80) cc_final: 0.7406 (m-80) REVERT: B 234 HIS cc_start: 0.8674 (t70) cc_final: 0.8322 (t70) REVERT: B 284 GLU cc_start: 0.7903 (mp0) cc_final: 0.7666 (mp0) REVERT: B 294 TRP cc_start: 0.8116 (p-90) cc_final: 0.7326 (p-90) REVERT: B 332 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8401 (p90) REVERT: B 366 LYS cc_start: 0.8327 (ptmm) cc_final: 0.8114 (ptmm) outliers start: 60 outliers final: 40 residues processed: 192 average time/residue: 0.2451 time to fit residues: 69.3108 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 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 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 295 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.107190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084537 restraints weight = 40018.455| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 4.33 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13617 Z= 0.140 Angle : 0.607 9.973 18712 Z= 0.309 Chirality : 0.045 0.321 2008 Planarity : 0.004 0.053 2105 Dihedral : 19.590 179.965 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.32 % Allowed : 28.81 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1402 helix: 0.39 (0.25), residues: 428 sheet: -1.11 (0.35), residues: 248 loop : -1.20 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 319 HIS 0.003 0.001 HIS D 340 PHE 0.012 0.001 PHE B 380 TYR 0.010 0.001 TYR D 210 ARG 0.004 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 456) hydrogen bonds : angle 5.03584 ( 1242) covalent geometry : bond 0.00319 (13617) covalent geometry : angle 0.60733 (18712) *********************** 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 207 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8769 (t0) cc_final: 0.8423 (t0) REVERT: A 79 GLU cc_start: 0.8030 (tp30) cc_final: 0.7533 (tp30) REVERT: A 95 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: A 303 MET cc_start: 0.6580 (ttm) cc_final: 0.6326 (ttm) REVERT: A 435 MET cc_start: 0.7168 (ttt) cc_final: 0.5991 (ptm) REVERT: C 72 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6444 (ptp90) REVERT: C 85 LYS cc_start: 0.8477 (tppt) cc_final: 0.8221 (tppt) REVERT: C 249 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: C 403 TYR cc_start: 0.6710 (p90) cc_final: 0.6206 (p90) REVERT: C 504 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8864 (ptmm) REVERT: D 167 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7261 (ptpt) REVERT: D 231 GLU cc_start: 0.8532 (pm20) cc_final: 0.8303 (pm20) REVERT: D 277 MET cc_start: 0.7583 (mmp) cc_final: 0.7295 (mmp) REVERT: D 294 TRP cc_start: 0.7733 (p-90) cc_final: 0.7336 (p-90) REVERT: D 309 MET cc_start: 0.7291 (mpp) cc_final: 0.6932 (mpp) REVERT: D 350 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8096 (mt) REVERT: D 376 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8992 (mttp) REVERT: D 394 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: B 179 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (mm) REVERT: B 185 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8075 (pp) REVERT: B 187 PHE cc_start: 0.8256 (m-80) cc_final: 0.7322 (m-80) REVERT: B 193 MET cc_start: 0.3680 (ppp) cc_final: 0.3437 (ppp) REVERT: B 234 HIS cc_start: 0.8749 (t70) cc_final: 0.8395 (t70) REVERT: B 294 TRP cc_start: 0.8119 (p-90) cc_final: 0.7317 (p-90) REVERT: B 332 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8394 (p90) outliers start: 67 outliers final: 41 residues processed: 195 average time/residue: 0.2340 time to fit residues: 66.9066 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 44 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 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 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 249 GLU Chi-restraints excluded: chain C residue 274 VAL 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 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 295 LEU 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 391 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 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 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 28 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.108271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.085689 restraints weight = 39940.201| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 4.30 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2570 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= 0.129 Angle : 0.610 10.099 18712 Z= 0.308 Chirality : 0.045 0.317 2008 Planarity : 0.004 0.054 2105 Dihedral : 19.549 179.167 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.16 % Allowed : 28.57 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1402 helix: 0.42 (0.25), residues: 431 sheet: -1.09 (0.35), residues: 248 loop : -1.18 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 319 HIS 0.003 0.001 HIS D 340 PHE 0.009 0.001 PHE A 245 TYR 0.010 0.001 TYR B 330 ARG 0.005 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 456) hydrogen bonds : angle 4.95251 ( 1242) covalent geometry : bond 0.00293 (13617) covalent geometry : angle 0.60999 (18712) *********************** 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 218 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8758 (t0) cc_final: 0.8414 (t0) REVERT: A 79 GLU cc_start: 0.8025 (tp30) cc_final: 0.7521 (tp30) REVERT: A 95 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: A 267 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7707 (mtmm) REVERT: A 435 MET cc_start: 0.7215 (ttt) cc_final: 0.6263 (ptm) REVERT: C 72 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6349 (ptt-90) REVERT: C 249 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: C 409 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (p0) REVERT: C 504 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8882 (ptmm) REVERT: D 167 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.6840 (mtmt) REVERT: D 229 LYS cc_start: 0.8026 (tttp) cc_final: 0.7822 (tmtt) REVERT: D 231 GLU cc_start: 0.8558 (pm20) cc_final: 0.8312 (pm20) REVERT: D 294 TRP cc_start: 0.7649 (p-90) cc_final: 0.7335 (p-90) REVERT: D 309 MET cc_start: 0.7229 (mpp) cc_final: 0.6860 (mpp) REVERT: D 350 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8092 (mt) REVERT: D 376 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8974 (mttp) REVERT: B 185 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B 187 PHE cc_start: 0.8223 (m-80) cc_final: 0.7301 (m-80) REVERT: B 234 HIS cc_start: 0.8664 (t70) cc_final: 0.8286 (t70) REVERT: B 284 GLU cc_start: 0.7637 (mp0) cc_final: 0.7274 (mp0) REVERT: B 294 TRP cc_start: 0.8074 (p-90) cc_final: 0.7261 (p-90) REVERT: B 332 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8354 (p90) outliers start: 65 outliers final: 43 residues processed: 204 average time/residue: 0.2605 time to fit residues: 76.7723 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 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 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 ILE 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 249 GLU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 409 ASN 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 269 LEU Chi-restraints excluded: chain D residue 295 LEU 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 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 416 TYR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 300 LEU 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 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.106516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083766 restraints weight = 40098.359| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 4.26 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2633 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= 0.160 Angle : 0.637 10.181 18712 Z= 0.321 Chirality : 0.045 0.324 2008 Planarity : 0.004 0.052 2105 Dihedral : 19.512 179.363 2440 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.48 % Allowed : 28.65 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1402 helix: 0.42 (0.25), residues: 433 sheet: -1.16 (0.34), residues: 245 loop : -1.21 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 319 HIS 0.015 0.001 HIS D 358 PHE 0.010 0.001 PHE A 245 TYR 0.010 0.001 TYR D 293 ARG 0.006 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 456) hydrogen bonds : angle 4.96016 ( 1242) covalent geometry : bond 0.00364 (13617) covalent geometry : angle 0.63665 (18712) *********************** 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 203 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 134 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8091 (tp30) cc_final: 0.7681 (tp30) REVERT: A 95 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: A 435 MET cc_start: 0.7395 (ttt) cc_final: 0.6425 (ptm) REVERT: A 476 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6476 (tp30) REVERT: C 72 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6360 (ptp90) REVERT: C 249 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: C 409 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8265 (p0) REVERT: C 504 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8851 (ptmm) REVERT: D 167 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7054 (mtmt) REVERT: D 231 GLU cc_start: 0.8631 (pm20) cc_final: 0.8366 (pm20) REVERT: D 277 MET cc_start: 0.7616 (mmp) cc_final: 0.7252 (mmp) REVERT: D 283 GLN cc_start: 0.7776 (mp10) cc_final: 0.6713 (mp10) REVERT: D 309 MET cc_start: 0.7299 (mpp) cc_final: 0.6933 (mpp) REVERT: D 350 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8140 (mt) REVERT: D 376 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9007 (mttp) REVERT: B 179 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8458 (mm) REVERT: B 193 MET cc_start: 0.3708 (ppp) cc_final: 0.3463 (ppp) REVERT: B 234 HIS cc_start: 0.8744 (t70) cc_final: 0.8364 (t70) REVERT: B 284 GLU cc_start: 0.7606 (mp0) cc_final: 0.7320 (mp0) REVERT: B 294 TRP cc_start: 0.8139 (p-90) cc_final: 0.7345 (p-90) REVERT: B 332 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8329 (p90) outliers start: 69 outliers final: 44 residues processed: 189 average time/residue: 0.2576 time to fit residues: 70.9399 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 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 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 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 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 249 GLU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 409 ASN 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 295 LEU 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 358 HIS Chi-restraints excluded: chain D residue 360 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 300 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 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.108177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085487 restraints weight = 39778.657| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 4.36 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13617 Z= 0.130 Angle : 0.626 10.164 18712 Z= 0.315 Chirality : 0.044 0.317 2008 Planarity : 0.004 0.054 2105 Dihedral : 19.469 178.981 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.76 % Allowed : 28.89 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1402 helix: 0.51 (0.25), residues: 430 sheet: -1.11 (0.34), residues: 246 loop : -1.17 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 294 HIS 0.016 0.001 HIS D 358 PHE 0.009 0.001 PHE D 391 TYR 0.010 0.001 TYR D 293 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 456) hydrogen bonds : angle 4.88243 ( 1242) covalent geometry : bond 0.00295 (13617) covalent geometry : angle 0.62575 (18712) *********************** 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 205 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8846 (t0) cc_final: 0.8541 (t0) REVERT: A 79 GLU cc_start: 0.8063 (tp30) cc_final: 0.7645 (tp30) REVERT: A 95 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: A 267 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7862 (mtmm) REVERT: A 303 MET cc_start: 0.6960 (mtp) cc_final: 0.6480 (mmm) REVERT: A 435 MET cc_start: 0.7297 (ttt) cc_final: 0.6361 (ptm) REVERT: C 72 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6319 (ptp90) REVERT: C 249 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: C 406 LEU cc_start: 0.8410 (mm) cc_final: 0.8115 (tp) REVERT: C 504 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8877 (ptmm) REVERT: D 167 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7570 (ptpt) REVERT: D 277 MET cc_start: 0.7629 (mmp) cc_final: 0.7224 (mmp) REVERT: D 309 MET cc_start: 0.7267 (mpp) cc_final: 0.6900 (mpp) REVERT: D 350 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7879 (mt) REVERT: D 376 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8981 (mttp) REVERT: B 179 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (mm) REVERT: B 187 PHE cc_start: 0.8349 (m-80) cc_final: 0.7496 (m-80) REVERT: B 193 MET cc_start: 0.3545 (ppp) cc_final: 0.3311 (ppp) REVERT: B 234 HIS cc_start: 0.8731 (t70) cc_final: 0.8336 (t70) REVERT: B 284 GLU cc_start: 0.7619 (mp0) cc_final: 0.7327 (mp0) REVERT: B 294 TRP cc_start: 0.8098 (p-90) cc_final: 0.7327 (p-90) REVERT: B 304 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8028 (ttpt) outliers start: 60 outliers final: 40 residues processed: 192 average time/residue: 0.2569 time to fit residues: 71.9020 Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 111 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 363 THR 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 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 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 391 PHE 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 300 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.108383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085876 restraints weight = 39583.860| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.32 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13617 Z= 0.129 Angle : 0.624 10.258 18712 Z= 0.313 Chirality : 0.045 0.314 2008 Planarity : 0.004 0.055 2105 Dihedral : 19.442 178.788 2440 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.37 % Allowed : 29.37 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1402 helix: 0.69 (0.26), residues: 430 sheet: -1.14 (0.34), residues: 247 loop : -1.16 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 319 HIS 0.016 0.001 HIS D 358 PHE 0.008 0.001 PHE D 391 TYR 0.010 0.001 TYR D 293 ARG 0.006 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 456) hydrogen bonds : angle 4.84361 ( 1242) covalent geometry : bond 0.00294 (13617) covalent geometry : angle 0.62431 (18712) *********************** 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 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8799 (t0) cc_final: 0.8532 (t0) REVERT: A 79 GLU cc_start: 0.8064 (tp30) cc_final: 0.7643 (tp30) REVERT: A 95 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: A 267 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7884 (mtmm) REVERT: A 303 MET cc_start: 0.6818 (mtp) cc_final: 0.6375 (mmm) REVERT: A 435 MET cc_start: 0.7202 (ttt) cc_final: 0.6375 (ptm) REVERT: C 72 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6331 (ptp90) REVERT: C 249 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: C 406 LEU cc_start: 0.8410 (mm) cc_final: 0.8140 (tp) REVERT: C 504 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8871 (ptmm) REVERT: D 167 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7549 (ptpt) REVERT: D 277 MET cc_start: 0.7629 (mmp) cc_final: 0.7216 (mmp) REVERT: D 350 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8044 (mt) REVERT: B 179 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8370 (mm) REVERT: B 187 PHE cc_start: 0.8356 (m-80) cc_final: 0.7504 (m-80) REVERT: B 193 MET cc_start: 0.3641 (ppp) cc_final: 0.3423 (ppp) REVERT: B 234 HIS cc_start: 0.8729 (t70) cc_final: 0.8324 (t70) REVERT: B 284 GLU cc_start: 0.7638 (mp0) cc_final: 0.7364 (mp0) REVERT: B 294 TRP cc_start: 0.8108 (p-90) cc_final: 0.7290 (p-90) outliers start: 55 outliers final: 42 residues processed: 188 average time/residue: 0.3264 time to fit residues: 89.0877 Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 36 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 120 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 363 THR 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 219 TRP 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 300 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 370 ASN 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 88 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.108171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085605 restraints weight = 39907.175| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.29 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13617 Z= 0.134 Angle : 0.635 10.292 18712 Z= 0.319 Chirality : 0.045 0.314 2008 Planarity : 0.004 0.054 2105 Dihedral : 19.438 179.075 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.60 % Allowed : 29.13 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1402 helix: 0.69 (0.26), residues: 431 sheet: -1.16 (0.33), residues: 251 loop : -1.20 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 319 HIS 0.019 0.001 HIS D 358 PHE 0.010 0.001 PHE D 391 TYR 0.008 0.001 TYR D 210 ARG 0.011 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 456) hydrogen bonds : angle 4.82843 ( 1242) covalent geometry : bond 0.00307 (13617) covalent geometry : angle 0.63475 (18712) ********************** 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 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8069 (tp30) cc_final: 0.7655 (tp30) REVERT: A 95 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: A 267 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7892 (mtmm) REVERT: A 316 GLU cc_start: 0.7959 (pm20) cc_final: 0.7641 (mp0) REVERT: A 435 MET cc_start: 0.7205 (ttt) cc_final: 0.6387 (ptm) REVERT: C 72 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6251 (ptp90) REVERT: C 249 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: C 406 LEU cc_start: 0.8432 (mm) cc_final: 0.8171 (tp) REVERT: C 504 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8848 (ptmm) REVERT: D 167 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7536 (ptpt) REVERT: D 350 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8048 (mt) REVERT: B 179 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 187 PHE cc_start: 0.8351 (m-80) cc_final: 0.7506 (m-80) REVERT: B 193 MET cc_start: 0.3370 (ppp) cc_final: 0.3168 (ppp) REVERT: B 234 HIS cc_start: 0.8742 (t70) cc_final: 0.8334 (t70) REVERT: B 284 GLU cc_start: 0.7628 (mp0) cc_final: 0.7355 (mp0) REVERT: B 294 TRP cc_start: 0.8109 (p-90) cc_final: 0.7308 (p-90) outliers start: 58 outliers final: 46 residues processed: 185 average time/residue: 0.2677 time to fit residues: 72.1567 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 36 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 111 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 363 THR 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 219 TRP Chi-restraints excluded: chain D residue 229 LYS 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 370 ASN Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 398 GLU 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 300 LEU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN 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 90 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 127 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.084471 restraints weight = 39905.592| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.29 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13617 Z= 0.149 Angle : 0.641 10.313 18712 Z= 0.323 Chirality : 0.045 0.315 2008 Planarity : 0.004 0.055 2105 Dihedral : 19.470 179.802 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.60 % Allowed : 28.89 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1402 helix: 0.69 (0.25), residues: 432 sheet: -1.17 (0.33), residues: 251 loop : -1.19 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 192 HIS 0.019 0.001 HIS D 358 PHE 0.010 0.001 PHE A 245 TYR 0.012 0.001 TYR A 321 ARG 0.009 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 456) hydrogen bonds : angle 4.84012 ( 1242) covalent geometry : bond 0.00342 (13617) covalent geometry : angle 0.64134 (18712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.55 seconds wall clock time: 96 minutes 52.81 seconds (5812.81 seconds total)