Starting phenix.real_space_refine on Thu May 15 12:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr8_36592/05_2025/8jr8_36592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr8_36592/05_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_36592/05_2025/8jr8_36592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr8_36592/05_2025/8jr8_36592.map" model { file = "/net/cci-nas-00/data/ceres_data/8jr8_36592/05_2025/8jr8_36592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr8_36592/05_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-5687/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: 7.73, per 1000 atoms: 0.59 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: 3.00 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: 4.43 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: 4.21 Time building geometry restraints manager: 3.50 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- 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 : 1.303 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: 0.2749 time to fit residues: 50.3112 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 : 1.288 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082185 restraints weight = 39788.492| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.16 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 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 = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- 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 : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8800 (t0) cc_final: 0.8483 (t0) REVERT: A 95 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: A 430 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: A 464 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7616 (tppt) REVERT: C 4 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8456 (mt) REVERT: C 249 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: D 231 GLU cc_start: 0.8648 (pm20) cc_final: 0.8440 (pm20) REVERT: D 350 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 376 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9068 (mttp) REVERT: D 394 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: B 234 HIS cc_start: 0.8564 (t70) cc_final: 0.8041 (m-70) REVERT: B 235 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: B 294 TRP cc_start: 0.8196 (p-90) cc_final: 0.7364 (p-90) REVERT: B 332 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8164 (p90) outliers start: 65 outliers final: 37 residues processed: 188 average time/residue: 0.2572 time to fit residues: 69.9038 Evaluate side-chains 167 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 4 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 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: 1.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.106897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.084504 restraints weight = 40246.545| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.21 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13617 Z= 0.147 Angle : 0.625 9.283 18712 Z= 0.320 Chirality : 0.046 0.324 2008 Planarity : 0.004 0.056 2105 Dihedral : 19.730 179.374 2446 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.16 % Allowed : 29.13 % Favored : 65.71 % 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: -1.36 (0.23), residues: 1402 helix: 0.11 (0.25), residues: 430 sheet: -1.55 (0.33), residues: 266 loop : -1.22 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 319 HIS 0.011 0.001 HIS D 358 PHE 0.011 0.001 PHE D 343 TYR 0.015 0.001 TYR D 210 ARG 0.005 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 456) hydrogen bonds : angle 5.54384 ( 1242) covalent geometry : bond 0.00329 (13617) covalent geometry : angle 0.62469 (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 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8827 (t0) cc_final: 0.8459 (t0) REVERT: A 95 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 54 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7946 (mtp85) REVERT: C 72 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6446 (ptp90) REVERT: C 85 LYS cc_start: 0.8471 (tppt) cc_final: 0.8182 (tppt) REVERT: C 369 GLU cc_start: 0.6351 (mp0) cc_final: 0.6097 (mp0) REVERT: D 167 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7092 (ptpt) REVERT: D 277 MET cc_start: 0.7720 (mmp) cc_final: 0.7295 (mmp) REVERT: D 376 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9000 (mttp) REVERT: B 179 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 234 HIS cc_start: 0.8544 (t70) cc_final: 0.8223 (t70) REVERT: B 284 GLU cc_start: 0.7772 (mp0) cc_final: 0.7319 (mp0) REVERT: B 294 TRP cc_start: 0.8127 (p-90) cc_final: 0.7282 (p-90) REVERT: B 332 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8241 (p90) outliers start: 65 outliers final: 38 residues processed: 196 average time/residue: 0.2647 time to fit residues: 74.0532 Evaluate side-chains 175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 227 SER 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 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 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 265 ILE 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 416 TYR 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: 5.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 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 18 GLN A 59 HIS ** A 251 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.104627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082145 restraints weight = 40103.980| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.15 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13617 Z= 0.202 Angle : 0.651 9.494 18712 Z= 0.335 Chirality : 0.046 0.324 2008 Planarity : 0.005 0.055 2105 Dihedral : 19.721 178.149 2443 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.95 % Allowed : 28.89 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.23), residues: 1402 helix: -0.02 (0.25), residues: 440 sheet: -1.58 (0.32), residues: 266 loop : -1.25 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 319 HIS 0.006 0.001 HIS D 340 PHE 0.011 0.001 PHE D 342 TYR 0.011 0.001 TYR D 210 ARG 0.004 0.001 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 456) hydrogen bonds : angle 5.42955 ( 1242) covalent geometry : bond 0.00458 (13617) covalent geometry : angle 0.65072 (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 206 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 131 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8897 (t0) cc_final: 0.8583 (t0) REVERT: A 79 GLU cc_start: 0.8059 (tp30) cc_final: 0.7743 (tp30) REVERT: A 95 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 303 MET cc_start: 0.6717 (ttm) cc_final: 0.6452 (ttm) REVERT: A 435 MET cc_start: 0.7101 (ttt) cc_final: 0.5913 (ptm) REVERT: C 72 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6670 (ptt-90) REVERT: C 85 LYS cc_start: 0.8568 (tppt) cc_final: 0.8261 (tppt) REVERT: C 267 LYS cc_start: 0.7272 (tptt) cc_final: 0.6775 (tptp) REVERT: C 504 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8846 (ptmm) REVERT: D 167 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7338 (ptpt) REVERT: D 179 LEU cc_start: 0.9150 (pt) cc_final: 0.8928 (pt) REVERT: D 350 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8099 (mp) REVERT: D 376 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9062 (mttp) REVERT: D 394 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6761 (pm20) REVERT: B 179 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 234 HIS cc_start: 0.8691 (t70) cc_final: 0.8356 (t70) REVERT: B 284 GLU cc_start: 0.7768 (mp0) cc_final: 0.7554 (mp0) REVERT: B 294 TRP cc_start: 0.8098 (p-90) cc_final: 0.7392 (p-90) REVERT: B 332 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8475 (p90) REVERT: B 366 LYS cc_start: 0.8321 (ptmm) cc_final: 0.8098 (ptmm) outliers start: 75 outliers final: 54 residues processed: 188 average time/residue: 0.2422 time to fit residues: 66.1384 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 460 LEU 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 13 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 111 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ILE 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 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 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: 5.9990 chunk 64 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** 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 = 0.3924 r_free = 0.3924 target = 0.104952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.082366 restraints weight = 40169.052| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.27 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13617 Z= 0.158 Angle : 0.618 9.865 18712 Z= 0.316 Chirality : 0.045 0.327 2008 Planarity : 0.004 0.053 2105 Dihedral : 19.683 178.726 2443 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.19 % Allowed : 28.10 % Favored : 65.71 % 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: -1.35 (0.23), residues: 1402 helix: 0.13 (0.25), residues: 438 sheet: -1.55 (0.33), residues: 264 loop : -1.25 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 319 HIS 0.012 0.001 HIS D 358 PHE 0.012 0.001 PHE B 380 TYR 0.011 0.001 TYR D 210 ARG 0.005 0.000 ARG C 54 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 456) hydrogen bonds : angle 5.21087 ( 1242) covalent geometry : bond 0.00358 (13617) covalent geometry : angle 0.61787 (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 218 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 140 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9068 (tp) cc_final: 0.8866 (tp) REVERT: A 74 MET cc_start: 0.4171 (ptt) cc_final: 0.3925 (ptt) REVERT: A 79 GLU cc_start: 0.8045 (tp30) cc_final: 0.7710 (tp30) REVERT: A 95 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: C 54 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.7993 (mtp85) REVERT: C 72 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6490 (ptt-90) REVERT: C 85 LYS cc_start: 0.8573 (tppt) cc_final: 0.8293 (tppt) REVERT: C 249 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: C 267 LYS cc_start: 0.7180 (tptt) cc_final: 0.6681 (tptp) REVERT: C 504 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8866 (ptmm) REVERT: D 167 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7408 (ptpt) REVERT: D 231 GLU cc_start: 0.8531 (pm20) cc_final: 0.8283 (pm20) REVERT: D 277 MET cc_start: 0.7728 (mmp) cc_final: 0.7437 (mmp) REVERT: D 294 TRP cc_start: 0.7722 (p-90) cc_final: 0.7322 (p-90) REVERT: D 376 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8993 (mttp) REVERT: D 394 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: B 179 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8542 (mm) REVERT: B 187 PHE cc_start: 0.8443 (m-80) cc_final: 0.7557 (m-80) REVERT: B 234 HIS cc_start: 0.8758 (t70) cc_final: 0.8409 (t70) REVERT: B 284 GLU cc_start: 0.7935 (mp0) cc_final: 0.7717 (mp0) REVERT: B 294 TRP cc_start: 0.8179 (p-90) cc_final: 0.7458 (p-90) REVERT: B 332 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8503 (p90) outliers start: 78 outliers final: 56 residues processed: 203 average time/residue: 0.2398 time to fit residues: 70.7971 Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU 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 111 HIS Chi-restraints excluded: chain C residue 120 LEU 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 357 VAL 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 234 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 265 ILE 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 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 393 LEU Chi-restraints excluded: chain D residue 394 GLU 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 332 PHE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 0.0770 chunk 128 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 118 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 0.0030 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 468 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.108838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.086527 restraints weight = 40079.109| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.31 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13617 Z= 0.122 Angle : 0.616 10.334 18712 Z= 0.310 Chirality : 0.045 0.324 2008 Planarity : 0.004 0.054 2105 Dihedral : 19.552 178.549 2443 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.97 % Allowed : 30.24 % Favored : 65.79 % 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: -1.04 (0.23), residues: 1402 helix: 0.53 (0.26), residues: 430 sheet: -1.17 (0.35), residues: 246 loop : -1.24 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 319 HIS 0.003 0.001 HIS B 320 PHE 0.019 0.001 PHE A 245 TYR 0.011 0.001 TYR B 330 ARG 0.006 0.001 ARG C 54 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 456) hydrogen bonds : angle 4.92755 ( 1242) covalent geometry : bond 0.00273 (13617) covalent geometry : angle 0.61603 (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 213 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8790 (t0) cc_final: 0.8536 (t0) REVERT: A 74 MET cc_start: 0.4506 (ptt) cc_final: 0.4298 (ptt) REVERT: A 95 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 303 MET cc_start: 0.6345 (mtp) cc_final: 0.5878 (ttm) REVERT: A 435 MET cc_start: 0.7183 (ttt) cc_final: 0.6111 (ptm) REVERT: C 72 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6288 (ptp90) REVERT: C 85 LYS cc_start: 0.8439 (tppt) cc_final: 0.8227 (tppt) REVERT: C 249 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: D 167 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.6804 (mtmt) REVERT: D 265 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9068 (mm) REVERT: D 376 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8934 (mttp) REVERT: D 394 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: B 187 PHE cc_start: 0.8365 (m-80) cc_final: 0.7511 (m-80) REVERT: B 193 MET cc_start: 0.3710 (ppp) cc_final: 0.3478 (ppp) REVERT: B 234 HIS cc_start: 0.8700 (t70) cc_final: 0.8330 (t70) REVERT: B 284 GLU cc_start: 0.7945 (mp0) cc_final: 0.7733 (mp0) REVERT: B 294 TRP cc_start: 0.8060 (p-90) cc_final: 0.7307 (p-90) REVERT: B 350 LEU cc_start: 0.8493 (mp) cc_final: 0.7953 (pt) outliers start: 50 outliers final: 32 residues processed: 206 average time/residue: 0.2554 time to fit residues: 75.6299 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 249 GLU Chi-restraints excluded: chain C residue 304 PHE 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 265 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 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 398 GLU 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 397 SER 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: 6.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 357 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.084083 restraints weight = 40068.174| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.33 r_work (final): 0.3523 ------------------------------------------------------------------------------- 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 = 0.82 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 = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13617 Z= 0.147 Angle : 0.633 10.328 18712 Z= 0.317 Chirality : 0.045 0.330 2008 Planarity : 0.004 0.052 2105 Dihedral : 19.454 178.837 2440 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.52 % Allowed : 29.92 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.06 (0.23), residues: 1402 helix: 0.52 (0.25), residues: 431 sheet: -1.40 (0.33), residues: 257 loop : -1.16 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 319 HIS 0.003 0.001 HIS D 340 PHE 0.022 0.001 PHE A 245 TYR 0.014 0.001 TYR C 403 ARG 0.007 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 456) hydrogen bonds : angle 4.93695 ( 1242) covalent geometry : bond 0.00336 (13617) covalent geometry : angle 0.63312 (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 200 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4416 (ptt) cc_final: 0.4199 (ptt) REVERT: A 95 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 303 MET cc_start: 0.6298 (mtp) cc_final: 0.5669 (ttm) REVERT: A 435 MET cc_start: 0.7324 (ttt) cc_final: 0.6238 (ptm) REVERT: C 72 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6391 (ptp90) REVERT: C 249 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: D 167 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7213 (mtmt) REVERT: D 231 GLU cc_start: 0.8490 (pm20) cc_final: 0.8268 (pm20) REVERT: D 277 MET cc_start: 0.7714 (mmp) cc_final: 0.7357 (mmp) REVERT: D 283 GLN cc_start: 0.7745 (mp10) cc_final: 0.7396 (mp10) REVERT: D 350 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8025 (mt) REVERT: D 376 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8997 (mttp) REVERT: D 394 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7429 (pp20) REVERT: B 179 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8464 (mm) REVERT: B 187 PHE cc_start: 0.8395 (m-80) cc_final: 0.7553 (m-80) REVERT: B 193 MET cc_start: 0.3905 (ppp) cc_final: 0.3661 (ppp) REVERT: B 234 HIS cc_start: 0.8759 (t70) cc_final: 0.8384 (t70) REVERT: B 294 TRP cc_start: 0.8108 (p-90) cc_final: 0.7246 (p-90) REVERT: B 332 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8352 (p90) outliers start: 57 outliers final: 38 residues processed: 188 average time/residue: 0.2458 time to fit residues: 67.3903 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE 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 321 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 476 GLU 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 243 ARG 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 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 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 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 394 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 265 ILE 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: 5.9990 chunk 119 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 D 358 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084243 restraints weight = 39876.034| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.30 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2788 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= 0.143 Angle : 0.639 10.267 18712 Z= 0.320 Chirality : 0.045 0.334 2008 Planarity : 0.004 0.053 2105 Dihedral : 19.436 178.741 2440 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.52 % Allowed : 30.32 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.25), residues: 432 sheet: -1.20 (0.34), residues: 246 loop : -1.21 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 319 HIS 0.015 0.001 HIS D 358 PHE 0.009 0.001 PHE D 391 TYR 0.011 0.001 TYR B 330 ARG 0.005 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 456) hydrogen bonds : angle 4.90314 ( 1242) covalent geometry : bond 0.00328 (13617) covalent geometry : angle 0.63853 (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 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4404 (ptt) cc_final: 0.4160 (ptt) REVERT: A 95 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: A 435 MET cc_start: 0.7288 (ttt) cc_final: 0.6203 (ptm) REVERT: C 72 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6390 (ptp90) REVERT: C 249 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7345 (mm-30) REVERT: C 409 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (p0) REVERT: D 167 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7651 (ptpt) REVERT: D 231 GLU cc_start: 0.8472 (pm20) cc_final: 0.8231 (pm20) REVERT: D 277 MET cc_start: 0.7749 (mmp) cc_final: 0.7363 (mmp) REVERT: D 283 GLN cc_start: 0.7758 (mp10) cc_final: 0.7442 (mp10) REVERT: D 350 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8020 (mt) REVERT: D 376 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8978 (mttp) REVERT: B 179 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 187 PHE cc_start: 0.8365 (m-80) cc_final: 0.7532 (m-80) REVERT: B 193 MET cc_start: 0.3978 (ppp) cc_final: 0.3753 (ppp) REVERT: B 234 HIS cc_start: 0.8779 (t70) cc_final: 0.8398 (t70) REVERT: B 284 GLU cc_start: 0.7689 (mp0) cc_final: 0.7137 (mp0) REVERT: B 294 TRP cc_start: 0.8121 (p-90) cc_final: 0.7255 (p-90) REVERT: B 332 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8403 (p90) outliers start: 57 outliers final: 45 residues processed: 182 average time/residue: 0.2518 time to fit residues: 66.6113 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 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 476 GLU 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 243 ARG 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 431 THR 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS ** D 364 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 = 0.3948 r_free = 0.3948 target = 0.106336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.083644 restraints weight = 39985.064| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.23 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13617 Z= 0.158 Angle : 0.643 10.297 18712 Z= 0.322 Chirality : 0.045 0.336 2008 Planarity : 0.004 0.052 2105 Dihedral : 19.441 179.659 2440 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.68 % Allowed : 30.63 % Favored : 64.68 % 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: -1.05 (0.23), residues: 1402 helix: 0.53 (0.25), residues: 430 sheet: -1.34 (0.33), residues: 253 loop : -1.18 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 319 HIS 0.017 0.001 HIS D 358 PHE 0.010 0.001 PHE D 391 TYR 0.010 0.001 TYR C 262 ARG 0.006 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 456) hydrogen bonds : angle 4.91389 ( 1242) covalent geometry : bond 0.00364 (13617) covalent geometry : angle 0.64277 (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: 59 poor density : 137 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4359 (ptt) cc_final: 0.4126 (ptt) REVERT: A 95 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: A 435 MET cc_start: 0.7351 (ttt) cc_final: 0.6294 (ptm) REVERT: C 72 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6319 (ptp90) REVERT: C 249 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: C 406 LEU cc_start: 0.8466 (mm) cc_final: 0.8171 (tp) REVERT: D 167 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7706 (ptpt) REVERT: D 231 GLU cc_start: 0.8441 (pm20) cc_final: 0.8202 (pm20) REVERT: D 283 GLN cc_start: 0.7783 (mp10) cc_final: 0.7474 (mp10) REVERT: D 350 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8048 (mt) REVERT: D 376 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8764 (mttp) REVERT: B 179 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8485 (mm) REVERT: B 187 PHE cc_start: 0.8361 (m-80) cc_final: 0.7530 (m-80) REVERT: B 234 HIS cc_start: 0.8756 (t70) cc_final: 0.8369 (t70) REVERT: B 284 GLU cc_start: 0.7703 (mp0) cc_final: 0.7138 (mp0) REVERT: B 294 TRP cc_start: 0.8108 (p-90) cc_final: 0.7241 (p-90) REVERT: B 332 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8477 (p90) outliers start: 59 outliers final: 47 residues processed: 183 average time/residue: 0.2469 time to fit residues: 65.3406 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 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 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 243 ARG 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 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 350 LEU Chi-restraints excluded: chain D residue 353 SER 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 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 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 395 MET 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: 3.9990 chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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** A 409 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 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 = 0.3905 r_free = 0.3905 target = 0.103807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.080794 restraints weight = 40426.432| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.23 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13617 Z= 0.217 Angle : 0.691 10.836 18712 Z= 0.348 Chirality : 0.047 0.349 2008 Planarity : 0.005 0.052 2105 Dihedral : 19.580 178.212 2440 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 4.92 % Allowed : 30.32 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.23), residues: 1402 helix: 0.19 (0.25), residues: 444 sheet: -1.51 (0.33), residues: 252 loop : -1.20 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 294 HIS 0.006 0.001 HIS D 340 PHE 0.013 0.001 PHE D 342 TYR 0.013 0.001 TYR D 251 ARG 0.008 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 456) hydrogen bonds : angle 5.10032 ( 1242) covalent geometry : bond 0.00498 (13617) covalent geometry : angle 0.69136 (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 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.4214 (ptt) cc_final: 0.3956 (ptt) REVERT: A 79 GLU cc_start: 0.8177 (tp30) cc_final: 0.7854 (tp30) REVERT: A 95 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 303 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5686 (ttm) REVERT: A 435 MET cc_start: 0.7445 (ttt) cc_final: 0.6359 (ptm) REVERT: A 464 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7735 (tppt) REVERT: C 11 LYS cc_start: 0.7867 (tptp) cc_final: 0.7618 (tptt) REVERT: C 72 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6309 (ptp90) REVERT: D 167 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7845 (ptpt) REVERT: D 231 GLU cc_start: 0.8418 (pm20) cc_final: 0.8197 (pm20) REVERT: D 277 MET cc_start: 0.7818 (mmp) cc_final: 0.7509 (mmp) REVERT: D 283 GLN cc_start: 0.7793 (mp10) cc_final: 0.7431 (mp10) REVERT: D 350 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8142 (mt) REVERT: D 376 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8808 (mttp) REVERT: B 179 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8647 (mm) REVERT: B 187 PHE cc_start: 0.8408 (m-80) cc_final: 0.7570 (m-80) REVERT: B 234 HIS cc_start: 0.8799 (t70) cc_final: 0.8421 (t70) REVERT: B 284 GLU cc_start: 0.7735 (mp0) cc_final: 0.7483 (mp0) REVERT: B 294 TRP cc_start: 0.8182 (p-90) cc_final: 0.7330 (p-90) outliers start: 62 outliers final: 46 residues processed: 183 average time/residue: 0.2545 time to fit residues: 67.4675 Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 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 243 ARG 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 431 THR 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 234 HIS 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 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 340 HIS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 395 MET 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: 3.9990 chunk 134 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.104030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081129 restraints weight = 40360.528| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 4.22 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 13617 Z= 0.232 Angle : 0.890 59.123 18712 Z= 0.493 Chirality : 0.050 0.862 2008 Planarity : 0.005 0.085 2105 Dihedral : 19.599 178.185 2440 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 4.76 % Allowed : 30.56 % Favored : 64.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.22 (0.23), residues: 1402 helix: 0.36 (0.25), residues: 432 sheet: -1.51 (0.33), residues: 252 loop : -1.22 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 319 HIS 0.008 0.001 HIS C 329 PHE 0.013 0.001 PHE D 342 TYR 0.058 0.002 TYR C 505 ARG 0.018 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 456) hydrogen bonds : angle 5.10522 ( 1242) covalent geometry : bond 0.00519 (13617) covalent geometry : angle 0.88965 (18712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.91 seconds wall clock time: 83 minutes 41.65 seconds (5021.65 seconds total)