Starting phenix.real_space_refine on Wed Sep 17 23:56:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlg_22243/09_2025/6xlg_22243.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlg_22243/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xlg_22243/09_2025/6xlg_22243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlg_22243/09_2025/6xlg_22243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xlg_22243/09_2025/6xlg_22243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlg_22243/09_2025/6xlg_22243.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.13, per 1000 atoms: 0.26 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: 0.89 Conformation dependent library (CDL) restraints added in 523.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.40 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: 2.22 Time building geometry restraints manager: 1.19 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 376 TYR 0.004 0.000 TYR C 230 PHE 0.006 0.001 PHE B 579 TRP 0.007 0.001 TRP B 273 HIS 0.001 0.000 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00119 (12486) covalent geometry : angle 0.35571 (16852) hydrogen bonds : bond 0.25419 ( 560) hydrogen bonds : angle 8.19289 ( 1608) *********************** 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 : 0.397 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: 0.7537 (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: 0.7604 (mtm110) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.7101 time to fit residues: 318.1294 Evaluate side-chains 192 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- 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 C 314 GLN D 212 ASN D 223 ASN D 284 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124059 restraints weight = 16809.589| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.76 r_work: 0.3412 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12486 Z= 0.160 Angle : 0.583 7.749 16852 Z= 0.300 Chirality : 0.044 0.148 1886 Planarity : 0.004 0.043 2148 Dihedral : 8.714 171.586 1644 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.86 % Allowed : 14.32 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.20), residues: 1484 helix: -0.60 (0.20), residues: 574 sheet: -0.82 (0.27), residues: 332 loop : -1.29 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 575 TYR 0.012 0.002 TYR B 565 PHE 0.019 0.002 PHE B 104 TRP 0.008 0.001 TRP C 285 HIS 0.006 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00373 (12486) covalent geometry : angle 0.58296 (16852) hydrogen bonds : bond 0.04199 ( 560) hydrogen bonds : angle 5.46706 ( 1608) *********************** 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 260 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: A 262 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 552 ASP cc_start: 0.7317 (p0) cc_final: 0.7093 (p0) REVERT: A 553 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6809 (mt) REVERT: A 633 LYS cc_start: 0.7749 (tppt) cc_final: 0.7393 (mmtm) REVERT: A 636 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7737 (ttpp) REVERT: B 105 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: B 183 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: B 262 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 297 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: B 462 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7297 (tm-30) REVERT: B 552 ASP cc_start: 0.7234 (p0) cc_final: 0.7005 (p0) REVERT: B 553 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6778 (mt) REVERT: B 633 LYS cc_start: 0.7775 (tppt) cc_final: 0.7435 (mmtm) REVERT: B 636 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7732 (ttpp) REVERT: C 227 SER cc_start: 0.8195 (p) cc_final: 0.7732 (t) REVERT: D 227 SER cc_start: 0.8216 (p) cc_final: 0.7729 (t) REVERT: D 271 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: D 333 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7404 (mt-10) outliers start: 52 outliers final: 14 residues processed: 247 average time/residue: 0.6686 time to fit residues: 177.3802 Evaluate side-chains 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 592 GLN C 223 ASN D 212 ASN D 223 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114672 restraints weight = 16794.372| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.77 r_work: 0.3277 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12486 Z= 0.179 Angle : 0.562 5.878 16852 Z= 0.293 Chirality : 0.044 0.162 1886 Planarity : 0.004 0.036 2148 Dihedral : 8.419 155.033 1644 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.23 % Allowed : 15.88 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.21), residues: 1484 helix: 0.01 (0.21), residues: 576 sheet: -0.78 (0.27), residues: 340 loop : -0.96 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 46 TYR 0.013 0.002 TYR B 504 PHE 0.016 0.002 PHE D 344 TRP 0.012 0.002 TRP D 285 HIS 0.005 0.002 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00422 (12486) covalent geometry : angle 0.56158 (16852) hydrogen bonds : bond 0.04119 ( 560) hydrogen bonds : angle 5.19607 ( 1608) *********************** 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 221 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 0.530 Fit side-chains REVERT: A 264 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: A 381 GLN cc_start: 0.6322 (pm20) cc_final: 0.6111 (pm20) REVERT: A 633 LYS cc_start: 0.7746 (tppt) cc_final: 0.7463 (mmtm) REVERT: A 666 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7449 (mtm-85) REVERT: B 14 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: B 105 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8434 (mmm) REVERT: B 165 GLU cc_start: 0.7511 (pm20) cc_final: 0.7310 (pp20) REVERT: B 381 GLN cc_start: 0.6244 (pm20) cc_final: 0.5958 (pm20) REVERT: B 623 LYS cc_start: 0.7235 (mtpp) cc_final: 0.6904 (mppt) REVERT: B 633 LYS cc_start: 0.7817 (tppt) cc_final: 0.7522 (mmtm) REVERT: B 666 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7432 (mtm-85) REVERT: C 238 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7278 (mtm180) REVERT: C 333 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7521 (tp30) outliers start: 57 outliers final: 17 residues processed: 199 average time/residue: 0.7019 time to fit residues: 149.9851 Evaluate side-chains 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 105 MET 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 576 THR Chi-restraints excluded: chain B residue 635 VAL 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 Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 123 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 A 578 GLN B 382 ASN B 430 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112871 restraints weight = 17044.249| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.81 r_work: 0.3247 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12486 Z= 0.108 Angle : 0.488 5.353 16852 Z= 0.254 Chirality : 0.042 0.147 1886 Planarity : 0.003 0.032 2148 Dihedral : 7.736 131.726 1644 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.97 % Allowed : 17.36 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1484 helix: 0.41 (0.22), residues: 578 sheet: -0.70 (0.27), residues: 348 loop : -0.69 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.010 0.001 TYR B 504 PHE 0.014 0.001 PHE B 6 TRP 0.014 0.001 TRP D 242 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00241 (12486) covalent geometry : angle 0.48799 (16852) hydrogen bonds : bond 0.03294 ( 560) hydrogen bonds : angle 4.91550 ( 1608) *********************** 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 206 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.492 Fit side-chains REVERT: A 165 GLU cc_start: 0.7578 (pm20) cc_final: 0.7367 (pp20) REVERT: A 620 GLU cc_start: 0.7344 (tp30) cc_final: 0.6781 (tp30) REVERT: A 623 LYS cc_start: 0.7221 (mtpp) cc_final: 0.6866 (mppt) REVERT: A 633 LYS cc_start: 0.7596 (tppt) cc_final: 0.7316 (mmtp) REVERT: B 14 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: B 336 ASN cc_start: 0.8176 (m110) cc_final: 0.7726 (p0) REVERT: B 381 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: B 620 GLU cc_start: 0.7282 (tp30) cc_final: 0.6723 (tp30) REVERT: B 623 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6827 (mppt) REVERT: B 633 LYS cc_start: 0.7636 (tppt) cc_final: 0.7367 (mmtm) REVERT: C 238 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7170 (mtm180) REVERT: C 262 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: D 240 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8583 (tt) outliers start: 40 outliers final: 15 residues processed: 191 average time/residue: 0.6541 time to fit residues: 134.5643 Evaluate side-chains 161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 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 D residue 218 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 A 430 GLN B 380 GLN B 382 ASN B 430 GLN B 578 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 314 GLN D 331 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107048 restraints weight = 17269.952| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.80 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12486 Z= 0.190 Angle : 0.562 5.663 16852 Z= 0.294 Chirality : 0.045 0.211 1886 Planarity : 0.004 0.032 2148 Dihedral : 7.991 124.322 1644 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.86 % Allowed : 17.14 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1484 helix: 0.32 (0.21), residues: 590 sheet: -0.67 (0.27), residues: 346 loop : -0.69 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 666 TYR 0.015 0.002 TYR B 184 PHE 0.018 0.002 PHE D 344 TRP 0.011 0.002 TRP D 242 HIS 0.005 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00449 (12486) covalent geometry : angle 0.56188 (16852) hydrogen bonds : bond 0.03812 ( 560) hydrogen bonds : angle 4.98291 ( 1608) *********************** 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 209 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 0.470 Fit side-chains REVERT: A 264 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: A 336 ASN cc_start: 0.8287 (m110) cc_final: 0.7597 (p0) REVERT: A 633 LYS cc_start: 0.7609 (tppt) cc_final: 0.7289 (mmtp) REVERT: B 14 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: B 264 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: B 297 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 336 ASN cc_start: 0.8242 (m110) cc_final: 0.7652 (p0) REVERT: B 531 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: B 633 LYS cc_start: 0.7606 (tppt) cc_final: 0.7271 (mmtp) REVERT: B 666 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7297 (mtm-85) REVERT: C 238 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7177 (mtm180) REVERT: C 247 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: C 262 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: D 240 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8719 (tt) REVERT: D 316 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7771 (tttm) outliers start: 52 outliers final: 20 residues processed: 190 average time/residue: 0.6557 time to fit residues: 134.2406 Evaluate side-chains 172 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 GLN 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 339 LEU Chi-restraints excluded: chain B residue 531 GLU 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 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 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 Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107974 restraints weight = 17192.231| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.80 r_work: 0.3176 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12486 Z= 0.145 Angle : 0.520 5.605 16852 Z= 0.271 Chirality : 0.043 0.188 1886 Planarity : 0.004 0.037 2148 Dihedral : 7.913 125.169 1644 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.78 % Allowed : 17.43 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1484 helix: 0.45 (0.21), residues: 590 sheet: -0.62 (0.27), residues: 346 loop : -0.55 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 46 TYR 0.018 0.001 TYR D 230 PHE 0.012 0.001 PHE B 6 TRP 0.015 0.001 TRP D 242 HIS 0.004 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00339 (12486) covalent geometry : angle 0.51963 (16852) hydrogen bonds : bond 0.03485 ( 560) hydrogen bonds : angle 4.88698 ( 1608) *********************** 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 202 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.534 Fit side-chains REVERT: A 336 ASN cc_start: 0.8292 (m110) cc_final: 0.7603 (p0) REVERT: A 381 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5919 (pm20) REVERT: A 633 LYS cc_start: 0.7557 (tppt) cc_final: 0.7263 (mmtm) REVERT: A 666 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7279 (mtm-85) REVERT: B 336 ASN cc_start: 0.8217 (m110) cc_final: 0.7617 (p0) REVERT: B 633 LYS cc_start: 0.7568 (tppt) cc_final: 0.7245 (mmtp) REVERT: B 666 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7232 (mtm-85) REVERT: C 238 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7210 (mtm180) REVERT: C 247 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: C 262 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: C 307 GLU cc_start: 0.6745 (pm20) cc_final: 0.6343 (tt0) REVERT: D 240 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8721 (tt) outliers start: 51 outliers final: 21 residues processed: 181 average time/residue: 0.6305 time to fit residues: 123.3265 Evaluate side-chains 166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 142 GLU 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 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 145 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 382 ASN B 380 GLN ** 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 C 331 ASN D 212 ASN D 223 ASN D 247 GLN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108968 restraints weight = 17024.488| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.80 r_work: 0.3192 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12486 Z= 0.116 Angle : 0.503 5.730 16852 Z= 0.261 Chirality : 0.043 0.169 1886 Planarity : 0.003 0.039 2148 Dihedral : 7.849 126.490 1644 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.89 % Allowed : 18.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.22), residues: 1484 helix: 0.60 (0.22), residues: 590 sheet: -0.63 (0.27), residues: 342 loop : -0.49 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.020 0.001 TYR D 230 PHE 0.013 0.001 PHE B 6 TRP 0.016 0.001 TRP D 242 HIS 0.005 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00265 (12486) covalent geometry : angle 0.50305 (16852) hydrogen bonds : bond 0.03250 ( 560) hydrogen bonds : angle 4.80157 ( 1608) *********************** 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 187 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.455 Fit side-chains REVERT: A 336 ASN cc_start: 0.8242 (m110) cc_final: 0.7577 (p0) REVERT: A 633 LYS cc_start: 0.7519 (tppt) cc_final: 0.7243 (mmtm) REVERT: A 666 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7241 (mtm-85) REVERT: B 297 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: B 336 ASN cc_start: 0.8185 (m110) cc_final: 0.7601 (p0) REVERT: B 382 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.7049 (p0) REVERT: B 620 GLU cc_start: 0.7378 (tp30) cc_final: 0.6747 (tp30) REVERT: B 633 LYS cc_start: 0.7548 (tppt) cc_final: 0.7258 (mmtm) REVERT: C 230 TYR cc_start: 0.8676 (t80) cc_final: 0.8168 (t80) REVERT: C 238 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7171 (mtm180) REVERT: C 262 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: C 307 GLU cc_start: 0.6709 (pm20) cc_final: 0.6247 (tt0) REVERT: D 240 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8695 (tt) REVERT: D 316 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7806 (tttm) outliers start: 39 outliers final: 24 residues processed: 169 average time/residue: 0.5455 time to fit residues: 100.7386 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 : 0.511 ------------------------------------------------------------------------------- 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 339 LEU 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 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 382 ASN Chi-restraints excluded: chain B residue 531 GLU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 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 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 380 GLN B 381 GLN B 382 ASN B 430 GLN C 223 ASN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 212 ASN D 223 ASN D 247 GLN D 284 HIS D 314 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109369 restraints weight = 17079.340| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.79 r_work: 0.3196 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12486 Z= 0.114 Angle : 0.495 5.441 16852 Z= 0.257 Chirality : 0.042 0.145 1886 Planarity : 0.004 0.044 2148 Dihedral : 7.821 126.720 1644 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.12 % Allowed : 18.77 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.22), residues: 1484 helix: 0.69 (0.22), residues: 590 sheet: -0.62 (0.27), residues: 346 loop : -0.43 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 666 TYR 0.022 0.001 TYR D 230 PHE 0.013 0.001 PHE B 6 TRP 0.016 0.001 TRP D 242 HIS 0.004 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00260 (12486) covalent geometry : angle 0.49472 (16852) hydrogen bonds : bond 0.03174 ( 560) hydrogen bonds : angle 4.74134 ( 1608) *********************** 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 184 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.415 Fit side-chains REVERT: A 336 ASN cc_start: 0.8239 (m110) cc_final: 0.7653 (p0) REVERT: A 381 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5844 (pm20) REVERT: A 633 LYS cc_start: 0.7500 (tppt) cc_final: 0.7231 (mmtm) REVERT: B 336 ASN cc_start: 0.8188 (m110) cc_final: 0.7748 (p0) REVERT: B 480 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8233 (mttm) REVERT: B 620 GLU cc_start: 0.7423 (tp30) cc_final: 0.6784 (tp30) REVERT: B 633 LYS cc_start: 0.7508 (tppt) cc_final: 0.7223 (mmtm) REVERT: B 666 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7285 (mtm-85) REVERT: C 230 TYR cc_start: 0.8675 (t80) cc_final: 0.8227 (t80) REVERT: C 238 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7233 (mtm180) REVERT: C 262 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: C 307 GLU cc_start: 0.6725 (pm20) cc_final: 0.6250 (tt0) REVERT: D 240 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8703 (tt) REVERT: D 316 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7790 (tttm) outliers start: 42 outliers final: 23 residues processed: 166 average time/residue: 0.5782 time to fit residues: 104.0166 Evaluate side-chains 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 142 GLU 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 370 LEU Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 480 LYS 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 D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 0.0060 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN B 381 GLN B 382 ASN 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 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108419 restraints weight = 17003.719| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.79 r_work: 0.3186 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12486 Z= 0.138 Angle : 0.516 5.568 16852 Z= 0.268 Chirality : 0.043 0.170 1886 Planarity : 0.004 0.052 2148 Dihedral : 7.862 125.660 1644 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.74 % Allowed : 18.84 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.22), residues: 1484 helix: 0.69 (0.22), residues: 590 sheet: -0.64 (0.27), residues: 348 loop : -0.36 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 46 TYR 0.023 0.001 TYR D 230 PHE 0.012 0.001 PHE B 6 TRP 0.015 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00320 (12486) covalent geometry : angle 0.51621 (16852) hydrogen bonds : bond 0.03278 ( 560) hydrogen bonds : angle 4.74190 ( 1608) *********************** 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 184 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.540 Fit side-chains REVERT: A 336 ASN cc_start: 0.8247 (m110) cc_final: 0.7652 (p0) REVERT: A 633 LYS cc_start: 0.7503 (tppt) cc_final: 0.7226 (mmtm) REVERT: A 666 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7232 (mtm-85) REVERT: B 336 ASN cc_start: 0.8200 (m110) cc_final: 0.7758 (p0) REVERT: B 480 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8250 (mttm) REVERT: B 633 LYS cc_start: 0.7519 (tppt) cc_final: 0.7230 (mmtm) REVERT: B 666 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7296 (mtm-85) REVERT: C 230 TYR cc_start: 0.8683 (t80) cc_final: 0.8190 (t80) REVERT: C 238 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7213 (mtm180) REVERT: C 262 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: C 307 GLU cc_start: 0.6755 (pm20) cc_final: 0.6321 (tt0) REVERT: D 240 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8704 (tt) REVERT: D 307 GLU cc_start: 0.6917 (pt0) cc_final: 0.6606 (tt0) outliers start: 37 outliers final: 24 residues processed: 169 average time/residue: 0.5745 time to fit residues: 105.4542 Evaluate side-chains 167 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 142 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 142 GLU 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 480 LYS 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 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 72 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 113 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** 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 247 GLN D 314 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110004 restraints weight = 17110.332| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.80 r_work: 0.3208 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12486 Z= 0.106 Angle : 0.497 6.269 16852 Z= 0.257 Chirality : 0.042 0.164 1886 Planarity : 0.003 0.032 2148 Dihedral : 7.802 128.167 1644 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.45 % Allowed : 19.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1484 helix: 0.81 (0.22), residues: 590 sheet: -0.65 (0.27), residues: 348 loop : -0.28 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.025 0.001 TYR D 230 PHE 0.013 0.001 PHE B 6 TRP 0.016 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00238 (12486) covalent geometry : angle 0.49663 (16852) hydrogen bonds : bond 0.03042 ( 560) hydrogen bonds : angle 4.67947 ( 1608) ********************** 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 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 336 ASN cc_start: 0.8173 (m110) cc_final: 0.7600 (p0) REVERT: A 633 LYS cc_start: 0.7507 (tppt) cc_final: 0.7243 (mmtm) REVERT: A 666 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7243 (mtm-85) REVERT: B 336 ASN cc_start: 0.8136 (m110) cc_final: 0.7713 (p0) REVERT: B 480 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8234 (mttm) REVERT: B 633 LYS cc_start: 0.7504 (tppt) cc_final: 0.7218 (mmtm) REVERT: B 666 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7293 (mtm-85) REVERT: C 230 TYR cc_start: 0.8669 (t80) cc_final: 0.8176 (t80) REVERT: C 231 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7737 (tp30) REVERT: C 262 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: C 307 GLU cc_start: 0.6739 (pm20) cc_final: 0.6249 (tt0) REVERT: D 231 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7500 (tt0) REVERT: D 240 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8716 (tt) REVERT: D 307 GLU cc_start: 0.6874 (pt0) cc_final: 0.6507 (tt0) REVERT: D 316 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7768 (tttm) outliers start: 33 outliers final: 22 residues processed: 167 average time/residue: 0.5623 time to fit residues: 102.3135 Evaluate side-chains 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 480 LYS 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 D residue 218 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 8 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 147 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN C 223 ASN C 314 GLN D 212 ASN D 223 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 = 0.3587 r_free = 0.3587 target = 0.130548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109974 restraints weight = 17086.802| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.79 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 12486 Z= 0.169 Angle : 0.801 59.073 16852 Z= 0.467 Chirality : 0.046 0.776 1886 Planarity : 0.003 0.033 2148 Dihedral : 7.797 128.159 1644 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.93 % Allowed : 20.18 % Favored : 77.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1484 helix: 0.81 (0.22), residues: 590 sheet: -0.65 (0.27), residues: 348 loop : -0.29 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 46 TYR 0.021 0.001 TYR D 230 PHE 0.012 0.001 PHE B 6 TRP 0.016 0.001 TRP D 242 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00345 (12486) covalent geometry : angle 0.80058 (16852) hydrogen bonds : bond 0.03042 ( 560) hydrogen bonds : angle 4.67926 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4527.40 seconds wall clock time: 77 minutes 57.11 seconds (4677.11 seconds total)