Starting phenix.real_space_refine on Fri Jun 13 00:04:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy9_60559/06_2025/8zy9_60559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy9_60559/06_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_60559/06_2025/8zy9_60559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy9_60559/06_2025/8zy9_60559.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy9_60559/06_2025/8zy9_60559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy9_60559/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.50, per 1000 atoms: 0.66 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: 3.41 Conformation dependent library (CDL) restraints added in 1.8 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: 1.47 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: 4.42 Time building geometry restraints manager: 4.08 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: 3.210 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.270 Find NCS groups from input model: 0.450 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.200 ------------------------------------------------------------------------------- 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 : 1.569 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: 1.3982 time to fit residues: 184.2107 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 : 1.728 ------------------------------------------------------------------------------- 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 = 0.077129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.047022 restraints weight = 39423.084| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.34 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 : 1.953 Fit side-chains revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8856 (m-30) cc_final: 0.8628 (m-30) REVERT: A 399 ARG cc_start: 0.9054 (ptm-80) cc_final: 0.8853 (ptm-80) REVERT: A 400 GLN cc_start: 0.9343 (mt0) cc_final: 0.8945 (tt0) REVERT: B 354 ASP cc_start: 0.6553 (t0) cc_final: 0.6296 (t0) REVERT: B 394 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8513 (ttpp) REVERT: B 396 ASP cc_start: 0.9150 (m-30) cc_final: 0.8887 (m-30) REVERT: B 397 ASP cc_start: 0.8826 (m-30) cc_final: 0.7845 (m-30) REVERT: B 399 ARG cc_start: 0.9317 (ptm-80) cc_final: 0.8962 (ptm-80) REVERT: B 400 GLN cc_start: 0.9171 (tt0) cc_final: 0.8269 (tt0) REVERT: B 405 GLN cc_start: 0.8990 (tt0) cc_final: 0.8581 (tt0) REVERT: B 411 ASP cc_start: 0.8526 (t0) cc_final: 0.8029 (t0) outliers start: 12 outliers final: 2 residues processed: 108 average time/residue: 1.4065 time to fit residues: 167.4231 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 : 1.559 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.8980 chunk 145 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.077380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.047330 restraints weight = 39310.155| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.34 r_work: 0.2568 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1608 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= 0.145 Angle : 0.545 9.375 20264 Z= 0.276 Chirality : 0.042 0.235 2149 Planarity : 0.004 0.050 2584 Dihedral : 5.955 55.844 2257 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.02 % Allowed : 9.15 % Favored : 89.83 % 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 : -0.81 (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 0.015 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 0.00144 ( 10) link_NAG-ASN : angle 1.59436 ( 30) link_BETA1-4 : bond 0.01005 ( 6) link_BETA1-4 : angle 2.54789 ( 18) hydrogen bonds : bond 0.04246 ( 564) hydrogen bonds : angle 4.39075 ( 1629) SS BOND : bond 0.00319 ( 10) SS BOND : angle 0.95153 ( 20) covalent geometry : bond 0.00327 (14883) covalent geometry : angle 0.53646 (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 117 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8832 (m-30) cc_final: 0.8615 (m-30) REVERT: A 399 ARG cc_start: 0.9071 (ptm-80) cc_final: 0.8854 (ptm-80) REVERT: A 400 GLN cc_start: 0.9355 (mt0) cc_final: 0.8941 (tt0) REVERT: D 366 MET cc_start: 0.8631 (ttt) cc_final: 0.8430 (ttt) REVERT: B 354 ASP cc_start: 0.6826 (t0) cc_final: 0.6547 (t0) REVERT: B 394 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8604 (ttpp) REVERT: B 396 ASP cc_start: 0.9206 (m-30) cc_final: 0.8969 (m-30) REVERT: B 397 ASP cc_start: 0.8891 (m-30) cc_final: 0.7855 (m-30) REVERT: B 399 ARG cc_start: 0.9279 (ptm-80) cc_final: 0.8915 (ptm-80) REVERT: B 400 GLN cc_start: 0.9216 (tt0) cc_final: 0.8308 (tt0) REVERT: B 405 GLN cc_start: 0.8957 (tt0) cc_final: 0.8480 (tt0) REVERT: B 411 ASP cc_start: 0.8493 (t0) cc_final: 0.8002 (t0) outliers start: 16 outliers final: 4 residues processed: 111 average time/residue: 1.3609 time to fit residues: 166.4269 Evaluate side-chains 103 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 0.0060 overall best weight: 1.4800 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.077070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.047042 restraints weight = 39263.879| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.34 r_work: 0.2551 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14909 Z= 0.147 Angle : 0.541 9.371 20264 Z= 0.272 Chirality : 0.041 0.233 2149 Planarity : 0.004 0.048 2584 Dihedral : 5.819 55.654 2257 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.15 % Allowed : 10.17 % Favored : 88.68 % 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: 0.20 (0.21), residues: 1733 helix: 1.16 (0.19), residues: 782 sheet: -0.31 (0.49), 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 0.016 0.001 PHE D 523 TYR 0.013 0.001 TYR D 207 ARG 0.004 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 10) link_NAG-ASN : angle 1.55588 ( 30) link_BETA1-4 : bond 0.00966 ( 6) link_BETA1-4 : angle 2.51912 ( 18) hydrogen bonds : bond 0.03968 ( 564) hydrogen bonds : angle 4.25615 ( 1629) SS BOND : bond 0.00415 ( 10) SS BOND : angle 0.94814 ( 20) covalent geometry : bond 0.00336 (14883) covalent geometry : angle 0.53290 (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 121 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8846 (m-30) cc_final: 0.8619 (m-30) REVERT: A 399 ARG cc_start: 0.9089 (ptm-80) cc_final: 0.8863 (ptm-80) REVERT: A 400 GLN cc_start: 0.9363 (mt0) cc_final: 0.8951 (tt0) REVERT: B 354 ASP cc_start: 0.7032 (t0) cc_final: 0.6703 (t0) REVERT: B 394 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8628 (ttpp) REVERT: B 396 ASP cc_start: 0.9234 (m-30) cc_final: 0.8976 (m-30) REVERT: B 397 ASP cc_start: 0.8926 (m-30) cc_final: 0.7935 (m-30) REVERT: B 399 ARG cc_start: 0.9296 (ptm-80) cc_final: 0.9024 (ptm-80) REVERT: B 400 GLN cc_start: 0.9268 (tt0) cc_final: 0.8349 (tt0) REVERT: B 405 GLN cc_start: 0.8974 (tt0) cc_final: 0.8481 (tt0) REVERT: B 411 ASP cc_start: 0.8495 (t0) cc_final: 0.8011 (t0) REVERT: B 415 LYS cc_start: 0.8579 (tptm) cc_final: 0.8174 (tppp) outliers start: 18 outliers final: 5 residues processed: 118 average time/residue: 1.4792 time to fit residues: 193.9821 Evaluate side-chains 102 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 138 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 150 optimal weight: 0.0050 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.076245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.046115 restraints weight = 39461.012| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.35 r_work: 0.2525 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1993 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= 0.183 Angle : 0.566 9.338 20264 Z= 0.284 Chirality : 0.042 0.230 2149 Planarity : 0.004 0.060 2584 Dihedral : 5.810 55.412 2257 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.22 % Allowed : 10.81 % Favored : 87.97 % 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: 0.29 (0.21), residues: 1733 helix: 1.27 (0.20), residues: 784 sheet: -0.33 (0.48), residues: 110 loop : -0.76 (0.22), residues: 839 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 0.016 0.001 TYR C 381 ARG 0.004 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 10) link_NAG-ASN : angle 1.63124 ( 30) link_BETA1-4 : bond 0.00934 ( 6) link_BETA1-4 : angle 2.53917 ( 18) hydrogen bonds : bond 0.04047 ( 564) hydrogen bonds : angle 4.21218 ( 1629) SS BOND : bond 0.00346 ( 10) SS BOND : angle 1.01703 ( 20) covalent geometry : bond 0.00421 (14883) covalent geometry : angle 0.55761 (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 116 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8879 (m-30) cc_final: 0.8637 (m-30) REVERT: A 399 ARG cc_start: 0.9114 (ptm-80) cc_final: 0.8881 (ptm-80) REVERT: A 400 GLN cc_start: 0.9381 (mt0) cc_final: 0.8976 (tt0) REVERT: B 354 ASP cc_start: 0.7287 (t0) cc_final: 0.6968 (t0) REVERT: B 394 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8596 (ttpp) REVERT: B 396 ASP cc_start: 0.9257 (m-30) cc_final: 0.9040 (m-30) REVERT: B 397 ASP cc_start: 0.8953 (m-30) cc_final: 0.7941 (m-30) REVERT: B 399 ARG cc_start: 0.9289 (ptm-80) cc_final: 0.8982 (ptm-80) REVERT: B 400 GLN cc_start: 0.9269 (tt0) cc_final: 0.8350 (tt0) REVERT: B 405 GLN cc_start: 0.8981 (tt0) cc_final: 0.8533 (tt0) REVERT: B 411 ASP cc_start: 0.8529 (t0) cc_final: 0.8039 (t0) REVERT: B 415 LYS cc_start: 0.8592 (tptm) cc_final: 0.8191 (tppt) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 1.3246 time to fit residues: 163.9048 Evaluate side-chains 103 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 79 LEU Chi-restraints excluded: chain D residue 95 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 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: 0.6980 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 127 optimal weight: 0.0470 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.8882 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.076110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.046089 restraints weight = 39710.826| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.34 r_work: 0.2523 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14909 Z= 0.174 Angle : 0.578 12.392 20264 Z= 0.288 Chirality : 0.042 0.229 2149 Planarity : 0.004 0.067 2584 Dihedral : 5.786 55.356 2257 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.22 % Allowed : 11.58 % Favored : 87.20 % 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: 0.38 (0.21), residues: 1733 helix: 1.38 (0.20), residues: 782 sheet: -0.28 (0.48), residues: 110 loop : -0.74 (0.22), residues: 841 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 0.017 0.001 PHE D 523 TYR 0.016 0.001 TYR C 381 ARG 0.004 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 10) link_NAG-ASN : angle 1.62742 ( 30) link_BETA1-4 : bond 0.00896 ( 6) link_BETA1-4 : angle 2.50552 ( 18) hydrogen bonds : bond 0.03970 ( 564) hydrogen bonds : angle 4.15936 ( 1629) SS BOND : bond 0.00459 ( 10) SS BOND : angle 1.08460 ( 20) covalent geometry : bond 0.00401 (14883) covalent geometry : angle 0.56927 (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 120 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8904 (m-30) cc_final: 0.8673 (m-30) REVERT: A 399 ARG cc_start: 0.9131 (ptm-80) cc_final: 0.8898 (ptm-80) REVERT: A 400 GLN cc_start: 0.9428 (mt0) cc_final: 0.9005 (tt0) REVERT: A 415 LYS cc_start: 0.8756 (tptm) cc_final: 0.8493 (tppp) REVERT: D 95 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8870 (tt) REVERT: B 354 ASP cc_start: 0.7315 (t0) cc_final: 0.6992 (t0) REVERT: B 394 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8593 (ttpp) REVERT: B 396 ASP cc_start: 0.9287 (m-30) cc_final: 0.9063 (m-30) REVERT: B 397 ASP cc_start: 0.8954 (m-30) cc_final: 0.7949 (m-30) REVERT: B 399 ARG cc_start: 0.9287 (ptm-80) cc_final: 0.8976 (ptm-80) REVERT: B 400 GLN cc_start: 0.9292 (tt0) cc_final: 0.8374 (tt0) REVERT: B 405 GLN cc_start: 0.8968 (tt0) cc_final: 0.8543 (tt0) REVERT: B 411 ASP cc_start: 0.8522 (t0) cc_final: 0.8042 (t0) REVERT: B 455 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8085 (mmm-85) REVERT: C 74 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9047 (pm20) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 1.2739 time to fit residues: 164.6111 Evaluate side-chains 109 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain D residue 705 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 79 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.046756 restraints weight = 39615.462| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.35 r_work: 0.2541 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14909 Z= 0.135 Angle : 0.559 9.925 20264 Z= 0.279 Chirality : 0.041 0.227 2149 Planarity : 0.004 0.066 2584 Dihedral : 5.686 55.449 2257 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.28 % Allowed : 11.90 % 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: 0.44 (0.21), residues: 1733 helix: 1.40 (0.20), residues: 788 sheet: -0.28 (0.48), residues: 110 loop : -0.70 (0.22), residues: 835 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 0.015 0.001 PHE D 523 TYR 0.014 0.001 TYR D 207 ARG 0.003 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 10) link_NAG-ASN : angle 1.58860 ( 30) link_BETA1-4 : bond 0.00983 ( 6) link_BETA1-4 : angle 2.47451 ( 18) hydrogen bonds : bond 0.03747 ( 564) hydrogen bonds : angle 4.08090 ( 1629) SS BOND : bond 0.00447 ( 10) SS BOND : angle 1.02628 ( 20) covalent geometry : bond 0.00309 (14883) covalent geometry : angle 0.55095 (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 119 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8890 (m-30) cc_final: 0.8651 (m-30) REVERT: A 399 ARG cc_start: 0.9143 (ptm-80) cc_final: 0.8896 (ptm-80) REVERT: A 400 GLN cc_start: 0.9429 (mt0) cc_final: 0.9076 (tt0) REVERT: A 415 LYS cc_start: 0.8794 (tptm) cc_final: 0.8533 (tppp) REVERT: D 95 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 354 ASP cc_start: 0.7308 (t0) cc_final: 0.6985 (t0) REVERT: B 394 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8603 (ttpp) REVERT: B 396 ASP cc_start: 0.9298 (m-30) cc_final: 0.9066 (m-30) REVERT: B 397 ASP cc_start: 0.8958 (m-30) cc_final: 0.7949 (m-30) REVERT: B 399 ARG cc_start: 0.9289 (ptm-80) cc_final: 0.8991 (ptm-80) REVERT: B 400 GLN cc_start: 0.9291 (tt0) cc_final: 0.8407 (tt0) REVERT: B 405 GLN cc_start: 0.8913 (tt0) cc_final: 0.8562 (tt0) REVERT: B 411 ASP cc_start: 0.8548 (t0) cc_final: 0.8066 (t0) REVERT: B 455 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8069 (mmm-85) REVERT: C 74 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9032 (pm20) outliers start: 20 outliers final: 9 residues processed: 116 average time/residue: 1.3486 time to fit residues: 172.1189 Evaluate side-chains 108 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 0.0270 chunk 5 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.0840 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.076986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.047193 restraints weight = 39086.323| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.33 r_work: 0.2555 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2225 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= 0.123 Angle : 0.557 11.195 20264 Z= 0.278 Chirality : 0.041 0.234 2149 Planarity : 0.004 0.063 2584 Dihedral : 5.615 55.510 2257 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: 0.50 (0.21), residues: 1733 helix: 1.50 (0.20), residues: 786 sheet: -0.32 (0.48), residues: 110 loop : -0.69 (0.22), residues: 837 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 0.014 0.001 TYR D 207 ARG 0.003 0.000 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 10) link_NAG-ASN : angle 1.57585 ( 30) link_BETA1-4 : bond 0.00994 ( 6) link_BETA1-4 : angle 2.46077 ( 18) hydrogen bonds : bond 0.03625 ( 564) hydrogen bonds : angle 4.03090 ( 1629) SS BOND : bond 0.00412 ( 10) SS BOND : angle 1.02938 ( 20) covalent geometry : bond 0.00281 (14883) covalent geometry : angle 0.54923 (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 114 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8893 (m-30) cc_final: 0.8648 (m-30) REVERT: A 399 ARG cc_start: 0.9140 (ptm-80) cc_final: 0.8895 (ptm-80) REVERT: A 400 GLN cc_start: 0.9433 (mt0) cc_final: 0.9002 (tt0) REVERT: D 95 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 354 ASP cc_start: 0.7314 (t0) cc_final: 0.7007 (t0) REVERT: B 394 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8611 (ttpp) REVERT: B 396 ASP cc_start: 0.9301 (m-30) cc_final: 0.9061 (m-30) REVERT: B 397 ASP cc_start: 0.8951 (m-30) cc_final: 0.7948 (m-30) REVERT: B 399 ARG cc_start: 0.9287 (ptm-80) cc_final: 0.9082 (ptm-80) REVERT: B 400 GLN cc_start: 0.9290 (tt0) cc_final: 0.8443 (tt0) REVERT: B 405 GLN cc_start: 0.8931 (tt0) cc_final: 0.8572 (tt0) REVERT: B 411 ASP cc_start: 0.8550 (t0) cc_final: 0.8080 (t0) REVERT: B 455 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8158 (mmm-85) REVERT: C 74 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9016 (pm20) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 1.8292 time to fit residues: 225.9221 Evaluate side-chains 107 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS ** 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 = 0.3490 r_free = 0.3490 target = 0.077623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.047906 restraints weight = 39405.286| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.36 r_work: 0.2588 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14909 Z= 0.104 Angle : 0.557 10.750 20264 Z= 0.276 Chirality : 0.041 0.235 2149 Planarity : 0.004 0.070 2584 Dihedral : 5.514 55.600 2257 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 12.99 % Favored : 86.18 % 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: 0.59 (0.21), residues: 1733 helix: 1.58 (0.20), residues: 786 sheet: -0.34 (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 D 163 HIS 0.003 0.001 HIS C 241 PHE 0.011 0.001 PHE D 523 TYR 0.013 0.001 TYR D 207 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 10) link_NAG-ASN : angle 1.52892 ( 30) link_BETA1-4 : bond 0.01026 ( 6) link_BETA1-4 : angle 2.43143 ( 18) hydrogen bonds : bond 0.03416 ( 564) hydrogen bonds : angle 3.97375 ( 1629) SS BOND : bond 0.00430 ( 10) SS BOND : angle 0.98457 ( 20) covalent geometry : bond 0.00235 (14883) covalent geometry : angle 0.54887 (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 110 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8862 (m-30) cc_final: 0.8650 (m-30) REVERT: A 399 ARG cc_start: 0.9142 (ptm-80) cc_final: 0.8894 (ptm-80) REVERT: A 400 GLN cc_start: 0.9411 (mt0) cc_final: 0.9003 (tt0) REVERT: D 95 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8769 (tt) REVERT: D 343 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8805 (m) REVERT: B 354 ASP cc_start: 0.7379 (t0) cc_final: 0.7091 (t0) REVERT: B 394 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8585 (ttpp) REVERT: B 396 ASP cc_start: 0.9300 (m-30) cc_final: 0.9039 (m-30) REVERT: B 397 ASP cc_start: 0.8958 (m-30) cc_final: 0.7919 (m-30) REVERT: B 399 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.8941 (ptm-80) REVERT: B 400 GLN cc_start: 0.9305 (tt0) cc_final: 0.8396 (tt0) REVERT: B 405 GLN cc_start: 0.8860 (tt0) cc_final: 0.8569 (tt0) REVERT: B 411 ASP cc_start: 0.8557 (t0) cc_final: 0.8097 (t0) REVERT: C 74 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9002 (pm20) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 1.5286 time to fit residues: 181.6170 Evaluate side-chains 106 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 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 111 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.076456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046619 restraints weight = 39416.945| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.35 r_work: 0.2548 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14909 Z= 0.157 Angle : 0.591 12.003 20264 Z= 0.292 Chirality : 0.042 0.231 2149 Planarity : 0.004 0.066 2584 Dihedral : 5.558 55.231 2257 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.02 % Allowed : 12.73 % Favored : 86.24 % 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: 0.63 (0.21), residues: 1733 helix: 1.64 (0.20), residues: 786 sheet: -0.36 (0.48), residues: 110 loop : -0.65 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 478 HIS 0.004 0.001 HIS C 378 PHE 0.017 0.001 PHE D 523 TYR 0.014 0.001 TYR D 207 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 10) link_NAG-ASN : angle 1.58403 ( 30) link_BETA1-4 : bond 0.00954 ( 6) link_BETA1-4 : angle 2.45713 ( 18) hydrogen bonds : bond 0.03714 ( 564) hydrogen bonds : angle 4.03380 ( 1629) SS BOND : bond 0.00452 ( 10) SS BOND : angle 1.10703 ( 20) covalent geometry : bond 0.00366 (14883) covalent geometry : angle 0.58275 (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: 16 poor density : 96 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASP cc_start: 0.8918 (m-30) cc_final: 0.8665 (m-30) REVERT: A 399 ARG cc_start: 0.9142 (ptm-80) cc_final: 0.8891 (ptm-80) REVERT: A 400 GLN cc_start: 0.9427 (mt0) cc_final: 0.9004 (tt0) REVERT: D 95 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8843 (tt) REVERT: D 343 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8808 (m) REVERT: B 354 ASP cc_start: 0.7465 (t0) cc_final: 0.7185 (t0) REVERT: B 394 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8588 (ttpp) REVERT: B 396 ASP cc_start: 0.9315 (m-30) cc_final: 0.9072 (m-30) REVERT: B 397 ASP cc_start: 0.8978 (m-30) cc_final: 0.7945 (m-30) REVERT: B 399 ARG cc_start: 0.9283 (ptm-80) cc_final: 0.8843 (ptm-80) REVERT: B 400 GLN cc_start: 0.9308 (tt0) cc_final: 0.8509 (tt0) REVERT: B 405 GLN cc_start: 0.8875 (tt0) cc_final: 0.8489 (tt0) REVERT: B 411 ASP cc_start: 0.8593 (t0) cc_final: 0.8135 (t0) REVERT: B 455 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8166 (mmm-85) REVERT: C 74 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8985 (pm20) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.7209 time to fit residues: 208.1726 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 : 1.546 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 147 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 150 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048114 restraints weight = 39473.126| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.37 r_work: 0.2591 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14909 Z= 0.102 Angle : 0.567 12.315 20264 Z= 0.279 Chirality : 0.040 0.234 2149 Planarity : 0.004 0.066 2584 Dihedral : 5.457 55.585 2257 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.83 % Allowed : 12.92 % Favored : 86.24 % 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: 1.64 (0.20), residues: 786 sheet: -0.42 (0.48), residues: 110 loop : -0.60 (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 D 374 PHE 0.011 0.001 PHE D 523 TYR 0.013 0.001 TYR D 207 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 10) link_NAG-ASN : angle 1.51152 ( 30) link_BETA1-4 : bond 0.01079 ( 6) link_BETA1-4 : angle 2.41301 ( 18) hydrogen bonds : bond 0.03344 ( 564) hydrogen bonds : angle 3.96882 ( 1629) SS BOND : bond 0.00371 ( 10) SS BOND : angle 0.94848 ( 20) covalent geometry : bond 0.00232 (14883) covalent geometry : angle 0.55957 (20196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10013.64 seconds wall clock time: 177 minutes 51.70 seconds (10671.70 seconds total)