Starting phenix.real_space_refine on Wed Mar 4 16:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhs_24468/03_2026/7rhs_24468.map" } resolution = 2.93 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= 0.002 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 Na 1 4.78 5 C 9644 2.51 5 N 2398 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14767 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 456, 3717 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} Conformer: "B" Number of residues, atoms: 456, 3717 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} bond proxies already assigned to first conformer: 3791 Chain: "B" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3692 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 14, 'TRANS': 438} Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Conformer: "B" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} bond proxies already assigned to first conformer: 3684 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.32 Number of scatterers: 14767 At special positions: 0 Unit cell: (129.478, 118.757, 109.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 Na 1 11.00 O 2658 8.00 N 2398 7.00 C 9644 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 720.7 milliseconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 67.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.955A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.093A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.767A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.980A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.266A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 removed outlier: 3.648A pdb=" N THR A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.700A pdb=" N ILE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 610 Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.718A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.939A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.913A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.692A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.002A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.371A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 407 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 6.421A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.758A pdb=" N TYR C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.852A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.721A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.959A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.212A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.052A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 407 Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 6.710A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'D' and resid 215 through 242 removed outlier: 3.722A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.513A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 3.767A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.830A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.824A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 315 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 329 removed outlier: 4.490A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.140A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.385A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.617A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.504A pdb=" N LEU D 595 " --> pdb=" O GLU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.585A pdb=" N ASN A 523 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.837A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.567A pdb=" N TYR B 508 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER B 570 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 510 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 527 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 540 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 529 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 503 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.791A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.098A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.628A pdb=" N SER D 588 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.687A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 607 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2722 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: 2.42 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3105 1.33 - 1.45: 3524 1.45 - 1.57: 8377 1.57 - 1.69: 1 1.69 - 1.81: 105 Bond restraints: 15112 Sorted by residual: bond pdb=" N PRO B 163 " pdb=" CD PRO B 163 " ideal model delta sigma weight residual 1.473 1.354 0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" C ARG D 442 " pdb=" O ARG D 442 " ideal model delta sigma weight residual 1.237 1.315 -0.079 1.17e-02 7.31e+03 4.52e+01 bond pdb=" C PHE A 392 " pdb=" O PHE A 392 " ideal model delta sigma weight residual 1.236 1.310 -0.074 1.25e-02 6.40e+03 3.53e+01 bond pdb=" N PRO D 309 " pdb=" CD PRO D 309 " ideal model delta sigma weight residual 1.473 1.413 0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" C PHE A 392 " pdb=" CA APHE A 392 " ideal model delta sigma weight residual 1.522 1.577 -0.055 1.39e-02 5.18e+03 1.58e+01 ... (remaining 15107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 19987 2.66 - 5.31: 453 5.31 - 7.97: 45 7.97 - 10.63: 12 10.63 - 13.28: 2 Bond angle restraints: 20499 Sorted by residual: angle pdb=" O PHE A 392 " pdb=" C PHE A 392 " pdb=" CA BPHE A 392 " ideal model delta sigma weight residual 120.10 129.67 -9.57 1.13e+00 7.83e-01 7.17e+01 angle pdb=" O ARG D 442 " pdb=" C ARG D 442 " pdb=" CA BARG D 442 " ideal model delta sigma weight residual 120.55 129.48 -8.93 1.06e+00 8.90e-01 7.10e+01 angle pdb=" O ARG D 442 " pdb=" C ARG D 442 " pdb=" CA AARG D 442 " ideal model delta sigma weight residual 120.55 129.46 -8.91 1.06e+00 8.90e-01 7.07e+01 angle pdb=" N SER B 560 " pdb=" CA SER B 560 " pdb=" C SER B 560 " ideal model delta sigma weight residual 111.14 120.19 -9.05 1.08e+00 8.57e-01 7.02e+01 angle pdb=" N PHE A 392 " pdb=" CA BPHE A 392 " pdb=" C PHE A 392 " ideal model delta sigma weight residual 111.71 118.98 -7.27 1.15e+00 7.56e-01 3.99e+01 ... (remaining 20494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 7987 16.38 - 32.75: 825 32.75 - 49.13: 140 49.13 - 65.51: 29 65.51 - 81.89: 13 Dihedral angle restraints: 8994 sinusoidal: 3666 harmonic: 5328 Sorted by residual: dihedral pdb=" CA ILE B 366 " pdb=" C ILE B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA MET A 607 " pdb=" C MET A 607 " pdb=" N LYS A 608 " pdb=" CA LYS A 608 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU B 227 " pdb=" C LEU B 227 " pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1971 0.073 - 0.147: 299 0.147 - 0.220: 52 0.220 - 0.293: 9 0.293 - 0.367: 1 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CB ILE D 564 " pdb=" CA ILE D 564 " pdb=" CG1 ILE D 564 " pdb=" CG2 ILE D 564 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE B 303 " pdb=" CA ILE B 303 " pdb=" CG1 ILE B 303 " pdb=" CG2 ILE B 303 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE C 159 " pdb=" CA ILE C 159 " pdb=" CG1 ILE C 159 " pdb=" CG2 ILE C 159 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2329 not shown) Planarity restraints: 2541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO D 273 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 504 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO C 505 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 505 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 505 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 546 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO D 547 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " -0.036 5.00e-02 4.00e+02 ... (remaining 2538 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4773 2.83 - 3.35: 13251 3.35 - 3.87: 25562 3.87 - 4.38: 29160 4.38 - 4.90: 50341 Nonbonded interactions: 123087 Sorted by model distance: nonbonded pdb=" O TRP A 358 " pdb=" OG1 THR A 362 " model vdw 2.318 3.040 nonbonded pdb=" O LYS A 431 " pdb=" OG1 THR A 435 " model vdw 2.332 3.040 nonbonded pdb=" O TRP D 482 " pdb=" OG1 THR D 486 " model vdw 2.334 3.040 nonbonded pdb=" O LEU D 222 " pdb=" OG1 THR D 226 " model vdw 2.342 3.040 nonbonded pdb=" O THR B 360 " pdb=" OG1 THR B 364 " model vdw 2.343 3.040 ... (remaining 123082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 391 or resid 393 through 611 or resid 801)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 801)) selection = (chain 'C' and (resid 159 through 391 or resid 393 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.006 0.119 15115 Z= 0.307 Angle : 0.956 13.282 20508 Z= 0.563 Chirality : 0.057 0.367 2332 Planarity : 0.008 0.078 2538 Dihedral : 13.639 81.887 5574 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.00 % 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 are not related in a simple way. whole: -3.90 (0.15), residues: 1798 helix: -3.08 (0.09), residues: 1122 sheet: -1.39 (0.64), residues: 53 loop : -1.22 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 294 TYR 0.025 0.002 TYR D 351 PHE 0.025 0.002 PHE C 301 TRP 0.028 0.003 TRP B 171 HIS 0.007 0.002 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00630 (15112) covalent geometry : angle 0.95532 (20499) hydrogen bonds : bond 0.13565 ( 945) hydrogen bonds : angle 6.95709 ( 2722) link_NAG-ASN : bond 0.00393 ( 3) link_NAG-ASN : angle 2.17965 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.567 Fit side-chains REVERT: A 265 LYS cc_start: 0.7604 (tmtt) cc_final: 0.7390 (tptt) REVERT: A 302 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7283 (mtp-110) REVERT: A 418 ASP cc_start: 0.8259 (m-30) cc_final: 0.7812 (m-30) REVERT: A 455 GLU cc_start: 0.7869 (mp0) cc_final: 0.7563 (mp0) REVERT: A 458 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8090 (pttm) REVERT: A 535 VAL cc_start: 0.8420 (m) cc_final: 0.8162 (t) REVERT: A 556 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7876 (mtmp) REVERT: A 603 ARG cc_start: 0.7206 (ttt-90) cc_final: 0.6864 (ttm-80) REVERT: B 228 GLU cc_start: 0.7687 (pp20) cc_final: 0.7424 (pp20) REVERT: B 499 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7417 (ttp-110) REVERT: B 575 ASP cc_start: 0.7963 (t0) cc_final: 0.7653 (t0) REVERT: C 193 ASP cc_start: 0.8105 (t0) cc_final: 0.7850 (t0) REVERT: C 217 ASP cc_start: 0.8689 (t70) cc_final: 0.8457 (t0) REVERT: C 467 GLU cc_start: 0.7397 (tp30) cc_final: 0.7073 (tp30) REVERT: C 499 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7423 (ptt90) REVERT: C 514 ASP cc_start: 0.7675 (m-30) cc_final: 0.7162 (m-30) REVERT: C 542 SER cc_start: 0.8342 (p) cc_final: 0.8009 (m) REVERT: D 268 MET cc_start: 0.8890 (mtp) cc_final: 0.8674 (mtp) REVERT: D 316 PHE cc_start: 0.8672 (m-80) cc_final: 0.8344 (m-10) REVERT: D 443 ASP cc_start: 0.8163 (t70) cc_final: 0.7907 (t70) REVERT: D 452 GLN cc_start: 0.7638 (tp-100) cc_final: 0.7282 (tm-30) REVERT: D 468 ASN cc_start: 0.8957 (t0) cc_final: 0.8733 (t0) REVERT: D 477 LYS cc_start: 0.7785 (tttm) cc_final: 0.7325 (tppt) REVERT: D 513 ASP cc_start: 0.8006 (t0) cc_final: 0.7706 (t0) REVERT: D 593 ILE cc_start: 0.9134 (tp) cc_final: 0.8837 (mt) outliers start: 1 outliers final: 2 residues processed: 284 average time/residue: 0.6252 time to fit residues: 193.8537 Evaluate side-chains 180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain D residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 229 GLN A 241 GLN A 248 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 473 HIS A 554 ASN A 604 GLN B 196 GLN B 229 GLN B 248 GLN C 241 GLN C 248 GLN C 398 ASN C 407 ASN C 422 GLN C 425 GLN C 473 HIS ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 340 HIS D 365 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102686 restraints weight = 36562.201| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.86 r_work: 0.3117 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15115 Z= 0.127 Angle : 0.538 8.064 20508 Z= 0.289 Chirality : 0.041 0.198 2332 Planarity : 0.005 0.049 2538 Dihedral : 5.390 59.622 2069 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.85 % Allowed : 12.28 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 1798 helix: -0.46 (0.13), residues: 1134 sheet: -1.07 (0.64), residues: 60 loop : -0.37 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 279 TYR 0.015 0.001 TYR C 263 PHE 0.015 0.001 PHE B 192 TRP 0.014 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00275 (15112) covalent geometry : angle 0.53592 (20499) hydrogen bonds : bond 0.04158 ( 945) hydrogen bonds : angle 4.53107 ( 2722) link_NAG-ASN : bond 0.00096 ( 3) link_NAG-ASN : angle 2.24663 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7447 (mtp-110) REVERT: A 405 ASN cc_start: 0.8204 (t0) cc_final: 0.7930 (m-40) REVERT: A 425 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6647 (mp-120) REVERT: A 455 GLU cc_start: 0.8239 (mp0) cc_final: 0.7932 (mp0) REVERT: A 458 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8202 (pttm) REVERT: A 481 ARG cc_start: 0.8728 (mtm180) cc_final: 0.8355 (mtm180) REVERT: A 535 VAL cc_start: 0.8495 (m) cc_final: 0.8282 (t) REVERT: A 556 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7779 (mtmp) REVERT: A 603 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6741 (ttm-80) REVERT: B 418 ASP cc_start: 0.8175 (m-30) cc_final: 0.7814 (m-30) REVERT: B 425 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6999 (mp-120) REVERT: B 499 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7864 (ttp-110) REVERT: B 575 ASP cc_start: 0.8286 (t0) cc_final: 0.8005 (t0) REVERT: C 193 ASP cc_start: 0.8451 (t0) cc_final: 0.8168 (t0) REVERT: C 402 MET cc_start: 0.8065 (ttp) cc_final: 0.7856 (ttp) REVERT: C 481 ARG cc_start: 0.8923 (mtm110) cc_final: 0.8695 (mtp180) REVERT: C 514 ASP cc_start: 0.7818 (m-30) cc_final: 0.7218 (m-30) REVERT: C 539 VAL cc_start: 0.8593 (t) cc_final: 0.8262 (p) REVERT: C 542 SER cc_start: 0.8331 (p) cc_final: 0.8034 (m) REVERT: D 316 PHE cc_start: 0.8636 (m-80) cc_final: 0.8265 (m-10) REVERT: D 378 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7838 (mt-10) REVERT: D 452 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7683 (tm-30) REVERT: D 477 LYS cc_start: 0.8202 (tttm) cc_final: 0.7725 (tppt) REVERT: D 513 ASP cc_start: 0.8474 (t0) cc_final: 0.8181 (t0) REVERT: D 593 ILE cc_start: 0.9050 (tp) cc_final: 0.8640 (mt) REVERT: D 636 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7611 (mtm110) outliers start: 30 outliers final: 6 residues processed: 218 average time/residue: 0.5880 time to fit residues: 141.1530 Evaluate side-chains 180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 142 optimal weight: 5.9990 chunk 156 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 405 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 241 GLN C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102121 restraints weight = 40768.404| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.91 r_work: 0.3101 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15115 Z= 0.131 Angle : 0.512 8.101 20508 Z= 0.274 Chirality : 0.041 0.193 2332 Planarity : 0.004 0.043 2538 Dihedral : 4.907 58.237 2064 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.91 % Allowed : 13.58 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 1798 helix: 0.71 (0.15), residues: 1128 sheet: -0.26 (0.68), residues: 50 loop : -0.16 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 279 TYR 0.012 0.001 TYR C 263 PHE 0.014 0.001 PHE B 192 TRP 0.013 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00291 (15112) covalent geometry : angle 0.51015 (20499) hydrogen bonds : bond 0.03879 ( 945) hydrogen bonds : angle 4.10626 ( 2722) link_NAG-ASN : bond 0.00095 ( 3) link_NAG-ASN : angle 2.15906 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.518 Fit side-chains REVERT: A 302 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7607 (mtp-110) REVERT: A 425 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6644 (mp-120) REVERT: A 455 GLU cc_start: 0.8275 (mp0) cc_final: 0.7984 (mp0) REVERT: A 458 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8232 (pttm) REVERT: A 481 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8368 (mtm180) REVERT: A 556 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7593 (mtmp) REVERT: A 599 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: A 603 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.6822 (ttm-80) REVERT: B 418 ASP cc_start: 0.8183 (m-30) cc_final: 0.7814 (m-30) REVERT: B 425 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.6990 (mp-120) REVERT: B 499 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8103 (ttp-110) REVERT: B 559 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7687 (mmtt) REVERT: C 193 ASP cc_start: 0.8370 (t0) cc_final: 0.7998 (t0) REVERT: C 514 ASP cc_start: 0.7837 (m-30) cc_final: 0.7282 (m-30) REVERT: C 542 SER cc_start: 0.8442 (p) cc_final: 0.8201 (m) REVERT: C 559 LYS cc_start: 0.6662 (mmtt) cc_final: 0.6397 (mmtt) REVERT: D 301 GLN cc_start: 0.8616 (mp-120) cc_final: 0.8303 (mm-40) REVERT: D 316 PHE cc_start: 0.8637 (m-80) cc_final: 0.8313 (m-10) REVERT: D 452 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7784 (tm-30) REVERT: D 477 LYS cc_start: 0.8317 (tttm) cc_final: 0.7896 (tppt) REVERT: D 513 ASP cc_start: 0.8407 (t0) cc_final: 0.8127 (t0) REVERT: D 593 ILE cc_start: 0.9122 (tp) cc_final: 0.8738 (mt) REVERT: D 636 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7703 (mtm110) outliers start: 31 outliers final: 10 residues processed: 208 average time/residue: 0.5794 time to fit residues: 132.5709 Evaluate side-chains 185 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 150 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 554 ASN C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101597 restraints weight = 33023.276| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.63 r_work: 0.3107 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15115 Z= 0.142 Angle : 0.511 8.352 20508 Z= 0.272 Chirality : 0.041 0.189 2332 Planarity : 0.004 0.057 2538 Dihedral : 4.673 57.164 2064 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.22 % Allowed : 13.52 % Favored : 84.26 % 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 are not related in a simple way. whole: 1.09 (0.20), residues: 1798 helix: 1.26 (0.15), residues: 1122 sheet: -0.14 (0.69), residues: 50 loop : -0.04 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 279 TYR 0.013 0.001 TYR B 297 PHE 0.015 0.001 PHE B 192 TRP 0.013 0.001 TRP D 373 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00322 (15112) covalent geometry : angle 0.50903 (20499) hydrogen bonds : bond 0.03850 ( 945) hydrogen bonds : angle 3.98792 ( 2722) link_NAG-ASN : bond 0.00078 ( 3) link_NAG-ASN : angle 2.09190 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7568 (mtp-110) REVERT: A 422 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8555 (tt0) REVERT: A 425 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6590 (mp-120) REVERT: A 431 LYS cc_start: 0.8578 (mppt) cc_final: 0.8237 (tppp) REVERT: A 455 GLU cc_start: 0.8287 (mp0) cc_final: 0.7938 (mp0) REVERT: A 458 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8251 (pttm) REVERT: A 556 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7587 (mtmp) REVERT: A 599 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: A 603 ARG cc_start: 0.7223 (ttt-90) cc_final: 0.6858 (ttm-80) REVERT: B 418 ASP cc_start: 0.8201 (m-30) cc_final: 0.7841 (m-30) REVERT: B 425 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.6927 (mp-120) REVERT: B 607 MET cc_start: 0.7719 (ttp) cc_final: 0.7268 (mtm) REVERT: C 193 ASP cc_start: 0.8314 (t0) cc_final: 0.7931 (t0) REVERT: C 514 ASP cc_start: 0.7795 (m-30) cc_final: 0.7236 (m-30) REVERT: C 542 SER cc_start: 0.8434 (p) cc_final: 0.8203 (m) REVERT: D 301 GLN cc_start: 0.8605 (mp-120) cc_final: 0.8299 (mm-40) REVERT: D 316 PHE cc_start: 0.8626 (m-80) cc_final: 0.8306 (m-10) REVERT: D 452 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7769 (tm-30) REVERT: D 477 LYS cc_start: 0.8280 (tttm) cc_final: 0.7863 (tppt) REVERT: D 513 ASP cc_start: 0.8458 (t0) cc_final: 0.8190 (t0) REVERT: D 593 ILE cc_start: 0.9108 (tp) cc_final: 0.8727 (mt) REVERT: D 636 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7674 (mtm110) outliers start: 36 outliers final: 12 residues processed: 198 average time/residue: 0.5823 time to fit residues: 126.8489 Evaluate side-chains 180 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 208 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 177 optimal weight: 0.0370 chunk 149 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 473 HIS C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103067 restraints weight = 32683.354| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.61 r_work: 0.3127 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15115 Z= 0.117 Angle : 0.492 10.107 20508 Z= 0.262 Chirality : 0.040 0.201 2332 Planarity : 0.004 0.051 2538 Dihedral : 4.346 52.441 2064 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 14.26 % Favored : 83.70 % 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 are not related in a simple way. whole: 1.47 (0.20), residues: 1798 helix: 1.58 (0.15), residues: 1126 sheet: -0.13 (0.69), residues: 50 loop : 0.07 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.014 0.001 TYR B 297 PHE 0.013 0.001 PHE C 301 TRP 0.013 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00257 (15112) covalent geometry : angle 0.49054 (20499) hydrogen bonds : bond 0.03634 ( 945) hydrogen bonds : angle 3.82347 ( 2722) link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 2.02393 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7591 (mtp-110) REVERT: A 425 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6625 (mp-120) REVERT: A 455 GLU cc_start: 0.8294 (mp0) cc_final: 0.7888 (mp0) REVERT: A 458 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8254 (pttm) REVERT: A 481 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8325 (mtm180) REVERT: A 599 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.5705 (mp0) REVERT: B 418 ASP cc_start: 0.8204 (m-30) cc_final: 0.7831 (m-30) REVERT: B 425 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.6978 (mp-120) REVERT: B 607 MET cc_start: 0.7727 (ttp) cc_final: 0.7263 (mtm) REVERT: C 193 ASP cc_start: 0.8205 (t0) cc_final: 0.7826 (t0) REVERT: C 272 GLU cc_start: 0.5566 (tt0) cc_final: 0.4903 (mp0) REVERT: C 514 ASP cc_start: 0.7837 (m-30) cc_final: 0.7218 (m-30) REVERT: C 542 SER cc_start: 0.8389 (p) cc_final: 0.8165 (m) REVERT: D 301 GLN cc_start: 0.8599 (mp-120) cc_final: 0.8345 (mm-40) REVERT: D 316 PHE cc_start: 0.8608 (m-80) cc_final: 0.8328 (m-10) REVERT: D 452 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7730 (tm-30) REVERT: D 477 LYS cc_start: 0.8267 (tttm) cc_final: 0.7829 (tppt) REVERT: D 513 ASP cc_start: 0.8461 (t0) cc_final: 0.8199 (t0) REVERT: D 593 ILE cc_start: 0.9127 (tp) cc_final: 0.8730 (mt) outliers start: 33 outliers final: 11 residues processed: 200 average time/residue: 0.5691 time to fit residues: 125.9281 Evaluate side-chains 185 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 405 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101880 restraints weight = 28045.162| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.39 r_work: 0.3118 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15115 Z= 0.140 Angle : 0.508 8.624 20508 Z= 0.270 Chirality : 0.041 0.204 2332 Planarity : 0.004 0.049 2538 Dihedral : 4.193 47.538 2064 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 14.75 % Favored : 83.33 % 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 are not related in a simple way. whole: 1.63 (0.20), residues: 1798 helix: 1.73 (0.15), residues: 1125 sheet: -0.21 (0.68), residues: 50 loop : 0.09 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 636 TYR 0.013 0.001 TYR B 297 PHE 0.015 0.001 PHE B 192 TRP 0.012 0.001 TRP D 373 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00319 (15112) covalent geometry : angle 0.50668 (20499) hydrogen bonds : bond 0.03730 ( 945) hydrogen bonds : angle 3.81773 ( 2722) link_NAG-ASN : bond 0.00103 ( 3) link_NAG-ASN : angle 2.03156 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7687 (mtp-110) REVERT: A 425 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6762 (mp-120) REVERT: A 455 GLU cc_start: 0.8474 (mp0) cc_final: 0.8049 (mp0) REVERT: A 458 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8269 (pttm) REVERT: A 481 ARG cc_start: 0.8854 (mtm180) cc_final: 0.8386 (mtm180) REVERT: A 537 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: A 556 LYS cc_start: 0.8037 (mtmp) cc_final: 0.7665 (pmtt) REVERT: A 599 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: B 418 ASP cc_start: 0.8348 (m-30) cc_final: 0.8000 (m-30) REVERT: B 425 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7115 (mp-120) REVERT: B 607 MET cc_start: 0.7755 (ttp) cc_final: 0.7455 (mtm) REVERT: C 193 ASP cc_start: 0.8281 (t0) cc_final: 0.7910 (t0) REVERT: C 344 GLU cc_start: 0.8379 (tp30) cc_final: 0.8089 (tp30) REVERT: C 524 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7530 (tt0) REVERT: C 542 SER cc_start: 0.8510 (p) cc_final: 0.8297 (m) REVERT: D 316 PHE cc_start: 0.8532 (m-80) cc_final: 0.8220 (m-10) REVERT: D 452 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7859 (tm-30) REVERT: D 477 LYS cc_start: 0.8402 (tttm) cc_final: 0.7958 (tppt) REVERT: D 513 ASP cc_start: 0.8579 (t0) cc_final: 0.8300 (t0) REVERT: D 593 ILE cc_start: 0.9171 (tp) cc_final: 0.8780 (mt) outliers start: 31 outliers final: 16 residues processed: 190 average time/residue: 0.5966 time to fit residues: 124.4937 Evaluate side-chains 182 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101675 restraints weight = 31198.885| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.54 r_work: 0.3108 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15115 Z= 0.134 Angle : 0.505 11.678 20508 Z= 0.267 Chirality : 0.041 0.196 2332 Planarity : 0.004 0.048 2538 Dihedral : 4.078 41.945 2064 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 15.00 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1798 helix: 1.85 (0.15), residues: 1118 sheet: -0.19 (0.69), residues: 50 loop : 0.10 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 636 TYR 0.013 0.001 TYR B 297 PHE 0.014 0.001 PHE C 301 TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00306 (15112) covalent geometry : angle 0.50350 (20499) hydrogen bonds : bond 0.03686 ( 945) hydrogen bonds : angle 3.78152 ( 2722) link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 2.00995 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7574 (mtp-110) REVERT: A 425 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6704 (mp-120) REVERT: A 455 GLU cc_start: 0.8343 (mp0) cc_final: 0.7887 (mp0) REVERT: A 458 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8253 (pttm) REVERT: A 537 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: A 556 LYS cc_start: 0.8059 (mtmp) cc_final: 0.7704 (pmtt) REVERT: A 599 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.5589 (mp0) REVERT: B 418 ASP cc_start: 0.8197 (m-30) cc_final: 0.7831 (m-30) REVERT: B 425 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.6945 (mp-120) REVERT: B 607 MET cc_start: 0.7688 (ttp) cc_final: 0.7459 (mtm) REVERT: C 193 ASP cc_start: 0.8097 (t0) cc_final: 0.7692 (t0) REVERT: C 344 GLU cc_start: 0.8179 (tp30) cc_final: 0.7938 (tp30) REVERT: C 542 SER cc_start: 0.8384 (p) cc_final: 0.8161 (m) REVERT: D 316 PHE cc_start: 0.8531 (m-80) cc_final: 0.8230 (m-10) REVERT: D 452 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7729 (tm-30) REVERT: D 477 LYS cc_start: 0.8266 (tttm) cc_final: 0.7841 (tppt) REVERT: D 513 ASP cc_start: 0.8471 (t0) cc_final: 0.8185 (t0) REVERT: D 593 ILE cc_start: 0.9130 (tp) cc_final: 0.8719 (mt) outliers start: 30 outliers final: 15 residues processed: 189 average time/residue: 0.5712 time to fit residues: 119.0321 Evaluate side-chains 177 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 155 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 169 optimal weight: 0.5980 chunk 139 optimal weight: 0.0050 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102337 restraints weight = 35814.819| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.75 r_work: 0.3109 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15115 Z= 0.116 Angle : 0.492 9.319 20508 Z= 0.261 Chirality : 0.040 0.187 2332 Planarity : 0.004 0.054 2538 Dihedral : 3.960 36.507 2064 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 15.68 % Favored : 82.59 % 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 are not related in a simple way. whole: 1.85 (0.20), residues: 1798 helix: 1.94 (0.16), residues: 1119 sheet: -0.16 (0.69), residues: 50 loop : 0.12 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 636 TYR 0.013 0.001 TYR B 297 PHE 0.013 0.001 PHE C 301 TRP 0.013 0.001 TRP B 171 HIS 0.002 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00257 (15112) covalent geometry : angle 0.49075 (20499) hydrogen bonds : bond 0.03563 ( 945) hydrogen bonds : angle 3.72234 ( 2722) link_NAG-ASN : bond 0.00103 ( 3) link_NAG-ASN : angle 1.93735 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7606 (mtp-110) REVERT: A 407 ASN cc_start: 0.7791 (p0) cc_final: 0.7577 (t0) REVERT: A 425 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6742 (mp-120) REVERT: A 431 LYS cc_start: 0.8701 (tppt) cc_final: 0.8433 (tppp) REVERT: A 455 GLU cc_start: 0.8351 (mp0) cc_final: 0.7936 (mp0) REVERT: A 458 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8254 (pttm) REVERT: A 481 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8317 (mtm180) REVERT: A 537 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: A 556 LYS cc_start: 0.8013 (mtmp) cc_final: 0.7687 (pmtt) REVERT: A 599 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.5610 (mp0) REVERT: B 418 ASP cc_start: 0.8224 (m-30) cc_final: 0.7855 (m-30) REVERT: B 425 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.6964 (mp-120) REVERT: B 607 MET cc_start: 0.7690 (ttp) cc_final: 0.7435 (mtm) REVERT: C 193 ASP cc_start: 0.8050 (t0) cc_final: 0.7527 (t0) REVERT: C 272 GLU cc_start: 0.5614 (tt0) cc_final: 0.4848 (mp0) REVERT: C 344 GLU cc_start: 0.8202 (tp30) cc_final: 0.7960 (tp30) REVERT: C 537 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7807 (mp-120) REVERT: C 542 SER cc_start: 0.8374 (p) cc_final: 0.8161 (m) REVERT: D 316 PHE cc_start: 0.8527 (m-80) cc_final: 0.8249 (m-10) REVERT: D 452 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7760 (tm-30) REVERT: D 477 LYS cc_start: 0.8286 (tttm) cc_final: 0.7857 (tppt) REVERT: D 513 ASP cc_start: 0.8456 (t0) cc_final: 0.8187 (t0) REVERT: D 593 ILE cc_start: 0.9129 (tp) cc_final: 0.8719 (mt) outliers start: 28 outliers final: 13 residues processed: 193 average time/residue: 0.5398 time to fit residues: 115.3905 Evaluate side-chains 187 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102243 restraints weight = 33132.157| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.64 r_work: 0.3114 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15115 Z= 0.125 Angle : 0.501 10.795 20508 Z= 0.265 Chirality : 0.041 0.188 2332 Planarity : 0.004 0.051 2538 Dihedral : 3.924 33.256 2064 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.60 % Allowed : 16.36 % Favored : 82.04 % 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 are not related in a simple way. whole: 1.87 (0.20), residues: 1798 helix: 1.96 (0.16), residues: 1119 sheet: -0.20 (0.68), residues: 50 loop : 0.13 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 636 TYR 0.013 0.001 TYR B 297 PHE 0.013 0.001 PHE C 301 TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 566 Details of bonding type rmsd covalent geometry : bond 0.00284 (15112) covalent geometry : angle 0.49952 (20499) hydrogen bonds : bond 0.03580 ( 945) hydrogen bonds : angle 3.71263 ( 2722) link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 1.91308 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7599 (mtp-110) REVERT: A 425 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6734 (mp-120) REVERT: A 455 GLU cc_start: 0.8353 (mp0) cc_final: 0.7937 (mp0) REVERT: A 458 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8274 (pttm) REVERT: A 481 ARG cc_start: 0.8712 (mtm180) cc_final: 0.8288 (mtm180) REVERT: A 537 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: A 556 LYS cc_start: 0.8013 (mtmp) cc_final: 0.7702 (pmtt) REVERT: A 599 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.5594 (mp0) REVERT: B 418 ASP cc_start: 0.8209 (m-30) cc_final: 0.7850 (m-30) REVERT: B 425 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.6898 (mp-120) REVERT: B 607 MET cc_start: 0.7696 (ttp) cc_final: 0.7477 (mtm) REVERT: C 193 ASP cc_start: 0.8052 (t0) cc_final: 0.7619 (t0) REVERT: C 272 GLU cc_start: 0.5617 (tt0) cc_final: 0.4842 (mp0) REVERT: C 344 GLU cc_start: 0.8200 (tp30) cc_final: 0.7961 (tp30) REVERT: C 454 LYS cc_start: 0.8712 (mptt) cc_final: 0.8510 (mmtm) REVERT: C 537 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7853 (mp-120) REVERT: C 542 SER cc_start: 0.8379 (p) cc_final: 0.8162 (m) REVERT: C 559 LYS cc_start: 0.6466 (mmtt) cc_final: 0.4959 (mtmm) REVERT: D 316 PHE cc_start: 0.8527 (m-80) cc_final: 0.8234 (m-10) REVERT: D 452 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7762 (tm-30) REVERT: D 477 LYS cc_start: 0.8275 (tttm) cc_final: 0.7845 (tppt) REVERT: D 513 ASP cc_start: 0.8461 (t0) cc_final: 0.8188 (t0) REVERT: D 593 ILE cc_start: 0.9127 (tp) cc_final: 0.8713 (mt) outliers start: 26 outliers final: 14 residues processed: 187 average time/residue: 0.5635 time to fit residues: 116.3723 Evaluate side-chains 183 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 176 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099568 restraints weight = 38556.051| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.81 r_work: 0.3063 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15115 Z= 0.165 Angle : 0.535 11.808 20508 Z= 0.282 Chirality : 0.042 0.203 2332 Planarity : 0.004 0.049 2538 Dihedral : 4.020 31.322 2064 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 17.04 % Favored : 81.67 % 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 are not related in a simple way. whole: 1.78 (0.20), residues: 1798 helix: 1.87 (0.15), residues: 1118 sheet: -0.27 (0.68), residues: 50 loop : 0.14 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 636 TYR 0.013 0.001 TYR A 354 PHE 0.017 0.001 PHE B 192 TRP 0.012 0.001 TRP D 373 HIS 0.003 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00387 (15112) covalent geometry : angle 0.53340 (20499) hydrogen bonds : bond 0.03827 ( 945) hydrogen bonds : angle 3.82805 ( 2722) link_NAG-ASN : bond 0.00134 ( 3) link_NAG-ASN : angle 1.96618 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7626 (mtp-110) REVERT: A 425 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6621 (mp-120) REVERT: A 455 GLU cc_start: 0.8374 (mp0) cc_final: 0.7950 (mp0) REVERT: A 458 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8281 (pttm) REVERT: A 537 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: A 556 LYS cc_start: 0.7934 (mtmp) cc_final: 0.7668 (pmtt) REVERT: A 599 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.5652 (mp0) REVERT: B 418 ASP cc_start: 0.8288 (m-30) cc_final: 0.7930 (m-30) REVERT: B 425 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6939 (mp-120) REVERT: B 607 MET cc_start: 0.7759 (ttp) cc_final: 0.7417 (mtp) REVERT: C 193 ASP cc_start: 0.8145 (t0) cc_final: 0.7695 (t0) REVERT: C 344 GLU cc_start: 0.8200 (tp30) cc_final: 0.7958 (tp30) REVERT: C 454 LYS cc_start: 0.8726 (mptt) cc_final: 0.8520 (mmtm) REVERT: C 537 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7906 (mp-120) REVERT: C 542 SER cc_start: 0.8460 (p) cc_final: 0.8231 (m) REVERT: D 316 PHE cc_start: 0.8545 (m-80) cc_final: 0.8233 (m-10) REVERT: D 452 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7809 (tm-30) REVERT: D 477 LYS cc_start: 0.8295 (tttm) cc_final: 0.7884 (tppt) REVERT: D 513 ASP cc_start: 0.8467 (t0) cc_final: 0.8192 (t0) REVERT: D 593 ILE cc_start: 0.9169 (tp) cc_final: 0.8769 (mt) REVERT: D 640 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7436 (tptp) outliers start: 21 outliers final: 12 residues processed: 180 average time/residue: 0.5951 time to fit residues: 118.2082 Evaluate side-chains 178 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 572 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 169 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100942 restraints weight = 30922.494| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.54 r_work: 0.3100 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15115 Z= 0.143 Angle : 0.521 11.777 20508 Z= 0.275 Chirality : 0.041 0.190 2332 Planarity : 0.004 0.048 2538 Dihedral : 3.963 28.465 2064 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.30 % Allowed : 16.85 % Favored : 81.85 % 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 are not related in a simple way. whole: 1.79 (0.20), residues: 1798 helix: 1.90 (0.15), residues: 1118 sheet: -0.29 (0.68), residues: 50 loop : 0.12 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 636 TYR 0.013 0.001 TYR B 297 PHE 0.014 0.001 PHE C 301 TRP 0.013 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00329 (15112) covalent geometry : angle 0.51983 (20499) hydrogen bonds : bond 0.03719 ( 945) hydrogen bonds : angle 3.78222 ( 2722) link_NAG-ASN : bond 0.00108 ( 3) link_NAG-ASN : angle 1.93440 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4867.51 seconds wall clock time: 83 minutes 39.32 seconds (5019.32 seconds total)