Starting phenix.real_space_refine on Thu Sep 26 06:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlg_22243/09_2024/6xlg_22243.cif" } resolution = 2.71 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= 0.004 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 7836 2.51 5 N 2010 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12258 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "B" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4906 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 20, 'TRANS': 586} Chain breaks: 3 Chain: "C" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1190 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.57, per 1000 atoms: 0.62 Number of scatterers: 12258 At special positions: 0 Unit cell: (106.038, 96.174, 131.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 24 16.00 P 6 15.00 Mg 2 11.99 O 2378 8.00 N 2010 7.00 C 7836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 41.4% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 4.460A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 50 removed outlier: 4.048A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 6.688A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 55 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.691A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 384 through 406 removed outlier: 4.006A pdb=" N ASP A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.127A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 475 through 480 removed outlier: 4.152A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 removed outlier: 4.568A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 510 removed outlier: 4.329A pdb=" N TYR A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.923A pdb=" N LYS A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 removed outlier: 3.606A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.593A pdb=" N GLY A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.757A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.464A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 50 removed outlier: 4.065A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 6.687A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 55 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 186 through 198 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.711A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 406 removed outlier: 3.999A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 428 removed outlier: 4.125A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 453 through 459 Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.161A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.575A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 removed outlier: 4.320A pdb=" N TYR B 504 " --> pdb=" O PRO B 500 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.834A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.622A pdb=" N ILE B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 590 Processing helix chain 'B' and resid 615 through 628 removed outlier: 3.594A pdb=" N GLY B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.845A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.670A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 3.665A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.564A pdb=" N ASN C 331 " --> pdb=" O ARG C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.743A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 removed outlier: 3.624A pdb=" N ALA D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.573A pdb=" N ASN D 331 " --> pdb=" O ARG D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.981A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.859A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.979A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 307 removed outlier: 7.291A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.006A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 7.264A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 4.004A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AB2, first strand: chain 'C' and resid 213 through 218 removed outlier: 5.492A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.659A pdb=" N LYS C 312 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 213 through 218 removed outlier: 5.496A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 213 through 218 removed outlier: 5.496A pdb=" N THR D 214 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 280 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS D 275 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL D 282 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 272 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 259 " --> pdb=" O LEU D 272 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4044 1.37 - 1.52: 3712 1.52 - 1.66: 4686 1.66 - 1.81: 40 1.81 - 1.95: 4 Bond restraints: 12486 Sorted by residual: bond pdb=" CA LYS D 279 " pdb=" CB LYS D 279 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.69e-02 3.50e+03 3.02e-01 bond pdb=" C GLY B 170 " pdb=" O GLY B 170 " ideal model delta sigma weight residual 1.230 1.236 -0.006 1.28e-02 6.10e+03 2.50e-01 bond pdb=" CA VAL B 122 " pdb=" C VAL B 122 " ideal model delta sigma weight residual 1.520 1.525 -0.005 1.00e-02 1.00e+04 2.36e-01 bond pdb=" C1' AGS A 801 " pdb=" C2' AGS A 801 " ideal model delta sigma weight residual 1.530 1.536 -0.006 1.30e-02 5.92e+03 2.04e-01 bond pdb=" N GLU A 351 " pdb=" CA GLU A 351 " ideal model delta sigma weight residual 1.463 1.458 0.005 1.08e-02 8.57e+03 1.94e-01 ... (remaining 12481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 16515 0.96 - 1.92: 257 1.92 - 2.88: 52 2.88 - 3.84: 21 3.84 - 4.80: 7 Bond angle restraints: 16852 Sorted by residual: angle pdb=" C LEU B 509 " pdb=" N LYS B 510 " pdb=" CA LYS B 510 " ideal model delta sigma weight residual 121.54 124.83 -3.29 1.91e+00 2.74e-01 2.97e+00 angle pdb=" C LEU A 509 " pdb=" N LYS A 510 " pdb=" CA LYS A 510 " ideal model delta sigma weight residual 121.54 124.78 -3.24 1.91e+00 2.74e-01 2.88e+00 angle pdb=" C GLU B 351 " pdb=" N ASP B 352 " pdb=" CA ASP B 352 " ideal model delta sigma weight residual 123.25 120.59 2.66 1.69e+00 3.50e-01 2.48e+00 angle pdb=" NE ARG D 327 " pdb=" CZ ARG D 327 " pdb=" NH1 ARG D 327 " ideal model delta sigma weight residual 121.50 119.99 1.51 1.00e+00 1.00e+00 2.29e+00 angle pdb=" NE ARG A 275 " pdb=" CZ ARG A 275 " pdb=" NH1 ARG A 275 " ideal model delta sigma weight residual 121.50 120.02 1.48 1.00e+00 1.00e+00 2.19e+00 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 7540 34.71 - 69.43: 47 69.43 - 104.14: 27 104.14 - 138.85: 0 138.85 - 173.57: 2 Dihedral angle restraints: 7616 sinusoidal: 3206 harmonic: 4410 Sorted by residual: dihedral pdb=" O1A AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PA AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sinusoidal sigma weight residual -67.73 105.84 -173.57 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 102.91 -170.64 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N GLU B 544 " pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " pdb=" CG GLU B 544 " ideal model delta sinusoidal sigma weight residual 180.00 -130.55 -49.45 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 7613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1114 0.025 - 0.051: 494 0.051 - 0.076: 157 0.076 - 0.102: 62 0.102 - 0.127: 59 Chirality restraints: 1886 Sorted by residual: chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE B 319 " pdb=" N ILE B 319 " pdb=" C ILE B 319 " pdb=" CB ILE B 319 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1883 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.60e-01 pdb=" N PRO A 355 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 354 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.07e-01 pdb=" N PRO B 355 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 355 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 355 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 320 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.11e-01 pdb=" N PRO C 321 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.013 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 313 2.71 - 3.32: 13686 3.32 - 3.93: 24064 3.93 - 4.53: 32934 4.53 - 5.14: 51454 Nonbonded interactions: 122451 Sorted by model distance: nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 2.105 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.137 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.141 2.170 nonbonded pdb=" O TRP D 242 " pdb=" OG SER D 339 " model vdw 2.253 3.040 ... (remaining 122446 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.620 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.001 0.012 12486 Z= 0.077 Angle : 0.356 4.802 16852 Z= 0.206 Chirality : 0.037 0.127 1886 Planarity : 0.002 0.024 2148 Dihedral : 10.467 173.566 4744 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.01 (0.18), residues: 1484 helix: -2.39 (0.16), residues: 568 sheet: -1.01 (0.27), residues: 338 loop : -1.96 (0.22), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 273 HIS 0.001 0.000 HIS B 463 PHE 0.006 0.001 PHE B 579 TYR 0.004 0.000 TYR C 230 ARG 0.001 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.6908 (t0) cc_final: 0.6646 (t70) REVERT: A 634 THR cc_start: 0.7770 (p) cc_final: 0.7536 (p) REVERT: B 634 THR cc_start: 0.7757 (p) cc_final: 0.7520 (p) REVERT: D 219 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6267 (mp0) REVERT: D 338 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7605 (mtm110) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 1.4475 time to fit residues: 649.9050 Evaluate side-chains 194 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 92 ASN A 135 GLN A 145 GLN A 282 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 430 GLN A 508 GLN A 557 GLN A 592 GLN A 640 ASN B 14 GLN B 92 ASN B 135 GLN B 145 GLN B 282 GLN B 409 GLN B 430 GLN B 508 GLN B 557 GLN B 640 ASN C 212 ASN C 223 ASN D 212 ASN D 223 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12486 Z= 0.198 Angle : 0.566 7.525 16852 Z= 0.291 Chirality : 0.043 0.149 1886 Planarity : 0.004 0.053 2148 Dihedral : 8.646 172.963 1644 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.56 % Allowed : 14.91 % Favored : 81.53 % 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: -1.47 (0.20), residues: 1484 helix: -0.60 (0.20), residues: 570 sheet: -0.80 (0.27), residues: 332 loop : -1.28 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 285 HIS 0.006 0.001 HIS C 284 PHE 0.018 0.002 PHE B 104 TYR 0.011 0.001 TYR B 565 ARG 0.011 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 214 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: A 262 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6571 (mm-30) REVERT: A 553 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6612 (mt) REVERT: A 633 LYS cc_start: 0.7772 (tppt) cc_final: 0.7474 (mmtm) REVERT: B 105 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: B 183 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: B 297 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: B 553 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6514 (mt) REVERT: B 633 LYS cc_start: 0.7790 (tppt) cc_final: 0.7488 (mmtm) REVERT: C 227 SER cc_start: 0.7857 (p) cc_final: 0.7464 (t) REVERT: D 227 SER cc_start: 0.7908 (p) cc_final: 0.7521 (t) REVERT: D 230 TYR cc_start: 0.8349 (t80) cc_final: 0.8084 (t80) outliers start: 48 outliers final: 14 residues processed: 249 average time/residue: 1.3895 time to fit residues: 372.8998 Evaluate side-chains 182 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 391 ASN A 430 GLN B 382 ASN B 391 ASN B 430 GLN B 578 GLN B 592 GLN C 223 ASN D 223 ASN D 284 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12486 Z= 0.297 Angle : 0.594 5.601 16852 Z= 0.311 Chirality : 0.046 0.182 1886 Planarity : 0.004 0.034 2148 Dihedral : 8.461 152.936 1644 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.67 % Allowed : 15.95 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1484 helix: -0.03 (0.21), residues: 576 sheet: -0.76 (0.27), residues: 340 loop : -0.97 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 285 HIS 0.005 0.002 HIS A 197 PHE 0.020 0.002 PHE D 344 TYR 0.015 0.002 TYR A 125 ARG 0.006 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 1.551 Fit side-chains REVERT: A 105 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8029 (mmm) REVERT: A 633 LYS cc_start: 0.7717 (tppt) cc_final: 0.7503 (mmtm) REVERT: A 666 ARG cc_start: 0.7409 (mtm110) cc_final: 0.7178 (mtm-85) REVERT: B 14 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: B 17 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8616 (m) REVERT: B 105 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8095 (mmm) REVERT: B 381 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: B 633 LYS cc_start: 0.7770 (tppt) cc_final: 0.7554 (mmtm) REVERT: C 238 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7171 (mtm180) REVERT: C 333 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: D 230 TYR cc_start: 0.8693 (t80) cc_final: 0.8397 (t80) outliers start: 63 outliers final: 19 residues processed: 212 average time/residue: 1.4131 time to fit residues: 322.9843 Evaluate side-chains 164 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 430 GLN B 382 ASN B 430 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 223 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12486 Z= 0.173 Angle : 0.501 5.505 16852 Z= 0.262 Chirality : 0.042 0.170 1886 Planarity : 0.003 0.036 2148 Dihedral : 7.802 127.168 1644 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.34 % Allowed : 17.51 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1484 helix: 0.32 (0.21), residues: 586 sheet: -0.75 (0.27), residues: 344 loop : -0.79 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 242 HIS 0.004 0.001 HIS C 284 PHE 0.014 0.001 PHE B 6 TYR 0.011 0.001 TYR B 504 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 1.323 Fit side-chains REVERT: A 620 GLU cc_start: 0.6908 (tp30) cc_final: 0.6542 (tp30) REVERT: A 633 LYS cc_start: 0.7630 (tppt) cc_final: 0.7406 (mmtp) REVERT: B 336 ASN cc_start: 0.7800 (m110) cc_final: 0.7429 (p0) REVERT: B 620 GLU cc_start: 0.6955 (tp30) cc_final: 0.6572 (tp30) REVERT: B 633 LYS cc_start: 0.7667 (tppt) cc_final: 0.7432 (mmtm) REVERT: C 238 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7078 (mtm180) REVERT: D 230 TYR cc_start: 0.8712 (t80) cc_final: 0.8422 (t80) REVERT: D 240 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8587 (tt) outliers start: 45 outliers final: 17 residues processed: 180 average time/residue: 1.2477 time to fit residues: 244.1713 Evaluate side-chains 150 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 381 GLN A 382 ASN A 578 GLN B 310 GLN B 380 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 430 GLN C 223 ASN C 237 GLN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 223 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12486 Z= 0.469 Angle : 0.676 6.506 16852 Z= 0.352 Chirality : 0.050 0.273 1886 Planarity : 0.004 0.033 2148 Dihedral : 8.305 124.706 1644 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.23 % Allowed : 17.14 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1484 helix: -0.06 (0.20), residues: 590 sheet: -0.82 (0.27), residues: 342 loop : -0.70 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 296 HIS 0.005 0.002 HIS C 303 PHE 0.029 0.002 PHE C 344 TYR 0.018 0.003 TYR B 565 ARG 0.006 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 1.457 Fit side-chains REVERT: A 264 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: A 336 ASN cc_start: 0.8005 (m110) cc_final: 0.7467 (p0) REVERT: A 633 LYS cc_start: 0.7723 (tppt) cc_final: 0.7478 (mmtm) REVERT: B 264 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: B 336 ASN cc_start: 0.7993 (m110) cc_final: 0.7466 (p0) REVERT: B 531 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: B 633 LYS cc_start: 0.7740 (tppt) cc_final: 0.7497 (mmtm) REVERT: B 666 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7287 (mtm-85) REVERT: C 238 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7137 (mtm180) REVERT: C 247 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: D 230 TYR cc_start: 0.8889 (t80) cc_final: 0.8592 (t80) REVERT: D 240 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8809 (tt) REVERT: D 316 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (tttm) outliers start: 57 outliers final: 23 residues processed: 188 average time/residue: 1.2550 time to fit residues: 255.1673 Evaluate side-chains 167 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 310 GLN B 381 GLN B 382 ASN B 430 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 295 ASN D 314 GLN D 331 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12486 Z= 0.186 Angle : 0.529 5.267 16852 Z= 0.277 Chirality : 0.043 0.213 1886 Planarity : 0.004 0.039 2148 Dihedral : 8.014 128.192 1644 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.49 % Allowed : 18.40 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1484 helix: 0.30 (0.21), residues: 590 sheet: -0.79 (0.26), residues: 346 loop : -0.46 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 242 HIS 0.005 0.001 HIS C 303 PHE 0.015 0.001 PHE B 6 TYR 0.014 0.001 TYR C 230 ARG 0.005 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.801 Fit side-chains REVERT: A 264 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: A 336 ASN cc_start: 0.7926 (m110) cc_final: 0.7382 (p0) REVERT: A 666 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7143 (mtm-85) REVERT: B 86 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (tttm) REVERT: B 633 LYS cc_start: 0.7651 (tppt) cc_final: 0.7443 (mmtm) REVERT: B 666 ARG cc_start: 0.7423 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: C 238 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7099 (mtm180) REVERT: C 247 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: D 230 TYR cc_start: 0.8847 (t80) cc_final: 0.8569 (t80) REVERT: D 240 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8790 (tt) REVERT: D 316 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7956 (tttm) outliers start: 47 outliers final: 21 residues processed: 179 average time/residue: 1.1315 time to fit residues: 220.0977 Evaluate side-chains 170 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 382 ASN B 119 GLN B 380 GLN B 381 GLN B 382 ASN B 430 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 284 HIS D 314 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12486 Z= 0.162 Angle : 0.504 5.210 16852 Z= 0.264 Chirality : 0.042 0.147 1886 Planarity : 0.004 0.041 2148 Dihedral : 7.910 127.915 1644 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.34 % Allowed : 18.84 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1484 helix: 0.54 (0.22), residues: 590 sheet: -0.73 (0.27), residues: 342 loop : -0.40 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 242 HIS 0.004 0.001 HIS D 284 PHE 0.014 0.001 PHE B 6 TYR 0.011 0.001 TYR C 230 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.489 Fit side-chains REVERT: A 336 ASN cc_start: 0.7910 (m110) cc_final: 0.7344 (p0) REVERT: B 86 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (tttm) REVERT: B 336 ASN cc_start: 0.7855 (m110) cc_final: 0.7366 (p0) REVERT: B 633 LYS cc_start: 0.7580 (tppt) cc_final: 0.7362 (mmtp) REVERT: C 238 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7130 (mtm180) REVERT: D 230 TYR cc_start: 0.8795 (t80) cc_final: 0.8490 (t80) REVERT: D 240 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8766 (tt) outliers start: 45 outliers final: 23 residues processed: 165 average time/residue: 1.2638 time to fit residues: 227.2014 Evaluate side-chains 164 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.0070 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 0.0370 chunk 129 optimal weight: 8.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 119 GLN B 381 GLN B 382 ASN C 284 HIS C 295 ASN C 314 GLN D 212 ASN D 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12486 Z= 0.189 Angle : 0.506 5.459 16852 Z= 0.264 Chirality : 0.043 0.146 1886 Planarity : 0.004 0.043 2148 Dihedral : 7.912 126.522 1644 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.04 % Allowed : 19.44 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1484 helix: 0.60 (0.22), residues: 590 sheet: -0.73 (0.27), residues: 342 loop : -0.33 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.011 0.001 TYR C 230 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.484 Fit side-chains REVERT: A 336 ASN cc_start: 0.7903 (m110) cc_final: 0.7343 (p0) REVERT: A 666 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7100 (mtm-85) REVERT: B 86 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7857 (tttm) REVERT: B 336 ASN cc_start: 0.7842 (m110) cc_final: 0.7484 (p0) REVERT: B 633 LYS cc_start: 0.7557 (tppt) cc_final: 0.7334 (mmtm) REVERT: B 666 ARG cc_start: 0.7481 (mtm110) cc_final: 0.7147 (mtm-85) REVERT: C 238 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7145 (mtm180) REVERT: D 230 TYR cc_start: 0.8801 (t80) cc_final: 0.8499 (t80) REVERT: D 238 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7919 (mtm180) REVERT: D 240 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8776 (tt) REVERT: D 316 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (tttm) outliers start: 41 outliers final: 24 residues processed: 169 average time/residue: 1.2624 time to fit residues: 231.8574 Evaluate side-chains 165 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 119 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN C 223 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12486 Z= 0.188 Angle : 0.511 5.456 16852 Z= 0.267 Chirality : 0.043 0.146 1886 Planarity : 0.004 0.039 2148 Dihedral : 7.910 126.543 1644 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.74 % Allowed : 20.10 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1484 helix: 0.65 (0.22), residues: 590 sheet: -0.77 (0.27), residues: 344 loop : -0.31 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.019 0.001 TYR C 230 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 1.532 Fit side-chains REVERT: A 336 ASN cc_start: 0.7896 (m110) cc_final: 0.7343 (p0) REVERT: A 381 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5016 (pm20) REVERT: A 666 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7104 (mtm-85) REVERT: B 86 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7852 (tttm) REVERT: B 336 ASN cc_start: 0.7833 (m110) cc_final: 0.7489 (p0) REVERT: B 381 GLN cc_start: 0.6027 (OUTLIER) cc_final: 0.4842 (pm20) REVERT: B 633 LYS cc_start: 0.7561 (tppt) cc_final: 0.7332 (mmtm) REVERT: B 666 ARG cc_start: 0.7477 (mtm110) cc_final: 0.7150 (mtm-85) REVERT: C 238 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7151 (mtm180) REVERT: D 230 TYR cc_start: 0.8790 (t80) cc_final: 0.8491 (t80) REVERT: D 238 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7916 (mtm180) REVERT: D 240 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8763 (tt) REVERT: D 316 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7960 (tttm) outliers start: 37 outliers final: 26 residues processed: 164 average time/residue: 1.2238 time to fit residues: 219.5472 Evaluate side-chains 165 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 119 GLN B 381 GLN B 382 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 331 ASN D 212 ASN D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12486 Z= 0.172 Angle : 0.507 5.809 16852 Z= 0.265 Chirality : 0.042 0.147 1886 Planarity : 0.004 0.046 2148 Dihedral : 7.895 127.109 1644 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.74 % Allowed : 20.18 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1484 helix: 0.73 (0.22), residues: 588 sheet: -0.72 (0.27), residues: 348 loop : -0.25 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 PHE 0.016 0.001 PHE B 120 TYR 0.019 0.001 TYR C 230 ARG 0.007 0.001 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 141 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 336 ASN cc_start: 0.7880 (m110) cc_final: 0.7333 (p0) REVERT: A 381 GLN cc_start: 0.6101 (OUTLIER) cc_final: 0.4989 (pm20) REVERT: B 86 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7827 (tttt) REVERT: B 336 ASN cc_start: 0.7817 (m110) cc_final: 0.7477 (p0) REVERT: B 633 LYS cc_start: 0.7583 (tppt) cc_final: 0.7344 (mmtm) REVERT: C 231 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7500 (tp30) REVERT: D 230 TYR cc_start: 0.8768 (t80) cc_final: 0.8477 (t80) REVERT: D 238 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7919 (mtm180) REVERT: D 240 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8744 (tt) REVERT: D 316 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7937 (tttm) outliers start: 37 outliers final: 26 residues processed: 163 average time/residue: 1.2190 time to fit residues: 216.8258 Evaluate side-chains 169 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.0030 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN B 119 GLN B 381 GLN B 382 ASN C 223 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108762 restraints weight = 17011.063| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.77 r_work: 0.3190 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12486 Z= 0.158 Angle : 0.507 6.963 16852 Z= 0.265 Chirality : 0.043 0.235 1886 Planarity : 0.004 0.045 2148 Dihedral : 7.877 127.664 1644 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.37 % Allowed : 20.85 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1484 helix: 0.80 (0.22), residues: 588 sheet: -0.71 (0.27), residues: 348 loop : -0.23 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.018 0.001 TYR C 230 ARG 0.007 0.001 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.97 seconds wall clock time: 88 minutes 49.38 seconds (5329.38 seconds total)