Starting phenix.real_space_refine on Wed Jun 11 03:52:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_22243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_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/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_22243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_22243.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_22243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlg_22243/06_2025/6xlg_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-5710/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: 7.78, per 1000 atoms: 0.63 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: 2.65 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: 1.57 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: 3.76 Time building geometry restraints manager: 3.19 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: 0.05 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: 1.380 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.540 Find NCS groups from input model: 0.360 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- 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= 0.067 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 Details of bonding type rmsd hydrogen bonds : bond 0.25419 ( 560) hydrogen bonds : angle 8.19289 ( 1608) covalent geometry : bond 0.00119 (12486) covalent geometry : angle 0.35571 (16852) *********************** 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 to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.313 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: 1.5138 time to fit residues: 677.7028 Evaluate side-chains 194 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126536 restraints weight = 16809.354| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.76 r_work: 0.3443 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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= 0.137 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 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 560) hydrogen bonds : angle 5.48754 ( 1608) covalent geometry : bond 0.00311 (12486) covalent geometry : angle 0.56624 (16852) *********************** 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 to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: A 262 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 552 ASP cc_start: 0.7278 (p0) cc_final: 0.7057 (p0) REVERT: A 553 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6737 (mt) REVERT: A 633 LYS cc_start: 0.7742 (tppt) cc_final: 0.7399 (mmtm) REVERT: B 105 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: B 183 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: B 297 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 552 ASP cc_start: 0.7241 (p0) cc_final: 0.7021 (p0) REVERT: B 553 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6653 (mt) REVERT: B 633 LYS cc_start: 0.7768 (tppt) cc_final: 0.7436 (mmtm) REVERT: B 636 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7728 (ttpp) REVERT: C 227 SER cc_start: 0.8148 (p) cc_final: 0.7680 (t) REVERT: D 227 SER cc_start: 0.8184 (p) cc_final: 0.7706 (t) REVERT: D 230 TYR cc_start: 0.8424 (t80) cc_final: 0.8137 (t80) REVERT: D 271 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: D 333 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7364 (mt-10) outliers start: 48 outliers final: 14 residues processed: 249 average time/residue: 1.4364 time to fit residues: 384.3305 Evaluate side-chains 185 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 271 GLU 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 40 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110394 restraints weight = 17115.915| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.81 r_work: 0.3209 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12486 Z= 0.190 Angle : 0.578 5.902 16852 Z= 0.303 Chirality : 0.045 0.184 1886 Planarity : 0.004 0.034 2148 Dihedral : 8.550 156.492 1644 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.45 % Allowed : 16.10 % Favored : 79.45 % 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: -0.89 (0.21), residues: 1484 helix: 0.03 (0.21), residues: 576 sheet: -0.75 (0.27), residues: 340 loop : -0.96 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 285 HIS 0.005 0.002 HIS A 197 PHE 0.018 0.002 PHE C 344 TYR 0.015 0.002 TYR A 125 ARG 0.005 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 560) hydrogen bonds : angle 5.18186 ( 1608) covalent geometry : bond 0.00449 (12486) covalent geometry : angle 0.57809 (16852) *********************** 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 226 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 1.514 Fit side-chains REVERT: A 105 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8485 (mmm) REVERT: A 381 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.6002 (pm20) REVERT: A 633 LYS cc_start: 0.7732 (tppt) cc_final: 0.7434 (mmtm) REVERT: A 666 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7407 (mtm-85) REVERT: B 14 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8301 (mp10) REVERT: B 105 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8492 (mmm) REVERT: B 165 GLU cc_start: 0.7651 (pm20) cc_final: 0.7425 (pp20) REVERT: B 381 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5918 (pm20) REVERT: B 382 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7058 (p0) REVERT: B 552 ASP cc_start: 0.7365 (p0) cc_final: 0.7142 (p0) REVERT: B 623 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6841 (mppt) REVERT: B 633 LYS cc_start: 0.7765 (tppt) cc_final: 0.7469 (mmtm) REVERT: B 666 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7407 (mtm-85) REVERT: C 238 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7260 (mtm180) REVERT: C 333 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: D 230 TYR cc_start: 0.8702 (t80) cc_final: 0.8406 (t80) outliers start: 60 outliers final: 18 residues processed: 206 average time/residue: 1.4213 time to fit residues: 315.2522 Evaluate side-chains 164 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 381 GLN 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 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 382 ASN 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 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 142 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108094 restraints weight = 17027.440| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.81 r_work: 0.3177 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12486 Z= 0.181 Angle : 0.550 5.874 16852 Z= 0.288 Chirality : 0.044 0.204 1886 Planarity : 0.004 0.036 2148 Dihedral : 7.914 126.950 1644 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.01 % Allowed : 16.54 % Favored : 79.45 % 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: -0.71 (0.21), residues: 1484 helix: 0.24 (0.21), residues: 580 sheet: -0.76 (0.27), residues: 342 loop : -0.86 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 242 HIS 0.004 0.001 HIS C 284 PHE 0.016 0.002 PHE D 344 TYR 0.013 0.002 TYR B 565 ARG 0.005 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 560) hydrogen bonds : angle 5.02718 ( 1608) covalent geometry : bond 0.00426 (12486) covalent geometry : angle 0.55021 (16852) *********************** 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 204 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 1.857 Fit side-chains REVERT: A 105 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8520 (mmm) REVERT: A 264 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 553 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7158 (pp) REVERT: A 620 GLU cc_start: 0.7351 (tp30) cc_final: 0.6786 (tp30) REVERT: A 623 LYS cc_start: 0.7222 (mtpp) cc_final: 0.6839 (mppt) REVERT: A 633 LYS cc_start: 0.7668 (tppt) cc_final: 0.7361 (mmtm) REVERT: B 264 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: B 297 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: B 336 ASN cc_start: 0.8215 (m110) cc_final: 0.7599 (p0) REVERT: B 553 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7173 (pp) REVERT: B 620 GLU cc_start: 0.7307 (tp30) cc_final: 0.6728 (tp30) REVERT: B 623 LYS cc_start: 0.7265 (mtpp) cc_final: 0.6872 (mppt) REVERT: B 633 LYS cc_start: 0.7699 (tppt) cc_final: 0.7381 (mmtm) REVERT: C 238 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: C 262 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: D 230 TYR cc_start: 0.8770 (t80) cc_final: 0.8448 (t80) REVERT: D 240 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8650 (tt) REVERT: D 316 LYS cc_start: 0.8360 (tptt) cc_final: 0.7793 (tttm) outliers start: 54 outliers final: 19 residues processed: 189 average time/residue: 1.6914 time to fit residues: 344.3366 Evaluate side-chains 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 264 GLU 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 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 264 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 312 GLU 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 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 262 GLU 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 291 SER 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 89 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 578 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 247 GLN D 331 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109953 restraints weight = 16981.971| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.80 r_work: 0.3203 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12486 Z= 0.115 Angle : 0.490 5.225 16852 Z= 0.256 Chirality : 0.042 0.161 1886 Planarity : 0.003 0.033 2148 Dihedral : 7.802 123.167 1644 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.04 % Allowed : 17.51 % Favored : 79.45 % 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: -0.48 (0.21), residues: 1484 helix: 0.43 (0.21), residues: 590 sheet: -0.73 (0.27), residues: 344 loop : -0.67 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.011 0.001 TYR B 504 ARG 0.003 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 560) hydrogen bonds : angle 4.86856 ( 1608) covalent geometry : bond 0.00263 (12486) covalent geometry : angle 0.49019 (16852) *********************** 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 195 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.738 Fit side-chains REVERT: A 336 ASN cc_start: 0.8235 (m110) cc_final: 0.7613 (p0) REVERT: A 620 GLU cc_start: 0.7369 (tp30) cc_final: 0.6779 (tp30) REVERT: A 623 LYS cc_start: 0.7307 (mtpp) cc_final: 0.6954 (mppt) REVERT: A 633 LYS cc_start: 0.7570 (tppt) cc_final: 0.7255 (mmtm) REVERT: B 14 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8329 (mp10) REVERT: B 297 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: B 336 ASN cc_start: 0.8205 (m110) cc_final: 0.7640 (p0) REVERT: B 620 GLU cc_start: 0.7364 (tp30) cc_final: 0.6776 (tp30) REVERT: B 623 LYS cc_start: 0.7302 (mtpp) cc_final: 0.6933 (mppt) REVERT: B 633 LYS cc_start: 0.7564 (tppt) cc_final: 0.7265 (mmtp) REVERT: C 238 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7192 (mtm180) REVERT: C 247 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 262 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: D 230 TYR cc_start: 0.8778 (t80) cc_final: 0.8425 (t80) REVERT: D 240 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8684 (tt) REVERT: D 316 LYS cc_start: 0.8329 (tptt) cc_final: 0.7752 (tttm) outliers start: 41 outliers final: 19 residues processed: 176 average time/residue: 1.5516 time to fit residues: 296.1690 Evaluate side-chains 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN 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 297 GLU Chi-restraints excluded: chain B residue 339 LEU 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 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 262 GLU 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 274 SER Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 111 optimal weight: 0.0870 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 132 optimal weight: 0.0770 chunk 10 optimal weight: 0.0050 overall best weight: 0.5732 ------------------------------------------------------------------------------- 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN 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 D 247 GLN D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110643 restraints weight = 17127.898| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.80 r_work: 0.3214 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12486 Z= 0.103 Angle : 0.474 5.015 16852 Z= 0.247 Chirality : 0.042 0.154 1886 Planarity : 0.003 0.032 2148 Dihedral : 7.731 125.256 1644 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.67 % Allowed : 18.47 % Favored : 78.86 % 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: -0.27 (0.22), residues: 1484 helix: 0.63 (0.22), residues: 590 sheet: -0.66 (0.27), residues: 344 loop : -0.56 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.009 0.001 TYR B 504 ARG 0.005 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 560) hydrogen bonds : angle 4.74258 ( 1608) covalent geometry : bond 0.00230 (12486) covalent geometry : angle 0.47405 (16852) *********************** 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 184 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.441 Fit side-chains REVERT: A 183 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: A 336 ASN cc_start: 0.8271 (m110) cc_final: 0.7637 (p0) REVERT: A 633 LYS cc_start: 0.7543 (tppt) cc_final: 0.7259 (mmtm) REVERT: A 666 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7263 (mtm-85) REVERT: B 14 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: B 297 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: B 336 ASN cc_start: 0.8150 (m110) cc_final: 0.7696 (p0) REVERT: B 382 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.7131 (p0) REVERT: B 620 GLU cc_start: 0.7428 (tp30) cc_final: 0.6815 (tp30) REVERT: B 633 LYS cc_start: 0.7568 (tppt) cc_final: 0.7280 (mmtm) REVERT: C 238 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7211 (mtm180) REVERT: C 262 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: D 230 TYR cc_start: 0.8749 (t80) cc_final: 0.8418 (t80) REVERT: D 240 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8678 (tt) outliers start: 36 outliers final: 19 residues processed: 170 average time/residue: 1.3486 time to fit residues: 249.3546 Evaluate side-chains 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 183 GLU 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 381 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL 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 262 GLU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 382 ASN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 247 GLN D 295 ASN D 314 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108465 restraints weight = 17136.519| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.80 r_work: 0.3183 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12486 Z= 0.154 Angle : 0.512 6.035 16852 Z= 0.266 Chirality : 0.044 0.180 1886 Planarity : 0.004 0.041 2148 Dihedral : 7.823 123.449 1644 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.04 % Allowed : 18.25 % Favored : 78.71 % 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: -0.24 (0.22), residues: 1484 helix: 0.64 (0.22), residues: 590 sheet: -0.66 (0.27), residues: 344 loop : -0.50 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 PHE 0.012 0.001 PHE B 104 TYR 0.009 0.001 TYR B 504 ARG 0.006 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 560) hydrogen bonds : angle 4.76895 ( 1608) covalent geometry : bond 0.00359 (12486) covalent geometry : angle 0.51216 (16852) *********************** 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 193 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.339 Fit side-chains REVERT: A 57 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6914 (mt-10) REVERT: A 336 ASN cc_start: 0.8324 (m110) cc_final: 0.7674 (p0) REVERT: A 633 LYS cc_start: 0.7554 (tppt) cc_final: 0.7269 (mmtm) REVERT: B 297 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: B 336 ASN cc_start: 0.8190 (m110) cc_final: 0.7713 (p0) REVERT: B 633 LYS cc_start: 0.7550 (tppt) cc_final: 0.7254 (mmtm) REVERT: C 230 TYR cc_start: 0.8741 (t80) cc_final: 0.8295 (t80) REVERT: C 238 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7236 (mtm180) REVERT: D 230 TYR cc_start: 0.8793 (t80) cc_final: 0.8418 (t80) REVERT: D 240 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8715 (tt) outliers start: 41 outliers final: 27 residues processed: 179 average time/residue: 1.2525 time to fit residues: 244.3607 Evaluate side-chains 169 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 ILE 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 576 THR Chi-restraints excluded: chain A residue 634 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 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 297 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 634 THR Chi-restraints excluded: chain B residue 635 VAL 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 C residue 334 GLU 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 274 SER Chi-restraints excluded: chain D residue 291 SER 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 123 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107634 restraints weight = 17183.094| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.80 r_work: 0.3172 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12486 Z= 0.150 Angle : 0.521 5.750 16852 Z= 0.270 Chirality : 0.043 0.182 1886 Planarity : 0.004 0.035 2148 Dihedral : 7.895 124.936 1644 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.12 % Allowed : 18.84 % Favored : 78.04 % 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: -0.15 (0.22), residues: 1484 helix: 0.69 (0.22), residues: 590 sheet: -0.68 (0.27), residues: 344 loop : -0.39 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 PHE 0.011 0.001 PHE C 344 TYR 0.010 0.001 TYR B 504 ARG 0.006 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 560) hydrogen bonds : angle 4.80359 ( 1608) covalent geometry : bond 0.00351 (12486) covalent geometry : angle 0.52071 (16852) *********************** 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 188 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.359 Fit side-chains REVERT: A 57 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7003 (mt-10) REVERT: A 264 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 336 ASN cc_start: 0.8325 (m110) cc_final: 0.7645 (p0) REVERT: A 633 LYS cc_start: 0.7519 (tppt) cc_final: 0.7243 (mmtm) REVERT: A 666 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7259 (mtm-85) REVERT: B 57 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: B 297 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7741 (mm-30) REVERT: B 336 ASN cc_start: 0.8212 (m110) cc_final: 0.7621 (p0) REVERT: B 382 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.7032 (p0) REVERT: B 633 LYS cc_start: 0.7526 (tppt) cc_final: 0.7227 (mmtm) REVERT: B 666 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7274 (mtm-85) REVERT: C 230 TYR cc_start: 0.8704 (t80) cc_final: 0.8166 (t80) REVERT: C 238 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7239 (mtm180) REVERT: C 247 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 262 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 307 GLU cc_start: 0.6681 (pm20) cc_final: 0.6292 (tt0) REVERT: D 230 TYR cc_start: 0.8819 (t80) cc_final: 0.8484 (t80) REVERT: D 240 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8737 (tt) REVERT: D 316 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7787 (tttm) outliers start: 42 outliers final: 28 residues processed: 172 average time/residue: 1.2609 time to fit residues: 236.0881 Evaluate side-chains 176 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 ILE 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 312 GLU Chi-restraints excluded: chain A residue 339 LEU 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 A residue 635 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 57 GLU 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 297 GLU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL 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 247 GLN Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 334 GLU 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 274 SER 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 73 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN B 382 ASN C 284 HIS C 295 ASN C 314 GLN D 212 ASN D 223 ASN D 247 GLN D 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109341 restraints weight = 17088.811| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.80 r_work: 0.3199 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12486 Z= 0.107 Angle : 0.496 5.800 16852 Z= 0.257 Chirality : 0.042 0.198 1886 Planarity : 0.004 0.037 2148 Dihedral : 7.815 127.183 1644 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.89 % Allowed : 19.36 % Favored : 77.74 % 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: -0.04 (0.22), residues: 1484 helix: 0.81 (0.22), residues: 590 sheet: -0.69 (0.27), residues: 344 loop : -0.31 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 PHE 0.013 0.001 PHE B 6 TYR 0.010 0.001 TYR B 504 ARG 0.005 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 560) hydrogen bonds : angle 4.72604 ( 1608) covalent geometry : bond 0.00238 (12486) covalent geometry : angle 0.49591 (16852) *********************** 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 188 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.411 Fit side-chains REVERT: A 57 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6967 (mt-10) REVERT: A 336 ASN cc_start: 0.8272 (m110) cc_final: 0.7610 (p0) REVERT: A 382 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.7138 (p0) REVERT: A 633 LYS cc_start: 0.7505 (tppt) cc_final: 0.7232 (mmtm) REVERT: A 666 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7267 (mtm-85) REVERT: B 297 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: B 336 ASN cc_start: 0.8183 (m110) cc_final: 0.7689 (p0) REVERT: B 633 LYS cc_start: 0.7486 (tppt) cc_final: 0.7205 (mmtm) REVERT: B 666 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7274 (mtm-85) REVERT: C 230 TYR cc_start: 0.8689 (t80) cc_final: 0.8170 (t80) REVERT: C 238 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7250 (mtm180) REVERT: C 262 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: C 307 GLU cc_start: 0.6634 (pm20) cc_final: 0.6167 (tt0) REVERT: D 230 TYR cc_start: 0.8791 (t80) cc_final: 0.8387 (t80) REVERT: D 240 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8712 (tt) REVERT: D 307 GLU cc_start: 0.6913 (pt0) cc_final: 0.6560 (tt0) outliers start: 39 outliers final: 24 residues processed: 169 average time/residue: 1.2422 time to fit residues: 228.6422 Evaluate side-chains 171 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 ILE 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 382 ASN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 339 LEU 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 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 262 GLU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 334 GLU 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 291 SER Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 314 GLN C 331 ASN D 212 ASN D 247 GLN D 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109135 restraints weight = 17077.837| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.80 r_work: 0.3194 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 12486 Z= 0.190 Angle : 0.956 59.200 16852 Z= 0.583 Chirality : 0.046 0.510 1886 Planarity : 0.004 0.044 2148 Dihedral : 7.818 127.162 1644 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.37 % Allowed : 20.03 % Favored : 77.60 % Cbeta Deviations : 0.14 % 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: -0.05 (0.22), residues: 1484 helix: 0.80 (0.22), residues: 590 sheet: -0.68 (0.27), residues: 344 loop : -0.32 (0.26), residues: 550 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 0.012 0.001 PHE B 6 TYR 0.010 0.001 TYR B 504 ARG 0.006 0.000 ARG C 329 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 560) hydrogen bonds : angle 4.71962 ( 1608) covalent geometry : bond 0.00394 (12486) covalent geometry : angle 0.95551 (16852) ********************** 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 173 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.353 Fit side-chains REVERT: A 57 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6970 (mt-10) REVERT: A 336 ASN cc_start: 0.8272 (m110) cc_final: 0.7616 (p0) REVERT: A 633 LYS cc_start: 0.7501 (tppt) cc_final: 0.7229 (mmtm) REVERT: A 666 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7286 (mtm-85) REVERT: B 297 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: B 336 ASN cc_start: 0.8183 (m110) cc_final: 0.7693 (p0) REVERT: B 633 LYS cc_start: 0.7503 (tppt) cc_final: 0.7215 (mmtm) REVERT: B 666 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7266 (mtm-85) REVERT: C 230 TYR cc_start: 0.8690 (t80) cc_final: 0.8169 (t80) REVERT: C 238 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: C 262 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: C 307 GLU cc_start: 0.6628 (pm20) cc_final: 0.6160 (tt0) REVERT: D 230 TYR cc_start: 0.8793 (t80) cc_final: 0.8459 (t80) REVERT: D 240 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8719 (tt) REVERT: D 307 GLU cc_start: 0.6900 (pt0) cc_final: 0.6579 (tt0) REVERT: D 316 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7838 (tttm) outliers start: 32 outliers final: 26 residues processed: 158 average time/residue: 1.1841 time to fit residues: 204.5460 Evaluate side-chains 170 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 19 ILE 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 381 GLN Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 339 LEU 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 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 262 GLU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 334 GLU 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 291 SER Chi-restraints excluded: chain D residue 298 ILE 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 59 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- 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** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 314 GLN D 212 ASN D 223 ASN D 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109114 restraints weight = 17159.545| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.80 r_work: 0.3194 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.361 12486 Z= 0.273 Angle : 1.091 59.191 16852 Z= 0.669 Chirality : 0.045 0.529 1886 Planarity : 0.004 0.081 2148 Dihedral : 7.829 127.128 1644 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.52 % Allowed : 19.73 % Favored : 77.74 % Cbeta Deviations : 0.07 % 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: -0.06 (0.22), residues: 1484 helix: 0.80 (0.22), residues: 590 sheet: -0.68 (0.27), residues: 344 loop : -0.33 (0.26), residues: 550 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 0.012 0.001 PHE B 6 TYR 0.010 0.001 TYR B 504 ARG 0.007 0.000 ARG C 329 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 560) hydrogen bonds : angle 4.71956 ( 1608) covalent geometry : bond 0.00557 (12486) covalent geometry : angle 1.09109 (16852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9807.89 seconds wall clock time: 170 minutes 34.98 seconds (10234.98 seconds total)