Starting phenix.real_space_refine on Thu Sep 18 05:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy9_60559/09_2025/8zy9_60559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy9_60559/09_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_60559/09_2025/8zy9_60559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy9_60559/09_2025/8zy9_60559.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy9_60559/09_2025/8zy9_60559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy9_60559/09_2025/8zy9_60559.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.67, per 1000 atoms: 0.25 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: 1.45 Conformation dependent library (CDL) restraints added in 804.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.51 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: 2.54 Time building geometry restraints manager: 1.86 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (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 ARG 0.005 0.000 ARG C 24 TYR 0.029 0.001 TYR A 442 PHE 0.017 0.001 PHE A 486 TRP 0.008 0.001 TRP D 478 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00357 (14883) covalent geometry : angle 0.72250 (20196) SS BOND : bond 0.00326 ( 10) SS BOND : angle 1.78604 ( 20) hydrogen bonds : bond 0.22444 ( 564) hydrogen bonds : angle 7.42432 ( 1629) link_BETA1-4 : bond 0.01581 ( 6) link_BETA1-4 : angle 3.83513 ( 18) link_NAG-ASN : bond 0.00153 ( 10) link_NAG-ASN : angle 1.72955 ( 30) *********************** 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 : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8751 (pptt) cc_final: 0.8310 (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: 0.8753 (tttm) REVERT: B 397 ASP cc_start: 0.8495 (m-30) cc_final: 0.7787 (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: 0.6843 time to fit residues: 89.7171 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 : 0.650 ------------------------------------------------------------------------------- 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 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049290 restraints weight = 39354.791| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.36 r_work: 0.2637 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14909 Z= 0.147 Angle : 0.572 9.473 20264 Z= 0.293 Chirality : 0.042 0.242 2149 Planarity : 0.005 0.056 2584 Dihedral : 6.137 56.345 2259 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.64 % Allowed : 6.21 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1733 helix: 0.24 (0.18), residues: 772 sheet: 0.08 (0.47), residues: 110 loop : -0.94 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.014 0.001 TYR C 207 PHE 0.013 0.001 PHE D 523 TRP 0.011 0.001 TRP C 478 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00324 (14883) covalent geometry : angle 0.56309 (20196) SS BOND : bond 0.00290 ( 10) SS BOND : angle 1.04494 ( 20) hydrogen bonds : bond 0.04932 ( 564) hydrogen bonds : angle 4.77476 ( 1629) link_BETA1-4 : bond 0.01036 ( 6) link_BETA1-4 : angle 2.71732 ( 18) link_NAG-ASN : bond 0.00280 ( 10) link_NAG-ASN : angle 1.49538 ( 30) *********************** 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 107 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.650 Fit side-chains REVERT: A 396 ASP cc_start: 0.8741 (m-30) cc_final: 0.8536 (m-30) REVERT: A 400 GLN cc_start: 0.9328 (mt0) cc_final: 0.8923 (tt0) REVERT: B 354 ASP cc_start: 0.6606 (t0) cc_final: 0.6327 (t0) REVERT: B 396 ASP cc_start: 0.9049 (m-30) cc_final: 0.8817 (m-30) REVERT: B 397 ASP cc_start: 0.8764 (m-30) cc_final: 0.7840 (m-30) REVERT: B 399 ARG cc_start: 0.9251 (ptm-80) cc_final: 0.8964 (ptm-80) REVERT: B 400 GLN cc_start: 0.9036 (tt0) cc_final: 0.8179 (tt0) REVERT: B 405 GLN cc_start: 0.8923 (tt0) cc_final: 0.8395 (tt0) outliers start: 10 outliers final: 2 residues processed: 101 average time/residue: 0.6892 time to fit residues: 75.9830 Evaluate side-chains 93 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.079625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049867 restraints weight = 39731.858| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.37 r_work: 0.2637 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14909 Z= 0.106 Angle : 0.524 9.479 20264 Z= 0.264 Chirality : 0.040 0.234 2149 Planarity : 0.004 0.053 2584 Dihedral : 5.810 56.128 2257 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.77 % Allowed : 8.51 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1733 helix: 0.80 (0.19), residues: 780 sheet: -0.05 (0.48), residues: 110 loop : -0.80 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 443 TYR 0.012 0.001 TYR C 207 PHE 0.012 0.001 PHE D 523 TRP 0.010 0.001 TRP C 478 HIS 0.003 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00231 (14883) covalent geometry : angle 0.51568 (20196) SS BOND : bond 0.00229 ( 10) SS BOND : angle 0.85237 ( 20) hydrogen bonds : bond 0.04019 ( 564) hydrogen bonds : angle 4.40020 ( 1629) link_BETA1-4 : bond 0.01064 ( 6) link_BETA1-4 : angle 2.51307 ( 18) link_NAG-ASN : bond 0.00143 ( 10) link_NAG-ASN : angle 1.48565 ( 30) *********************** 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 116 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ASN cc_start: 0.9136 (m-40) cc_final: 0.8363 (p0) REVERT: A 396 ASP cc_start: 0.8670 (m-30) cc_final: 0.8401 (m-30) REVERT: A 399 ARG cc_start: 0.8955 (ptm-80) cc_final: 0.8718 (ptm-80) REVERT: A 400 GLN cc_start: 0.9299 (mt0) cc_final: 0.8959 (tt0) REVERT: B 354 ASP cc_start: 0.6733 (t0) cc_final: 0.6462 (t0) REVERT: B 397 ASP cc_start: 0.8850 (m-30) cc_final: 0.7852 (m-30) REVERT: B 399 ARG cc_start: 0.9281 (ptm-80) cc_final: 0.8970 (ptm-80) REVERT: B 400 GLN cc_start: 0.9138 (tt0) cc_final: 0.8300 (tt0) REVERT: B 405 GLN cc_start: 0.8820 (tt0) cc_final: 0.8393 (tt0) REVERT: B 411 ASP cc_start: 0.8475 (t0) cc_final: 0.8001 (t0) outliers start: 12 outliers final: 5 residues processed: 113 average time/residue: 0.6580 time to fit residues: 81.8306 Evaluate side-chains 103 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN 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 109 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.047411 restraints weight = 39766.128| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.34 r_work: 0.2566 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14909 Z= 0.186 Angle : 0.564 9.328 20264 Z= 0.284 Chirality : 0.043 0.233 2149 Planarity : 0.004 0.051 2584 Dihedral : 5.783 55.538 2257 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.09 % Allowed : 9.85 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1733 helix: 1.12 (0.20), residues: 778 sheet: -0.24 (0.48), residues: 110 loop : -0.75 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 169 TYR 0.014 0.001 TYR D 385 PHE 0.019 0.001 PHE D 523 TRP 0.013 0.001 TRP C 478 HIS 0.004 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00430 (14883) covalent geometry : angle 0.55572 (20196) SS BOND : bond 0.00242 ( 10) SS BOND : angle 0.90369 ( 20) hydrogen bonds : bond 0.04161 ( 564) hydrogen bonds : angle 4.31448 ( 1629) link_BETA1-4 : bond 0.00944 ( 6) link_BETA1-4 : angle 2.56772 ( 18) link_NAG-ASN : bond 0.00201 ( 10) link_NAG-ASN : angle 1.56860 ( 30) *********************** 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 119 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ASN cc_start: 0.9155 (m-40) cc_final: 0.8418 (p0) REVERT: A 396 ASP cc_start: 0.8767 (m-30) cc_final: 0.8540 (m-30) REVERT: A 400 GLN cc_start: 0.9310 (mt0) cc_final: 0.8959 (tt0) REVERT: A 455 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8351 (mmm-85) REVERT: B 354 ASP cc_start: 0.6984 (t0) cc_final: 0.6663 (t0) REVERT: B 397 ASP cc_start: 0.8879 (m-30) cc_final: 0.7894 (m-30) REVERT: B 399 ARG cc_start: 0.9261 (ptm-80) cc_final: 0.8975 (ptm-80) REVERT: B 400 GLN cc_start: 0.9197 (tt0) cc_final: 0.8311 (tt0) REVERT: B 405 GLN cc_start: 0.8980 (tt0) cc_final: 0.8486 (tt0) REVERT: B 411 ASP cc_start: 0.8524 (t0) cc_final: 0.8027 (t0) outliers start: 17 outliers final: 8 residues processed: 115 average time/residue: 0.6739 time to fit residues: 85.2258 Evaluate side-chains 110 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 674 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 5 optimal weight: 40.0000 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.077962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.048003 restraints weight = 39366.470| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.35 r_work: 0.2589 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14909 Z= 0.122 Angle : 0.543 9.396 20264 Z= 0.271 Chirality : 0.041 0.235 2149 Planarity : 0.004 0.055 2584 Dihedral : 5.679 55.806 2257 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.96 % Allowed : 10.75 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1733 helix: 1.26 (0.20), residues: 778 sheet: -0.27 (0.48), residues: 110 loop : -0.73 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 399 TYR 0.014 0.001 TYR A 371 PHE 0.013 0.001 PHE D 523 TRP 0.009 0.001 TRP D 163 HIS 0.003 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00277 (14883) covalent geometry : angle 0.53438 (20196) SS BOND : bond 0.00310 ( 10) SS BOND : angle 0.94550 ( 20) hydrogen bonds : bond 0.03753 ( 564) hydrogen bonds : angle 4.18393 ( 1629) link_BETA1-4 : bond 0.00967 ( 6) link_BETA1-4 : angle 2.48435 ( 18) link_NAG-ASN : bond 0.00113 ( 10) link_NAG-ASN : angle 1.52002 ( 30) *********************** 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 121 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ASN cc_start: 0.9162 (m-40) cc_final: 0.8461 (p0) REVERT: A 396 ASP cc_start: 0.8755 (m-30) cc_final: 0.8506 (m-30) REVERT: A 400 GLN cc_start: 0.9302 (mt0) cc_final: 0.8917 (tt0) REVERT: B 354 ASP cc_start: 0.7099 (t0) cc_final: 0.6746 (t0) REVERT: B 397 ASP cc_start: 0.8885 (m-30) cc_final: 0.7838 (m-30) REVERT: B 399 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.9031 (ptm-80) REVERT: B 400 GLN cc_start: 0.9234 (tt0) cc_final: 0.8313 (tt0) REVERT: B 405 GLN cc_start: 0.8967 (tt0) cc_final: 0.8436 (tt0) REVERT: B 411 ASP cc_start: 0.8515 (t0) cc_final: 0.8017 (t0) outliers start: 15 outliers final: 8 residues processed: 118 average time/residue: 0.6709 time to fit residues: 87.1415 Evaluate side-chains 112 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 79 LEU 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 34 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.076582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046489 restraints weight = 39620.872| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.35 r_work: 0.2531 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14909 Z= 0.194 Angle : 0.586 11.082 20264 Z= 0.293 Chirality : 0.043 0.228 2149 Planarity : 0.004 0.062 2584 Dihedral : 5.750 55.316 2257 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.96 % Allowed : 11.13 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.21), residues: 1733 helix: 1.34 (0.20), residues: 778 sheet: -0.27 (0.48), residues: 110 loop : -0.75 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 399 TYR 0.016 0.001 TYR C 381 PHE 0.019 0.001 PHE D 523 TRP 0.011 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00449 (14883) covalent geometry : angle 0.57799 (20196) SS BOND : bond 0.00636 ( 10) SS BOND : angle 1.06047 ( 20) hydrogen bonds : bond 0.04073 ( 564) hydrogen bonds : angle 4.19618 ( 1629) link_BETA1-4 : bond 0.00934 ( 6) link_BETA1-4 : angle 2.51699 ( 18) link_NAG-ASN : bond 0.00250 ( 10) link_NAG-ASN : angle 1.60302 ( 30) *********************** 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 121 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ASN cc_start: 0.9184 (m-40) cc_final: 0.8486 (p0) REVERT: A 396 ASP cc_start: 0.8844 (m-30) cc_final: 0.8610 (m-30) REVERT: A 400 GLN cc_start: 0.9315 (mt0) cc_final: 0.8969 (tt0) REVERT: A 415 LYS cc_start: 0.8755 (tptm) cc_final: 0.8533 (tppp) REVERT: B 354 ASP cc_start: 0.7282 (t0) cc_final: 0.6948 (t0) REVERT: B 397 ASP cc_start: 0.8934 (m-30) cc_final: 0.8012 (m-30) REVERT: B 399 ARG cc_start: 0.9272 (ptm-80) cc_final: 0.9062 (ptm-80) REVERT: B 400 GLN cc_start: 0.9260 (tt0) cc_final: 0.8421 (tt0) REVERT: B 405 GLN cc_start: 0.8858 (tt0) cc_final: 0.8513 (tt0) REVERT: B 411 ASP cc_start: 0.8530 (t0) cc_final: 0.8069 (t0) REVERT: B 415 LYS cc_start: 0.8437 (tppt) cc_final: 0.8107 (tppt) outliers start: 15 outliers final: 13 residues processed: 119 average time/residue: 0.6339 time to fit residues: 83.5107 Evaluate side-chains 112 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 674 LEU 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 480 MET 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 117 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 167 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046449 restraints weight = 39314.001| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.32 r_work: 0.2530 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14909 Z= 0.179 Angle : 0.578 9.338 20264 Z= 0.290 Chirality : 0.043 0.228 2149 Planarity : 0.004 0.065 2584 Dihedral : 5.720 55.354 2257 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.41 % Allowed : 11.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1733 helix: 1.36 (0.20), residues: 778 sheet: -0.25 (0.48), residues: 110 loop : -0.73 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.016 0.001 TYR C 381 PHE 0.017 0.001 PHE D 523 TRP 0.010 0.001 TRP C 478 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00414 (14883) covalent geometry : angle 0.56940 (20196) SS BOND : bond 0.00401 ( 10) SS BOND : angle 1.07016 ( 20) hydrogen bonds : bond 0.03958 ( 564) hydrogen bonds : angle 4.15268 ( 1629) link_BETA1-4 : bond 0.00929 ( 6) link_BETA1-4 : angle 2.49511 ( 18) link_NAG-ASN : bond 0.00231 ( 10) link_NAG-ASN : angle 1.62564 ( 30) *********************** 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 124 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8879 (m-30) cc_final: 0.8669 (m-30) REVERT: A 400 GLN cc_start: 0.9318 (mt0) cc_final: 0.8911 (tt0) REVERT: A 454 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: B 354 ASP cc_start: 0.7321 (t0) cc_final: 0.6993 (t0) REVERT: B 397 ASP cc_start: 0.8921 (m-30) cc_final: 0.7932 (m-30) REVERT: B 399 ARG cc_start: 0.9257 (ptm-80) cc_final: 0.9010 (ptm-80) REVERT: B 400 GLN cc_start: 0.9283 (tt0) cc_final: 0.8433 (tt0) REVERT: B 405 GLN cc_start: 0.8815 (tt0) cc_final: 0.8521 (tt0) REVERT: B 411 ASP cc_start: 0.8557 (t0) cc_final: 0.8088 (t0) REVERT: C 74 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.9030 (pm20) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 0.6479 time to fit residues: 86.4002 Evaluate side-chains 114 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 674 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 674 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 40 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 5 optimal weight: 30.0000 chunk 83 optimal weight: 0.0050 chunk 158 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 23 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 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 = 0.3510 r_free = 0.3510 target = 0.078545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048731 restraints weight = 39158.739| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.36 r_work: 0.2612 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14909 Z= 0.097 Angle : 0.553 10.509 20264 Z= 0.274 Chirality : 0.040 0.227 2149 Planarity : 0.004 0.073 2584 Dihedral : 5.521 55.794 2257 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.83 % Allowed : 12.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1733 helix: 1.40 (0.20), residues: 782 sheet: -0.27 (0.48), residues: 110 loop : -0.68 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.013 0.001 TYR D 207 PHE 0.009 0.001 PHE D 523 TRP 0.011 0.001 TRP D 163 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00212 (14883) covalent geometry : angle 0.54515 (20196) SS BOND : bond 0.00464 ( 10) SS BOND : angle 0.83686 ( 20) hydrogen bonds : bond 0.03354 ( 564) hydrogen bonds : angle 4.03452 ( 1629) link_BETA1-4 : bond 0.01098 ( 6) link_BETA1-4 : angle 2.42689 ( 18) link_NAG-ASN : bond 0.00129 ( 10) link_NAG-ASN : angle 1.48941 ( 30) *********************** 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 116 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8790 (m-30) cc_final: 0.8571 (m-30) REVERT: A 399 ARG cc_start: 0.8833 (ptm-80) cc_final: 0.8564 (ptm-80) REVERT: A 400 GLN cc_start: 0.9316 (mt0) cc_final: 0.9010 (tt0) REVERT: B 354 ASP cc_start: 0.7275 (t0) cc_final: 0.6971 (t0) REVERT: B 397 ASP cc_start: 0.8884 (m-30) cc_final: 0.7787 (m-30) REVERT: B 399 ARG cc_start: 0.9274 (ptm-80) cc_final: 0.8934 (ptm-80) REVERT: B 400 GLN cc_start: 0.9268 (tt0) cc_final: 0.8352 (tt0) REVERT: B 405 GLN cc_start: 0.8938 (tt0) cc_final: 0.8573 (tt0) REVERT: B 411 ASP cc_start: 0.8563 (t0) cc_final: 0.8081 (t0) REVERT: C 74 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9030 (pm20) outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 0.6411 time to fit residues: 80.5105 Evaluate side-chains 107 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 90 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 0.0070 chunk 151 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048171 restraints weight = 39473.413| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.36 r_work: 0.2581 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2190 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= 0.120 Angle : 0.568 11.241 20264 Z= 0.283 Chirality : 0.041 0.236 2149 Planarity : 0.004 0.070 2584 Dihedral : 5.483 55.564 2257 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.83 % Allowed : 12.41 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1733 helix: 1.49 (0.20), residues: 782 sheet: -0.25 (0.48), residues: 110 loop : -0.64 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.012 0.001 TYR D 207 PHE 0.014 0.001 PHE D 523 TRP 0.011 0.001 TRP D 478 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00278 (14883) covalent geometry : angle 0.56050 (20196) SS BOND : bond 0.00413 ( 10) SS BOND : angle 1.02866 ( 20) hydrogen bonds : bond 0.03522 ( 564) hydrogen bonds : angle 4.01194 ( 1629) link_BETA1-4 : bond 0.00999 ( 6) link_BETA1-4 : angle 2.43974 ( 18) link_NAG-ASN : bond 0.00117 ( 10) link_NAG-ASN : angle 1.52221 ( 30) *********************** 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: 13 poor density : 99 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8815 (m-30) cc_final: 0.8607 (m-30) REVERT: A 400 GLN cc_start: 0.9326 (mt0) cc_final: 0.9016 (tt0) REVERT: A 415 LYS cc_start: 0.8715 (tptm) cc_final: 0.8372 (tppt) REVERT: A 439 ASN cc_start: 0.7797 (m-40) cc_final: 0.7264 (p0) REVERT: A 451 LYS cc_start: 0.9450 (tppt) cc_final: 0.9244 (tptp) REVERT: B 354 ASP cc_start: 0.7310 (t0) cc_final: 0.7014 (t0) REVERT: B 397 ASP cc_start: 0.8896 (m-30) cc_final: 0.7847 (m-30) REVERT: B 399 ARG cc_start: 0.9278 (ptm-80) cc_final: 0.8939 (ptm-80) REVERT: B 400 GLN cc_start: 0.9278 (tt0) cc_final: 0.8403 (tt0) REVERT: B 405 GLN cc_start: 0.8849 (tt0) cc_final: 0.8536 (tt0) REVERT: B 411 ASP cc_start: 0.8573 (t0) cc_final: 0.8097 (t0) REVERT: C 74 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9009 (pm20) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.6876 time to fit residues: 82.9638 Evaluate side-chains 108 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASN 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 90 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 158 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048634 restraints weight = 39367.175| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.36 r_work: 0.2602 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14909 Z= 0.108 Angle : 0.569 11.400 20264 Z= 0.283 Chirality : 0.041 0.233 2149 Planarity : 0.004 0.068 2584 Dihedral : 5.450 55.597 2257 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.83 % Allowed : 12.48 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.21), residues: 1733 helix: 1.52 (0.20), residues: 784 sheet: -0.28 (0.48), residues: 110 loop : -0.62 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.039 0.001 TYR A 371 PHE 0.012 0.001 PHE D 523 TRP 0.011 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00248 (14883) covalent geometry : angle 0.56103 (20196) SS BOND : bond 0.00371 ( 10) SS BOND : angle 0.99919 ( 20) hydrogen bonds : bond 0.03403 ( 564) hydrogen bonds : angle 3.99722 ( 1629) link_BETA1-4 : bond 0.01054 ( 6) link_BETA1-4 : angle 2.43044 ( 18) link_NAG-ASN : bond 0.00095 ( 10) link_NAG-ASN : angle 1.50424 ( 30) ********************** 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 111 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8796 (m-30) cc_final: 0.8577 (m-30) REVERT: A 399 ARG cc_start: 0.8844 (ptm-80) cc_final: 0.8606 (ptm-80) REVERT: A 400 GLN cc_start: 0.9310 (mt0) cc_final: 0.8988 (tt0) REVERT: A 415 LYS cc_start: 0.8751 (tptm) cc_final: 0.8401 (tppt) REVERT: A 439 ASN cc_start: 0.7729 (m-40) cc_final: 0.7247 (p0) REVERT: A 451 LYS cc_start: 0.9453 (tppt) cc_final: 0.9208 (ttpp) REVERT: A 454 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: B 354 ASP cc_start: 0.7371 (t0) cc_final: 0.7092 (t0) REVERT: B 397 ASP cc_start: 0.8899 (m-30) cc_final: 0.7816 (m-30) REVERT: B 399 ARG cc_start: 0.9280 (ptm-80) cc_final: 0.8948 (ptm-80) REVERT: B 400 GLN cc_start: 0.9283 (tt0) cc_final: 0.8380 (tt0) REVERT: B 405 GLN cc_start: 0.8863 (tt0) cc_final: 0.8554 (tt0) REVERT: B 411 ASP cc_start: 0.8575 (t0) cc_final: 0.8107 (t0) REVERT: C 74 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8979 (pm20) outliers start: 13 outliers final: 13 residues processed: 110 average time/residue: 0.6704 time to fit residues: 80.8728 Evaluate side-chains 113 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 674 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 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 147 optimal weight: 0.4980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.048486 restraints weight = 39287.714| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.36 r_work: 0.2600 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14909 Z= 0.112 Angle : 0.573 11.766 20264 Z= 0.283 Chirality : 0.041 0.235 2149 Planarity : 0.004 0.066 2584 Dihedral : 5.421 55.548 2257 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.83 % Allowed : 12.67 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.21), residues: 1733 helix: 1.56 (0.20), residues: 784 sheet: -0.33 (0.48), residues: 110 loop : -0.62 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.030 0.001 TYR A 371 PHE 0.013 0.001 PHE D 523 TRP 0.010 0.001 TRP D 478 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00259 (14883) covalent geometry : angle 0.56566 (20196) SS BOND : bond 0.00363 ( 10) SS BOND : angle 0.93592 ( 20) hydrogen bonds : bond 0.03423 ( 564) hydrogen bonds : angle 3.99329 ( 1629) link_BETA1-4 : bond 0.00991 ( 6) link_BETA1-4 : angle 2.38949 ( 18) link_NAG-ASN : bond 0.00095 ( 10) link_NAG-ASN : angle 1.49713 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4499.90 seconds wall clock time: 77 minutes 43.34 seconds (4663.34 seconds total)