Starting phenix.real_space_refine on Fri May 16 13:04:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy9_60559/05_2025/8zy9_60559.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 9243 2.51 5 N 2401 2.21 5 O 2759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14481 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain breaks: 1 Chain: "D" Number of atoms: 5730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5730 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 34, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Chain: "C" Number of atoms: 5730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5730 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 34, 'TRANS': 663} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.06, per 1000 atoms: 0.63 Number of scatterers: 14481 At special positions: 0 Unit cell: (131.4, 124.83, 133.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2759 8.00 N 2401 7.00 C 9243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG C 801 " - " ASN C 322 " " NAG C 802 " - " ASN C 432 " " NAG D 801 " - " ASN D 322 " " NAG D 802 " - " ASN D 432 " " NAG E 1 " - " ASN D 53 " " NAG F 1 " - " ASN D 689 " " NAG G 1 " - " ASN D 546 " " NAG H 1 " - " ASN C 53 " " NAG I 1 " - " ASN C 689 " " NAG J 1 " - " ASN C 546 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3294 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 14 sheets defined 50.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.933A pdb=" N PHE A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.208A pdb=" N TYR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'D' and resid 21 through 52 removed outlier: 3.784A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.859A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.655A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.581A pdb=" N TYR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.729A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.523A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.662A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 removed outlier: 4.110A pdb=" N ASN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.508A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 409 removed outlier: 3.811A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.704A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.388A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.585A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 removed outlier: 3.536A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 553 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL D 560 " --> pdb=" O GLN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.881A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.713A pdb=" N GLU D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 4.244A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 641 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 658 " --> pdb=" O TYR D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 706 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.861A pdb=" N ALA D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 removed outlier: 4.138A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.836A pdb=" N TYR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'C' and resid 24 through 52 removed outlier: 3.891A pdb=" N GLU C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.767A pdb=" N MET C 62 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 80 removed outlier: 3.582A pdb=" N TRP C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.649A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 194 Proline residue: C 178 - end of helix removed outlier: 3.622A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.613A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 248 removed outlier: 3.520A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.536A pdb=" N VAL C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.545A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.139A pdb=" N ASN C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.592A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.525A pdb=" N ARG C 393 " --> pdb=" O TYR C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 411 removed outlier: 4.283A pdb=" N HIS C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 431 through 444 removed outlier: 3.509A pdb=" N GLU C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 465 removed outlier: 3.502A pdb=" N GLU C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 533 removed outlier: 4.053A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.607A pdb=" N CYS C 542 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.758A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.926A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 removed outlier: 4.081A pdb=" N GLU C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 657 removed outlier: 3.521A pdb=" N LYS C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 706 removed outlier: 3.564A pdb=" N MET C 705 " --> pdb=" O GLY C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 removed outlier: 3.580A pdb=" N ASP C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367 removed outlier: 7.317A pdb=" N PHE A 365 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN A 428 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 367 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 426 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.949A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.061A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 618 through 621 Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345 removed outlier: 4.418A pdb=" N GLU B 344 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 390 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 389 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 386 removed outlier: 4.006A pdb=" N SER B 385 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 441 through 443 Processing sheet with id=AB2, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.916A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.164A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 618 through 621 564 hydrogen bonds defined for protein. 1629 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: 4.50 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4595 1.34 - 1.46: 3822 1.46 - 1.58: 6338 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 14883 Sorted by residual: bond pdb=" CA SER C 602 " pdb=" CB SER C 602 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.61e-02 3.86e+03 7.98e+00 bond pdb=" CA SER D 602 " pdb=" CB SER D 602 " ideal model delta sigma weight residual 1.530 1.484 0.047 1.68e-02 3.54e+03 7.70e+00 bond pdb=" N SER C 602 " pdb=" CA SER C 602 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.30e-02 5.92e+03 7.33e+00 bond pdb=" N PHE C 142 " pdb=" CA PHE C 142 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.26e-02 6.30e+03 6.30e+00 bond pdb=" N CYS C 141 " pdb=" CA CYS C 141 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.24e+00 ... (remaining 14878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 19755 2.16 - 4.33: 362 4.33 - 6.49: 58 6.49 - 8.66: 19 8.66 - 10.82: 2 Bond angle restraints: 20196 Sorted by residual: angle pdb=" C THR D 90 " pdb=" N VAL D 91 " pdb=" CA VAL D 91 " ideal model delta sigma weight residual 120.33 124.86 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" C THR C 90 " pdb=" N VAL C 91 " pdb=" CA VAL C 91 " ideal model delta sigma weight residual 120.33 124.68 -4.35 8.00e-01 1.56e+00 2.96e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 115.66 108.93 6.73 1.56e+00 4.11e-01 1.86e+01 angle pdb=" C TRP D 168 " pdb=" N ARG D 169 " pdb=" CA ARG D 169 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" N GLN C 139 " pdb=" CA GLN C 139 " pdb=" C GLN C 139 " ideal model delta sigma weight residual 112.90 107.32 5.58 1.31e+00 5.83e-01 1.82e+01 ... (remaining 20191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8143 17.68 - 35.35: 706 35.35 - 53.03: 122 53.03 - 70.71: 27 70.71 - 88.38: 10 Dihedral angle restraints: 9008 sinusoidal: 3875 harmonic: 5133 Sorted by residual: dihedral pdb=" CB CYS A 469 " pdb=" SG CYS A 469 " pdb=" SG CYS A 477 " pdb=" CB CYS A 477 " ideal model delta sinusoidal sigma weight residual -86.00 -1.00 -85.00 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 423 " pdb=" CB CYS A 423 " ideal model delta sinusoidal sigma weight residual -86.00 -144.58 58.58 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA CYS C 133 " pdb=" C CYS C 133 " pdb=" N LYS C 134 " pdb=" CA LYS C 134 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1798 0.061 - 0.123: 304 0.123 - 0.184: 41 0.184 - 0.246: 3 0.246 - 0.307: 3 Chirality restraints: 2149 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL C 581 " pdb=" CA VAL C 581 " pdb=" CG1 VAL C 581 " pdb=" CG2 VAL C 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2146 not shown) Planarity restraints: 2594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 326 " 0.045 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO B 327 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 327 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 327 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 582 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO D 583 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 582 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO C 583 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 583 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 583 " 0.036 5.00e-02 4.00e+02 ... (remaining 2591 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3276 2.78 - 3.31: 13095 3.31 - 3.84: 24489 3.84 - 4.37: 28756 4.37 - 4.90: 48926 Nonbonded interactions: 118542 Sorted by model distance: nonbonded pdb=" O LEU C 333 " pdb=" OG1 THR C 362 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR C 207 " pdb=" OG1 THR C 517 " model vdw 2.265 3.040 nonbonded pdb=" O VAL A 432 " pdb=" NZ LYS A 435 " model vdw 2.288 3.120 nonbonded pdb=" OH TYR C 217 " pdb=" OD2 ASP C 225 " model vdw 2.294 3.040 nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.298 3.040 ... (remaining 118537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 324 through 504) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 34.400 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 49.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.004 0.048 14909 Z= 0.189 Angle : 0.735 10.824 20264 Z= 0.393 Chirality : 0.048 0.307 2149 Planarity : 0.006 0.070 2584 Dihedral : 13.655 88.384 5684 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 1733 helix: -1.20 (0.16), residues: 754 sheet: 0.14 (0.45), residues: 110 loop : -1.33 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.005 0.001 HIS D 374 PHE 0.017 0.001 PHE A 486 TYR 0.029 0.001 TYR A 442 ARG 0.005 0.000 ARG C 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 10) link_NAG-ASN : angle 1.72955 ( 30) link_BETA1-4 : bond 0.01581 ( 6) link_BETA1-4 : angle 3.83513 ( 18) hydrogen bonds : bond 0.22444 ( 564) hydrogen bonds : angle 7.42432 ( 1629) SS BOND : bond 0.00326 ( 10) SS BOND : angle 1.78604 ( 20) covalent geometry : bond 0.00357 (14883) covalent geometry : angle 0.72250 (20196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8751 (pptt) cc_final: 0.8357 (ttpp) REVERT: B 336 ASN cc_start: 0.8704 (m-40) cc_final: 0.7958 (p0) REVERT: B 394 LYS cc_start: 0.8982 (ttpt) cc_final: 0.8716 (tttm) REVERT: B 397 ASP cc_start: 0.8495 (m-30) cc_final: 0.7819 (m-30) REVERT: B 405 GLN cc_start: 0.8630 (tt0) cc_final: 0.8231 (tt0) outliers start: 0 outliers final: 1 residues processed: 120 average time/residue: 1.3185 time to fit residues: 173.9153 Evaluate side-chains 97 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN D 117 ASN C 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.046969 restraints weight = 39436.216| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.35 r_work: 0.2558 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14909 Z= 0.232 Angle : 0.623 9.270 20264 Z= 0.320 Chirality : 0.044 0.242 2149 Planarity : 0.005 0.056 2584 Dihedral : 6.224 56.311 2259 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.77 % Allowed : 6.97 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1733 helix: 0.25 (0.18), residues: 784 sheet: -0.01 (0.48), residues: 110 loop : -0.93 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 478 HIS 0.006 0.001 HIS C 378 PHE 0.019 0.001 PHE D 523 TYR 0.024 0.001 TYR C 207 ARG 0.008 0.001 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 10) link_NAG-ASN : angle 1.56757 ( 30) link_BETA1-4 : bond 0.00820 ( 6) link_BETA1-4 : angle 2.72855 ( 18) hydrogen bonds : bond 0.04786 ( 564) hydrogen bonds : angle 4.66080 ( 1629) SS BOND : bond 0.00407 ( 10) SS BOND : angle 1.33609 ( 20) covalent geometry : bond 0.00530 (14883) covalent geometry : angle 0.61394 (20196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8855 (m-30) cc_final: 0.8626 (m-30) REVERT: A 399 ARG cc_start: 0.9055 (ptm-80) cc_final: 0.8854 (ptm-80) REVERT: A 400 GLN cc_start: 0.9343 (mt0) cc_final: 0.8946 (tt0) REVERT: B 354 ASP cc_start: 0.6549 (t0) cc_final: 0.6294 (t0) REVERT: B 394 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8510 (ttpp) REVERT: B 396 ASP cc_start: 0.9150 (m-30) cc_final: 0.8887 (m-30) REVERT: B 397 ASP cc_start: 0.8827 (m-30) cc_final: 0.7845 (m-30) REVERT: B 399 ARG cc_start: 0.9317 (ptm-80) cc_final: 0.8963 (ptm-80) REVERT: B 400 GLN cc_start: 0.9171 (tt0) cc_final: 0.8270 (tt0) REVERT: B 405 GLN cc_start: 0.8986 (tt0) cc_final: 0.8581 (tt0) REVERT: B 411 ASP cc_start: 0.8526 (t0) cc_final: 0.8027 (t0) outliers start: 12 outliers final: 2 residues processed: 108 average time/residue: 1.2861 time to fit residues: 153.4024 Evaluate side-chains 98 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 254 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 171 optimal weight: 0.3980 chunk 145 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.077490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.047480 restraints weight = 39291.360| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.35 r_work: 0.2573 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14909 Z= 0.138 Angle : 0.543 9.386 20264 Z= 0.275 Chirality : 0.041 0.235 2149 Planarity : 0.004 0.050 2584 Dihedral : 5.949 55.874 2257 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.02 % Allowed : 9.02 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1733 helix: 0.90 (0.19), residues: 780 sheet: -0.21 (0.49), residues: 110 loop : -0.80 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 PHE 0.014 0.001 PHE D 523 TYR 0.013 0.001 TYR D 207 ARG 0.005 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 10) link_NAG-ASN : angle 1.58902 ( 30) link_BETA1-4 : bond 0.01071 ( 6) link_BETA1-4 : angle 2.56989 ( 18) hydrogen bonds : bond 0.04229 ( 564) hydrogen bonds : angle 4.39259 ( 1629) SS BOND : bond 0.00347 ( 10) SS BOND : angle 0.96738 ( 20) covalent geometry : bond 0.00312 (14883) covalent geometry : angle 0.53444 (20196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8828 (m-30) cc_final: 0.8611 (m-30) REVERT: A 399 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8849 (ptm-80) REVERT: A 400 GLN cc_start: 0.9355 (mt0) cc_final: 0.8942 (tt0) REVERT: D 366 MET cc_start: 0.8618 (ttt) cc_final: 0.8416 (ttt) REVERT: B 354 ASP cc_start: 0.6746 (t0) cc_final: 0.6472 (t0) REVERT: B 394 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8611 (ttpp) REVERT: B 396 ASP cc_start: 0.9205 (m-30) cc_final: 0.8969 (m-30) REVERT: B 397 ASP cc_start: 0.8886 (m-30) cc_final: 0.7848 (m-30) REVERT: B 399 ARG cc_start: 0.9280 (ptm-80) cc_final: 0.8914 (ptm-80) REVERT: B 400 GLN cc_start: 0.9212 (tt0) cc_final: 0.8307 (tt0) REVERT: B 405 GLN cc_start: 0.8947 (tt0) cc_final: 0.8501 (tt0) REVERT: B 411 ASP cc_start: 0.8500 (t0) cc_final: 0.8017 (t0) outliers start: 16 outliers final: 4 residues processed: 112 average time/residue: 1.3220 time to fit residues: 163.0357 Evaluate side-chains 102 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.046854 restraints weight = 39304.446| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.35 r_work: 0.2546 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14909 Z= 0.155 Angle : 0.546 9.370 20264 Z= 0.274 Chirality : 0.042 0.233 2149 Planarity : 0.004 0.050 2584 Dihedral : 5.816 55.608 2257 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.15 % Allowed : 10.24 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1733 helix: 1.13 (0.19), residues: 782 sheet: -0.32 (0.49), residues: 110 loop : -0.76 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 PHE 0.016 0.001 PHE D 523 TYR 0.013 0.001 TYR D 385 ARG 0.004 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 10) link_NAG-ASN : angle 1.56575 ( 30) link_BETA1-4 : bond 0.00950 ( 6) link_BETA1-4 : angle 2.52785 ( 18) hydrogen bonds : bond 0.03995 ( 564) hydrogen bonds : angle 4.25214 ( 1629) SS BOND : bond 0.00379 ( 10) SS BOND : angle 0.99025 ( 20) covalent geometry : bond 0.00354 (14883) covalent geometry : angle 0.53766 (20196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8852 (m-30) cc_final: 0.8625 (m-30) REVERT: A 399 ARG cc_start: 0.9090 (ptm-80) cc_final: 0.8862 (ptm-80) REVERT: A 400 GLN cc_start: 0.9364 (mt0) cc_final: 0.8950 (tt0) REVERT: D 107 VAL cc_start: 0.9535 (OUTLIER) cc_final: 0.9335 (p) REVERT: B 354 ASP cc_start: 0.7032 (t0) cc_final: 0.6701 (t0) REVERT: B 394 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8634 (ttpp) REVERT: B 396 ASP cc_start: 0.9236 (m-30) cc_final: 0.8974 (m-30) REVERT: B 397 ASP cc_start: 0.8930 (m-30) cc_final: 0.7956 (m-30) REVERT: B 399 ARG cc_start: 0.9291 (ptm-80) cc_final: 0.9017 (ptm-80) REVERT: B 400 GLN cc_start: 0.9270 (tt0) cc_final: 0.8349 (tt0) REVERT: B 405 GLN cc_start: 0.8982 (tt0) cc_final: 0.8499 (tt0) REVERT: B 411 ASP cc_start: 0.8507 (t0) cc_final: 0.8024 (t0) REVERT: B 415 LYS cc_start: 0.8584 (tptm) cc_final: 0.8188 (tppp) outliers start: 18 outliers final: 5 residues processed: 117 average time/residue: 1.2908 time to fit residues: 166.8003 Evaluate side-chains 103 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 125 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 150 optimal weight: 0.2980 chunk 160 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.046015 restraints weight = 39506.533| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.34 r_work: 0.2529 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14909 Z= 0.186 Angle : 0.569 9.340 20264 Z= 0.285 Chirality : 0.043 0.229 2149 Planarity : 0.004 0.051 2584 Dihedral : 5.816 55.347 2257 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.28 % Allowed : 10.94 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1733 helix: 1.31 (0.20), residues: 782 sheet: -0.32 (0.48), residues: 110 loop : -0.77 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 PHE 0.018 0.001 PHE D 523 TYR 0.018 0.001 TYR C 381 ARG 0.004 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 10) link_NAG-ASN : angle 1.66290 ( 30) link_BETA1-4 : bond 0.00950 ( 6) link_BETA1-4 : angle 2.53941 ( 18) hydrogen bonds : bond 0.04087 ( 564) hydrogen bonds : angle 4.21150 ( 1629) SS BOND : bond 0.00460 ( 10) SS BOND : angle 1.08780 ( 20) covalent geometry : bond 0.00428 (14883) covalent geometry : angle 0.55973 (20196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8884 (m-30) cc_final: 0.8638 (m-30) REVERT: A 399 ARG cc_start: 0.9120 (ptm-80) cc_final: 0.8887 (ptm-80) REVERT: A 400 GLN cc_start: 0.9378 (mt0) cc_final: 0.8974 (tt0) REVERT: A 411 ASP cc_start: 0.8690 (t70) cc_final: 0.8371 (t70) REVERT: A 449 LYS cc_start: 0.9464 (tppt) cc_final: 0.9108 (tppp) REVERT: B 354 ASP cc_start: 0.7306 (t0) cc_final: 0.6985 (t0) REVERT: B 394 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8582 (ttpp) REVERT: B 396 ASP cc_start: 0.9263 (m-30) cc_final: 0.9056 (m-30) REVERT: B 397 ASP cc_start: 0.8962 (m-30) cc_final: 0.8006 (m-30) REVERT: B 399 ARG cc_start: 0.9282 (ptm-80) cc_final: 0.9022 (ptm-80) REVERT: B 400 GLN cc_start: 0.9268 (tt0) cc_final: 0.8410 (tt0) REVERT: B 405 GLN cc_start: 0.8990 (tt0) cc_final: 0.8616 (tt0) REVERT: B 411 ASP cc_start: 0.8522 (t0) cc_final: 0.8050 (t0) REVERT: B 415 LYS cc_start: 0.8553 (tptm) cc_final: 0.8334 (tppp) REVERT: B 479 GLU cc_start: 0.8009 (tp30) cc_final: 0.7581 (tp30) REVERT: C 74 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.8989 (pm20) outliers start: 20 outliers final: 7 residues processed: 116 average time/residue: 1.3547 time to fit residues: 173.1328 Evaluate side-chains 105 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 54 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 102 GLN C 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.045735 restraints weight = 39796.492| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.35 r_work: 0.2521 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14909 Z= 0.192 Angle : 0.585 11.242 20264 Z= 0.292 Chirality : 0.043 0.228 2149 Planarity : 0.004 0.062 2584 Dihedral : 5.813 55.254 2257 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.15 % Allowed : 11.52 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1733 helix: 1.39 (0.20), residues: 782 sheet: -0.30 (0.48), residues: 110 loop : -0.74 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 PHE 0.017 0.001 PHE D 523 TYR 0.017 0.001 TYR C 381 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 10) link_NAG-ASN : angle 1.65234 ( 30) link_BETA1-4 : bond 0.00958 ( 6) link_BETA1-4 : angle 2.53619 ( 18) hydrogen bonds : bond 0.04059 ( 564) hydrogen bonds : angle 4.17929 ( 1629) SS BOND : bond 0.00426 ( 10) SS BOND : angle 1.11269 ( 20) covalent geometry : bond 0.00443 (14883) covalent geometry : angle 0.57629 (20196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8922 (m-30) cc_final: 0.8675 (m-30) REVERT: A 399 ARG cc_start: 0.9135 (ptm-80) cc_final: 0.8901 (ptm-80) REVERT: A 400 GLN cc_start: 0.9425 (mt0) cc_final: 0.8994 (tt0) REVERT: A 415 LYS cc_start: 0.8732 (tptm) cc_final: 0.8530 (tppp) REVERT: D 95 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 354 ASP cc_start: 0.7311 (t0) cc_final: 0.6986 (t0) REVERT: B 394 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8588 (ttpp) REVERT: B 396 ASP cc_start: 0.9296 (m-30) cc_final: 0.9079 (m-30) REVERT: B 397 ASP cc_start: 0.8967 (m-30) cc_final: 0.7965 (m-30) REVERT: B 399 ARG cc_start: 0.9276 (ptm-80) cc_final: 0.9008 (ptm-80) REVERT: B 400 GLN cc_start: 0.9291 (tt0) cc_final: 0.8364 (tt0) REVERT: B 405 GLN cc_start: 0.8961 (tt0) cc_final: 0.8551 (tt0) REVERT: B 411 ASP cc_start: 0.8536 (t0) cc_final: 0.8071 (t0) REVERT: B 455 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8175 (mmm-85) REVERT: B 479 GLU cc_start: 0.8006 (tp30) cc_final: 0.7664 (tp30) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 1.3014 time to fit residues: 165.3832 Evaluate side-chains 111 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN D 34 HIS D 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046587 restraints weight = 39573.954| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.35 r_work: 0.2541 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14909 Z= 0.135 Angle : 0.559 9.877 20264 Z= 0.279 Chirality : 0.041 0.232 2149 Planarity : 0.004 0.065 2584 Dihedral : 5.688 55.528 2257 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.47 % Allowed : 11.71 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1733 helix: 1.44 (0.20), residues: 786 sheet: -0.30 (0.48), residues: 110 loop : -0.71 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS C 241 PHE 0.014 0.001 PHE D 523 TYR 0.015 0.001 TYR D 207 ARG 0.003 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 10) link_NAG-ASN : angle 1.58580 ( 30) link_BETA1-4 : bond 0.00956 ( 6) link_BETA1-4 : angle 2.46435 ( 18) hydrogen bonds : bond 0.03729 ( 564) hydrogen bonds : angle 4.08026 ( 1629) SS BOND : bond 0.00378 ( 10) SS BOND : angle 0.99117 ( 20) covalent geometry : bond 0.00309 (14883) covalent geometry : angle 0.55131 (20196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8922 (m-30) cc_final: 0.8668 (m-30) REVERT: A 399 ARG cc_start: 0.9143 (ptm-80) cc_final: 0.8893 (ptm-80) REVERT: A 400 GLN cc_start: 0.9429 (mt0) cc_final: 0.9077 (tt0) REVERT: A 415 LYS cc_start: 0.8815 (tptm) cc_final: 0.8579 (tppp) REVERT: D 95 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 354 ASP cc_start: 0.7303 (t0) cc_final: 0.6983 (t0) REVERT: B 394 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8605 (ttpp) REVERT: B 396 ASP cc_start: 0.9305 (m-30) cc_final: 0.9093 (m-30) REVERT: B 397 ASP cc_start: 0.8969 (m-30) cc_final: 0.7959 (m-30) REVERT: B 399 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.9028 (ptm-80) REVERT: B 400 GLN cc_start: 0.9291 (tt0) cc_final: 0.8392 (tt0) REVERT: B 405 GLN cc_start: 0.8933 (tt0) cc_final: 0.8537 (tt0) REVERT: B 411 ASP cc_start: 0.8534 (t0) cc_final: 0.8079 (t0) REVERT: B 415 LYS cc_start: 0.8663 (tptm) cc_final: 0.8381 (tppp) REVERT: B 479 GLU cc_start: 0.7954 (tp30) cc_final: 0.7599 (tp30) REVERT: C 74 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9032 (pm20) outliers start: 23 outliers final: 10 residues processed: 119 average time/residue: 1.2743 time to fit residues: 167.6903 Evaluate side-chains 108 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 65 optimal weight: 0.0070 chunk 2 optimal weight: 0.6980 chunk 143 optimal weight: 0.0670 chunk 153 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN D 34 HIS D 82 ASN C 603 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.046030 restraints weight = 39204.754| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.33 r_work: 0.2527 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14909 Z= 0.166 Angle : 0.575 10.046 20264 Z= 0.287 Chirality : 0.042 0.230 2149 Planarity : 0.004 0.069 2584 Dihedral : 5.706 55.266 2257 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.15 % Allowed : 12.54 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1733 helix: 1.47 (0.20), residues: 790 sheet: -0.37 (0.48), residues: 110 loop : -0.67 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 PHE 0.017 0.001 PHE D 523 TYR 0.014 0.001 TYR C 381 ARG 0.002 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 10) link_NAG-ASN : angle 1.62919 ( 30) link_BETA1-4 : bond 0.00939 ( 6) link_BETA1-4 : angle 2.48846 ( 18) hydrogen bonds : bond 0.03893 ( 564) hydrogen bonds : angle 4.08931 ( 1629) SS BOND : bond 0.00434 ( 10) SS BOND : angle 1.16160 ( 20) covalent geometry : bond 0.00383 (14883) covalent geometry : angle 0.56614 (20196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8939 (m-30) cc_final: 0.8678 (m-30) REVERT: A 399 ARG cc_start: 0.9134 (ptm-80) cc_final: 0.8888 (ptm-80) REVERT: A 400 GLN cc_start: 0.9431 (mt0) cc_final: 0.9014 (tt0) REVERT: D 95 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 354 ASP cc_start: 0.7321 (t0) cc_final: 0.7009 (t0) REVERT: B 394 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8648 (ttpp) REVERT: B 396 ASP cc_start: 0.9331 (m-30) cc_final: 0.9124 (m-30) REVERT: B 397 ASP cc_start: 0.8975 (m-30) cc_final: 0.8008 (m-30) REVERT: B 399 ARG cc_start: 0.9279 (ptm-80) cc_final: 0.9075 (ptm-80) REVERT: B 400 GLN cc_start: 0.9292 (tt0) cc_final: 0.8460 (tt0) REVERT: B 405 GLN cc_start: 0.8927 (tt0) cc_final: 0.8566 (tt0) REVERT: B 411 ASP cc_start: 0.8553 (t0) cc_final: 0.8100 (t0) REVERT: B 415 LYS cc_start: 0.8662 (tptm) cc_final: 0.8424 (tppp) REVERT: B 455 ARG cc_start: 0.8442 (mmm160) cc_final: 0.7999 (mmm-85) REVERT: B 479 GLU cc_start: 0.7965 (tp30) cc_final: 0.7606 (tp30) REVERT: C 74 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9017 (pm20) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 1.3209 time to fit residues: 161.8249 Evaluate side-chains 109 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 8.9990 chunk 158 optimal weight: 0.0010 chunk 168 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN D 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.046737 restraints weight = 39335.829| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.35 r_work: 0.2553 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14909 Z= 0.128 Angle : 0.564 10.965 20264 Z= 0.280 Chirality : 0.041 0.232 2149 Planarity : 0.004 0.066 2584 Dihedral : 5.618 55.425 2257 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.96 % Allowed : 12.92 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1733 helix: 1.55 (0.20), residues: 786 sheet: -0.44 (0.48), residues: 110 loop : -0.66 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.004 0.001 HIS C 378 PHE 0.014 0.001 PHE D 523 TYR 0.015 0.001 TYR D 207 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 10) link_NAG-ASN : angle 1.58104 ( 30) link_BETA1-4 : bond 0.00967 ( 6) link_BETA1-4 : angle 2.44499 ( 18) hydrogen bonds : bond 0.03642 ( 564) hydrogen bonds : angle 4.03105 ( 1629) SS BOND : bond 0.00491 ( 10) SS BOND : angle 1.10730 ( 20) covalent geometry : bond 0.00293 (14883) covalent geometry : angle 0.55596 (20196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8920 (m-30) cc_final: 0.8662 (m-30) REVERT: A 399 ARG cc_start: 0.9141 (ptm-80) cc_final: 0.8892 (ptm-80) REVERT: A 400 GLN cc_start: 0.9417 (mt0) cc_final: 0.8995 (tt0) REVERT: D 95 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8853 (tt) REVERT: B 354 ASP cc_start: 0.7371 (t0) cc_final: 0.7068 (t0) REVERT: B 394 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8614 (ttpp) REVERT: B 396 ASP cc_start: 0.9334 (m-30) cc_final: 0.9117 (m-30) REVERT: B 397 ASP cc_start: 0.8965 (m-30) cc_final: 0.7955 (m-30) REVERT: B 400 GLN cc_start: 0.9293 (tt0) cc_final: 0.8468 (tt0) REVERT: B 405 GLN cc_start: 0.8923 (tt0) cc_final: 0.8643 (tt0) REVERT: B 411 ASP cc_start: 0.8556 (t0) cc_final: 0.8100 (t0) REVERT: B 479 GLU cc_start: 0.7903 (tp30) cc_final: 0.7549 (tp30) REVERT: C 74 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.8978 (pm20) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 1.3012 time to fit residues: 157.6051 Evaluate side-chains 109 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** C 373 HIS ** 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 = 0.3478 r_free = 0.3478 target = 0.077093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047371 restraints weight = 39238.717| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.34 r_work: 0.2577 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14909 Z= 0.114 Angle : 0.565 12.099 20264 Z= 0.279 Chirality : 0.041 0.234 2149 Planarity : 0.004 0.063 2584 Dihedral : 5.544 55.442 2257 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.96 % Allowed : 13.05 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1733 helix: 1.63 (0.20), residues: 786 sheet: -0.50 (0.48), residues: 110 loop : -0.64 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 478 HIS 0.003 0.001 HIS C 241 PHE 0.013 0.001 PHE D 523 TYR 0.014 0.001 TYR D 207 ARG 0.004 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 10) link_NAG-ASN : angle 1.55634 ( 30) link_BETA1-4 : bond 0.01012 ( 6) link_BETA1-4 : angle 2.43257 ( 18) hydrogen bonds : bond 0.03494 ( 564) hydrogen bonds : angle 3.98797 ( 1629) SS BOND : bond 0.00405 ( 10) SS BOND : angle 1.02047 ( 20) covalent geometry : bond 0.00260 (14883) covalent geometry : angle 0.55707 (20196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8916 (m-30) cc_final: 0.8649 (m-30) REVERT: A 399 ARG cc_start: 0.9147 (ptm-80) cc_final: 0.8894 (ptm-80) REVERT: A 400 GLN cc_start: 0.9414 (mt0) cc_final: 0.9002 (tt0) REVERT: A 415 LYS cc_start: 0.8732 (tptm) cc_final: 0.8427 (tppt) REVERT: D 95 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D 343 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8798 (m) REVERT: D 408 MET cc_start: 0.9334 (mmp) cc_final: 0.9128 (mmm) REVERT: B 354 ASP cc_start: 0.7462 (t0) cc_final: 0.7190 (t0) REVERT: B 396 ASP cc_start: 0.9344 (m-30) cc_final: 0.9132 (m-30) REVERT: B 397 ASP cc_start: 0.8963 (m-30) cc_final: 0.8015 (m-30) REVERT: B 400 GLN cc_start: 0.9274 (tt0) cc_final: 0.8562 (tt0) REVERT: B 405 GLN cc_start: 0.8829 (tt0) cc_final: 0.8553 (tt0) REVERT: B 411 ASP cc_start: 0.8570 (t0) cc_final: 0.8116 (t0) REVERT: B 479 GLU cc_start: 0.7876 (tp30) cc_final: 0.7507 (tp30) REVERT: C 74 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8976 (pm20) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 1.3315 time to fit residues: 161.6568 Evaluate side-chains 108 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 705 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 0.4980 chunk 147 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.047694 restraints weight = 39455.163| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.37 r_work: 0.2579 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14909 Z= 0.108 Angle : 0.563 12.478 20264 Z= 0.277 Chirality : 0.041 0.234 2149 Planarity : 0.004 0.064 2584 Dihedral : 5.486 55.450 2257 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.96 % Allowed : 12.99 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1733 helix: 1.68 (0.20), residues: 786 sheet: -0.51 (0.47), residues: 110 loop : -0.62 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS C 241 PHE 0.012 0.001 PHE D 523 TYR 0.014 0.001 TYR D 207 ARG 0.008 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 10) link_NAG-ASN : angle 1.53014 ( 30) link_BETA1-4 : bond 0.01007 ( 6) link_BETA1-4 : angle 2.41442 ( 18) hydrogen bonds : bond 0.03426 ( 564) hydrogen bonds : angle 3.97124 ( 1629) SS BOND : bond 0.00383 ( 10) SS BOND : angle 0.93686 ( 20) covalent geometry : bond 0.00247 (14883) covalent geometry : angle 0.55515 (20196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.15 seconds wall clock time: 152 minutes 57.05 seconds (9177.05 seconds total)