Starting phenix.real_space_refine on Sun Sep 13 17:01:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d03_7783/09_2026/6d03_7783.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 132 5.16 5 C 15757 2.51 5 N 4200 2.21 5 O 4749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24844 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 614} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 455} 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 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 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 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 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 chiralities: 2 Chain: "K" 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 chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.19 Number of scatterers: 24844 At special positions: 0 Unit cell: (144.45, 149.85, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 132 16.00 O 4749 8.00 N 4200 7.00 C 15757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.02 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.02 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.02 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.02 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.01 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.01 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.02 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.02 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.05 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " BETA2-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG F 1 " - " ASN A 317 " " NAG G 1 " - " ASN A 727 " " NAG H 1 " - " ASN B 317 " " NAG I 1 " - " ASN B 727 " " NAG J 1 " - " ASN C 413 " " NAG K 1 " - " ASN D 413 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 26 sheets defined 44.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.195A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.644A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.883A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.680A pdb=" N THR A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 541 through 549 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.773A pdb=" N VAL A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 626 removed outlier: 3.973A pdb=" N GLN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.715A pdb=" N GLU A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.691A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.656A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 719 through 722 Processing helix chain 'A' and resid 727 through 750 removed outlier: 3.584A pdb=" N SER A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.741A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 159 through 176 removed outlier: 3.808A pdb=" N ARG B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.576A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 439 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.535A pdb=" N THR B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 582 through 603 removed outlier: 3.812A pdb=" N VAL B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 627 removed outlier: 3.754A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.521A pdb=" N GLU B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 635 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.597A pdb=" N TYR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.912A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 removed outlier: 4.336A pdb=" N HIS B 684 " --> pdb=" O VAL B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 717 through 722 removed outlier: 4.274A pdb=" N GLN B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 722' Processing helix chain 'B' and resid 727 through 750 removed outlier: 3.882A pdb=" N SER B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 30 removed outlier: 4.778A pdb=" N LYS C 18 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 29 " --> pdb=" O HIS C 25 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.842A pdb=" N TYR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 5.323A pdb=" N ILE C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 136 through 139 Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.727A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.761A pdb=" N LEU C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 removed outlier: 3.596A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 275 removed outlier: 3.809A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 350 through 362 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.680A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 460 through 472 removed outlier: 4.047A pdb=" N ASN C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 497 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.705A pdb=" N GLY C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 593 through 609 removed outlier: 3.804A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 608 " --> pdb=" O GLN C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.520A pdb=" N GLY C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 668 through 675 Processing helix chain 'D' and resid 12 through 29 removed outlier: 3.981A pdb=" N VAL D 29 " --> pdb=" O HIS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.948A pdb=" N TYR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.777A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.706A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.733A pdb=" N LEU D 170 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN D 172 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 removed outlier: 3.599A pdb=" N PHE D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 310 through 316 removed outlier: 3.504A pdb=" N GLY D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.746A pdb=" N ARG D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 4.067A pdb=" N LYS D 354 " --> pdb=" O HIS D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.736A pdb=" N CYS D 377 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.793A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.625A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.547A pdb=" N GLY D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 593 through 608 removed outlier: 3.867A pdb=" N VAL D 597 " --> pdb=" O LYS D 593 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.699A pdb=" N GLY D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 662 through 666 Processing helix chain 'D' and resid 668 through 675 removed outlier: 3.519A pdb=" N GLU D 672 " --> pdb=" O SER D 668 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 678 No H-bonds generated for 'chain 'D' and resid 676 through 678' Processing helix chain 'E' and resid 197 through 210 removed outlier: 3.540A pdb=" N PHE E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 240 removed outlier: 4.528A pdb=" N LYS E 223 " --> pdb=" O GLU E 219 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 224 " --> pdb=" O ASP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 256 removed outlier: 4.012A pdb=" N LYS E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 262 Processing helix chain 'E' and resid 266 through 288 removed outlier: 3.840A pdb=" N ARG E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 309 removed outlier: 3.949A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 335 removed outlier: 3.788A pdb=" N ASP E 323 " --> pdb=" O ASN E 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 362 removed outlier: 3.719A pdb=" N ARG E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 405 Processing helix chain 'E' and resid 415 through 459 removed outlier: 4.519A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 439 " --> pdb=" O PHE E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 477 removed outlier: 4.377A pdb=" N GLU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG E 468 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 510 removed outlier: 3.964A pdb=" N ASN E 484 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 566 removed outlier: 4.298A pdb=" N ASN E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 589 Processing helix chain 'E' and resid 591 through 632 removed outlier: 4.027A pdb=" N LEU E 616 " --> pdb=" O LYS E 612 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.871A pdb=" N LYS A 180 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA A 478 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A 402 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR A 480 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.728A pdb=" N VAL A 213 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.361A pdb=" N VAL A 233 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ARG A 258 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 282 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 279 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.641A pdb=" N LYS B 180 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP B 453 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 210 through 214 removed outlier: 6.999A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.667A pdb=" N MET B 349 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 367 " --> pdb=" O MET B 349 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY B 351 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.677A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 81 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C 301 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.823A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA C 99 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 233 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.823A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.703A pdb=" N VAL C 342 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 369 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP C 344 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA C 371 " --> pdb=" O TRP C 344 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 346 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 389 through 391 removed outlier: 3.712A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 449 through 450 removed outlier: 5.112A pdb=" N ALA C 430 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 561 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 449 through 450 removed outlier: 3.907A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AC2, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.692A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 251 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.542A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.542A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 345 removed outlier: 6.159A pdb=" N VAL D 342 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL D 369 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TRP D 344 " --> pdb=" O VAL D 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 388 through 391 removed outlier: 6.697A pdb=" N VAL D 587 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D 637 " --> pdb=" O ASN D 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.415A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA D 430 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 561 " --> pdb=" O LYS D 569 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 569 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.415A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) 1081 hydrogen bonds defined for protein. 3156 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: 5.06 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8008 1.34 - 1.47: 6440 1.47 - 1.60: 10762 1.60 - 1.73: 1 1.73 - 1.87: 176 Bond restraints: 25387 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C1 NAG D 707 " pdb=" O5 NAG D 707 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CA GLU B 582 " pdb=" CB GLU B 582 " ideal model delta sigma weight residual 1.527 1.607 -0.080 2.48e-02 1.63e+03 1.04e+01 bond pdb=" CG1 ILE E 175 " pdb=" CD1 ILE E 175 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 bond pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.14e+00 ... (remaining 25382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 33413 3.00 - 6.00: 778 6.00 - 8.99: 101 8.99 - 11.99: 25 11.99 - 14.99: 10 Bond angle restraints: 34327 Sorted by residual: angle pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta sigma weight residual 122.07 135.44 -13.37 1.43e+00 4.89e-01 8.74e+01 angle pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta sigma weight residual 121.70 136.69 -14.99 1.80e+00 3.09e-01 6.93e+01 angle pdb=" C ILE A 756 " pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta sigma weight residual 121.70 136.04 -14.34 1.80e+00 3.09e-01 6.35e+01 angle pdb=" C ASN A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 120.82 130.15 -9.33 1.50e+00 4.44e-01 3.87e+01 angle pdb=" C ASP E 407 " pdb=" N GLY E 408 " pdb=" CA GLY E 408 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 ... (remaining 34322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 14723 26.95 - 53.89: 484 53.89 - 80.84: 29 80.84 - 107.79: 8 107.79 - 134.73: 1 Dihedral angle restraints: 15245 sinusoidal: 6183 harmonic: 9062 Sorted by residual: dihedral pdb=" CA ALA E 569 " pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta harmonic sigma weight residual 180.00 45.27 134.73 0 5.00e+00 4.00e-02 7.26e+02 dihedral pdb=" CB CYS C 161 " pdb=" SG CYS C 161 " pdb=" SG CYS C 179 " pdb=" CB CYS C 179 " ideal model delta sinusoidal sigma weight residual -86.00 -175.56 89.56 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 345 " pdb=" SG CYS C 345 " pdb=" SG CYS C 377 " pdb=" CB CYS C 377 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 15242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 3770 0.480 - 0.960: 1 0.960 - 1.440: 0 1.440 - 1.920: 0 1.920 - 2.400: 1 Chirality restraints: 3772 Sorted by residual: chirality pdb=" C2 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C1 NAG J 2 " pdb=" C1 NAG J 2 " both_signs ideal model delta sigma weight residual False 2.40 0.00 2.40 2.00e-02 2.50e+03 1.44e+04 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 317 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CG LEU E 447 " pdb=" CB LEU E 447 " pdb=" CD1 LEU E 447 " pdb=" CD2 LEU E 447 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3769 not shown) Planarity restraints: 4436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 691 " -0.058 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 692 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 692 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 692 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 521 " -0.021 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE E 521 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 521 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 521 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE E 521 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 521 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 521 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO C 335 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.041 5.00e-02 4.00e+02 ... (remaining 4433 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 156 2.55 - 3.14: 18382 3.14 - 3.72: 37249 3.72 - 4.31: 51187 4.31 - 4.90: 85187 Nonbonded interactions: 192161 Sorted by model distance: nonbonded pdb="FE FE C 703 " pdb=" O1 CO3 C 704 " model vdw 1.960 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.005 2.260 nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.012 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.015 2.260 nonbonded pdb=" OH TYR D 188 " pdb="FE FE D 703 " model vdw 2.040 2.260 ... (remaining 192156 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.470 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 : 0.009 0.104 25447 Z= 0.399 Angle : 1.233 38.483 34462 Z= 0.671 Chirality : 0.074 2.400 3772 Planarity : 0.008 0.089 4426 Dihedral : 11.860 134.734 9285 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 1.12 % Allowed : 7.30 % Favored : 91.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.83 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.12), residues: 3096 helix: -2.78 (0.10), residues: 1242 sheet: -1.75 (0.26), residues: 346 loop : -2.17 (0.13), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 339 TYR 0.037 0.004 TYR B 643 PHE 0.055 0.004 PHE E 521 TRP 0.044 0.004 TRP C 358 HIS 0.023 0.003 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.40 (25387) covalent geometry : angle 1.19230 / 0.66 (34327) SS BOND : bond 0.00775 / 0.45 ( 44) SS BOND : angle 2.50754 / 1.63 ( 88) hydrogen bonds : bond 0.16551 / 10.65 ( 1057) hydrogen bonds : angle 8.78672 / 6.15 ( 3156) glycosidic custom : bond 0.06047 / 3.18 ( 1) glycosidic custom : angle 27.38013 / 14.43 ( 2) link_BETA1-4 : bond 0.01187 / 0.63 ( 5) link_BETA1-4 : angle 3.82650 / 2.29 ( 15) link_NAG-ASN : bond 0.00792 / 0.40 ( 10) link_NAG-ASN : angle 6.63965 / 4.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 343 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9006 (mt) REVERT: A 671 MET cc_start: 0.8625 (mmm) cc_final: 0.8195 (mmt) REVERT: B 365 MET cc_start: 0.9058 (mmm) cc_final: 0.8612 (mmm) REVERT: B 384 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9138 (pp) REVERT: C 367 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 389 MET cc_start: 0.8760 (ttt) cc_final: 0.8453 (ttt) REVERT: D 26 MET cc_start: 0.8538 (mmm) cc_final: 0.7985 (mpp) REVERT: D 267 LEU cc_start: 0.8731 (tm) cc_final: 0.8204 (tp) REVERT: D 323 ILE cc_start: 0.9427 (tt) cc_final: 0.9029 (tt) REVERT: E 185 ASN cc_start: 0.7972 (m-40) cc_final: 0.7739 (t0) REVERT: E 220 ASP cc_start: 0.7914 (t0) cc_final: 0.7291 (p0) REVERT: E 244 LYS cc_start: 0.8203 (tmmm) cc_final: 0.7876 (ttmt) REVERT: E 261 LYS cc_start: 0.8297 (tmtp) cc_final: 0.8072 (mmtp) REVERT: E 321 TYR cc_start: 0.7008 (t80) cc_final: 0.6566 (t80) REVERT: E 525 TYR cc_start: 0.7577 (t80) cc_final: 0.7147 (t80) REVERT: E 601 MET cc_start: 0.7740 (mtt) cc_final: 0.7486 (mtm) REVERT: E 626 GLN cc_start: 0.7571 (tt0) cc_final: 0.7363 (tm-30) outliers start: 30 outliers final: 6 residues processed: 367 average time/residue: 0.1709 time to fit residues: 97.1940 Evaluate side-chains 175 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 171 ASN A 206 ASN A 348 ASN A 379 ASN A 475 HIS A 493 ASN A 515 HIS A 603 HIS A 626 ASN A 715 ASN B 171 ASN B 302 HIS B 401 HIS B 483 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN C 25 HIS C 55 ASN C 300 HIS C 536 GLN C 546 ASN C 603 GLN C 618 ASN D 25 HIS D 55 ASN D 172 GLN D 268 ASN D 383 ASN D 411 ASN D 417 ASN D 469 ASN D 541 ASN D 618 ASN E 174 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 252 ASN E 289 ASN E 444 ASN E 483 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107457 restraints weight = 39297.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108019 restraints weight = 39579.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108952 restraints weight = 33129.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109406 restraints weight = 25510.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109475 restraints weight = 22711.930| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25447 Z= 0.185 Angle : 0.717 10.694 34462 Z= 0.374 Chirality : 0.060 2.400 3772 Planarity : 0.005 0.058 4426 Dihedral : 6.415 74.064 3371 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.42 % Allowed : 10.01 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.14), residues: 3096 helix: -0.77 (0.13), residues: 1273 sheet: -1.32 (0.27), residues: 346 loop : -1.70 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 272 TYR 0.029 0.002 TYR C 514 PHE 0.026 0.002 PHE E 521 TRP 0.027 0.002 TRP B 740 HIS 0.008 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (25387) covalent geometry : angle 0.70230 / 0.37 (34327) SS BOND : bond 0.00447 / 0.26 ( 44) SS BOND : angle 1.86511 / 1.29 ( 88) hydrogen bonds : bond 0.06174 / 4.00 ( 1057) hydrogen bonds : angle 5.57087 / 3.91 ( 3156) glycosidic custom : bond 0.00685 / 0.36 ( 1) glycosidic custom : angle 1.45527 / 0.77 ( 2) link_BETA1-4 : bond 0.00568 / 0.33 ( 5) link_BETA1-4 : angle 1.86451 / 1.12 ( 15) link_NAG-ASN : bond 0.00468 / 0.25 ( 10) link_NAG-ASN : angle 3.70169 / 2.35 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7639 (mm-40) REVERT: A 375 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7757 (pt) REVERT: A 454 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8865 (t) REVERT: A 603 HIS cc_start: 0.9133 (OUTLIER) cc_final: 0.8822 (p90) REVERT: B 209 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6857 (mt) REVERT: B 295 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 384 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9157 (pt) REVERT: C 367 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 389 MET cc_start: 0.8774 (ttt) cc_final: 0.8436 (ttt) REVERT: C 421 THR cc_start: 0.8573 (m) cc_final: 0.8125 (p) REVERT: D 26 MET cc_start: 0.8691 (mmm) cc_final: 0.7987 (mpp) REVERT: D 323 ILE cc_start: 0.9325 (tt) cc_final: 0.8908 (tt) REVERT: D 382 MET cc_start: 0.8399 (mtp) cc_final: 0.8071 (mtp) REVERT: D 411 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8431 (m110) REVERT: D 497 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8778 (tt) REVERT: D 527 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8496 (ptpp) REVERT: E 220 ASP cc_start: 0.7568 (t0) cc_final: 0.7275 (p0) REVERT: E 244 LYS cc_start: 0.8300 (tmmm) cc_final: 0.7943 (ttmt) REVERT: E 264 ARG cc_start: 0.8707 (mpp80) cc_final: 0.8018 (mmm160) REVERT: E 321 TYR cc_start: 0.6931 (t80) cc_final: 0.6621 (t80) REVERT: E 335 MET cc_start: 0.7280 (tpp) cc_final: 0.6843 (ttt) REVERT: E 612 LYS cc_start: 0.8624 (tptp) cc_final: 0.8399 (tptt) outliers start: 65 outliers final: 29 residues processed: 244 average time/residue: 0.1647 time to fit residues: 63.6687 Evaluate side-chains 192 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 LYS Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 385 ILE Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 3.9990 chunk 149 optimal weight: 0.3980 chunk 307 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 198 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 604 GLN D 383 ASN D 411 ASN D 584 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108918 restraints weight = 38921.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109498 restraints weight = 34774.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110102 restraints weight = 28160.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110493 restraints weight = 23895.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110698 restraints weight = 21277.957| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25447 Z= 0.138 Angle : 0.627 10.858 34462 Z= 0.325 Chirality : 0.058 2.400 3772 Planarity : 0.004 0.049 4426 Dihedral : 5.951 70.285 3368 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.68 % Allowed : 11.21 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3096 helix: 0.20 (0.14), residues: 1267 sheet: -1.12 (0.27), residues: 346 loop : -1.49 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 121 TYR 0.034 0.002 TYR C 514 PHE 0.025 0.001 PHE A 237 TRP 0.023 0.001 TRP B 740 HIS 0.006 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25387) covalent geometry : angle 0.61385 / 0.32 (34327) SS BOND : bond 0.00352 / 0.20 ( 44) SS BOND : angle 1.59822 / 1.13 ( 88) hydrogen bonds : bond 0.05322 / 3.44 ( 1057) hydrogen bonds : angle 5.08419 / 3.56 ( 3156) glycosidic custom : bond 0.00701 / 0.37 ( 1) glycosidic custom : angle 1.92121 / 1.02 ( 2) link_BETA1-4 : bond 0.00756 / 0.44 ( 5) link_BETA1-4 : angle 1.72003 / 1.03 ( 15) link_NAG-ASN : bond 0.00400 / 0.22 ( 10) link_NAG-ASN : angle 3.35173 / 2.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 166 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7880 (pt) REVERT: A 603 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8322 (p-80) REVERT: A 604 ASP cc_start: 0.7745 (t0) cc_final: 0.7533 (t0) REVERT: B 384 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9156 (pt) REVERT: C 367 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 389 MET cc_start: 0.8750 (ttt) cc_final: 0.8376 (ttt) REVERT: C 421 THR cc_start: 0.8563 (m) cc_final: 0.8129 (p) REVERT: C 514 TYR cc_start: 0.8188 (m-80) cc_final: 0.7925 (m-80) REVERT: D 26 MET cc_start: 0.8758 (mmm) cc_final: 0.7982 (mpp) REVERT: D 323 ILE cc_start: 0.9285 (tt) cc_final: 0.8844 (tt) REVERT: D 361 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8870 (t160) REVERT: D 382 MET cc_start: 0.8360 (mtp) cc_final: 0.8014 (mtp) REVERT: D 497 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8760 (tt) REVERT: D 527 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (ptpp) REVERT: E 220 ASP cc_start: 0.7624 (t0) cc_final: 0.7280 (p0) REVERT: E 244 LYS cc_start: 0.8224 (tmmm) cc_final: 0.7881 (ttmt) REVERT: E 321 TYR cc_start: 0.6840 (t80) cc_final: 0.6591 (t80) REVERT: E 612 LYS cc_start: 0.8579 (tptp) cc_final: 0.8356 (tptt) outliers start: 72 outliers final: 31 residues processed: 230 average time/residue: 0.1523 time to fit residues: 57.3002 Evaluate side-chains 173 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 LYS Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 603 GLN Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 743 GLN C 119 HIS ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 383 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 292 ASN E 456 ASN E 628 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104914 restraints weight = 39195.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105224 restraints weight = 40122.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106176 restraints weight = 33571.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106640 restraints weight = 26352.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106717 restraints weight = 23160.227| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25447 Z= 0.222 Angle : 0.686 11.227 34462 Z= 0.355 Chirality : 0.060 2.400 3772 Planarity : 0.004 0.050 4426 Dihedral : 5.834 67.648 3368 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 3.16 % Allowed : 11.88 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3096 helix: 0.52 (0.14), residues: 1294 sheet: -1.21 (0.26), residues: 358 loop : -1.37 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 121 TYR 0.023 0.002 TYR B 683 PHE 0.022 0.002 PHE A 442 TRP 0.023 0.002 TRP A 740 HIS 0.007 0.001 HIS D 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (25387) covalent geometry : angle 0.67406 / 0.35 (34327) SS BOND : bond 0.00407 / 0.24 ( 44) SS BOND : angle 1.56053 / 1.06 ( 88) hydrogen bonds : bond 0.05673 / 3.67 ( 1057) hydrogen bonds : angle 4.98469 / 3.50 ( 3156) glycosidic custom : bond 0.00740 / 0.39 ( 1) glycosidic custom : angle 1.69601 / 0.90 ( 2) link_BETA1-4 : bond 0.00785 / 0.45 ( 5) link_BETA1-4 : angle 1.93585 / 1.17 ( 15) link_NAG-ASN : bond 0.00421 / 0.21 ( 10) link_NAG-ASN : angle 3.47904 / 2.25 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 138 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7962 (pt) REVERT: B 384 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9178 (pt) REVERT: B 565 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7202 (p90) REVERT: B 570 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7844 (mtp) REVERT: C 225 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7817 (pp) REVERT: C 389 MET cc_start: 0.8807 (ttt) cc_final: 0.8522 (ttt) REVERT: D 323 ILE cc_start: 0.9287 (tt) cc_final: 0.8808 (tt) REVERT: D 361 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8928 (t160) REVERT: D 382 MET cc_start: 0.8503 (mtp) cc_final: 0.8142 (mtp) REVERT: D 411 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8587 (m110) REVERT: D 497 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8728 (tt) REVERT: D 527 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8406 (ptpp) REVERT: E 220 ASP cc_start: 0.7756 (t0) cc_final: 0.7315 (p0) REVERT: E 244 LYS cc_start: 0.8255 (tmmm) cc_final: 0.7951 (ttmt) REVERT: E 321 TYR cc_start: 0.6722 (t80) cc_final: 0.6496 (t80) outliers start: 85 outliers final: 47 residues processed: 215 average time/residue: 0.1502 time to fit residues: 53.2095 Evaluate side-chains 189 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 642 HIS Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 527 LYS Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 603 GLN Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 238 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS B 684 HIS ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN D 540 GLN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108174 restraints weight = 38856.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108549 restraints weight = 37848.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109222 restraints weight = 32198.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109786 restraints weight = 26987.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109787 restraints weight = 22997.517| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25447 Z= 0.130 Angle : 0.595 10.821 34462 Z= 0.306 Chirality : 0.058 2.400 3772 Planarity : 0.004 0.048 4426 Dihedral : 5.532 63.518 3368 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 3.28 % Allowed : 11.95 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3096 helix: 1.00 (0.14), residues: 1294 sheet: -1.13 (0.26), residues: 370 loop : -1.22 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 632 TYR 0.025 0.002 TYR D 412 PHE 0.019 0.001 PHE A 237 TRP 0.020 0.001 TRP B 740 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (25387) covalent geometry : angle 0.58348 / 0.30 (34327) SS BOND : bond 0.00294 / 0.17 ( 44) SS BOND : angle 1.41457 / 1.02 ( 88) hydrogen bonds : bond 0.04811 / 3.11 ( 1057) hydrogen bonds : angle 4.64521 / 3.26 ( 3156) glycosidic custom : bond 0.00687 / 0.36 ( 1) glycosidic custom : angle 1.66649 / 0.88 ( 2) link_BETA1-4 : bond 0.00806 / 0.49 ( 5) link_BETA1-4 : angle 1.67997 / 1.01 ( 15) link_NAG-ASN : bond 0.00403 / 0.22 ( 10) link_NAG-ASN : angle 3.11018 / 1.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 149 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8040 (pt) REVERT: A 603 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8758 (p90) REVERT: B 384 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9171 (pt) REVERT: B 565 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6962 (p90) REVERT: C 225 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7879 (pp) REVERT: C 389 MET cc_start: 0.8748 (ttt) cc_final: 0.8505 (ttt) REVERT: C 421 THR cc_start: 0.8448 (m) cc_final: 0.7993 (p) REVERT: D 192 PHE cc_start: 0.8355 (t80) cc_final: 0.8077 (t80) REVERT: D 323 ILE cc_start: 0.9281 (tt) cc_final: 0.8837 (tt) REVERT: D 361 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8859 (t160) REVERT: D 411 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8632 (m110) REVERT: D 564 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6444 (mt) REVERT: E 211 TYR cc_start: 0.6761 (m-10) cc_final: 0.6491 (m-10) REVERT: E 220 ASP cc_start: 0.7547 (t0) cc_final: 0.7271 (p0) REVERT: E 321 TYR cc_start: 0.6765 (t80) cc_final: 0.6524 (t80) REVERT: E 335 MET cc_start: 0.7537 (ttt) cc_final: 0.6766 (tpp) REVERT: E 452 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8299 (tttp) outliers start: 88 outliers final: 48 residues processed: 227 average time/residue: 0.1544 time to fit residues: 57.5254 Evaluate side-chains 186 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 452 LYS Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain E residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 139 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 158 optimal weight: 0.0060 chunk 298 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 302 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 285 GLN B 615 ASN D 383 ASN E 185 ASN E 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109132 restraints weight = 38897.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109495 restraints weight = 39891.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110280 restraints weight = 32559.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110854 restraints weight = 25648.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110890 restraints weight = 23040.267| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25447 Z= 0.117 Angle : 0.584 15.881 34462 Z= 0.298 Chirality : 0.057 2.400 3772 Planarity : 0.003 0.043 4426 Dihedral : 5.368 60.053 3368 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 2.64 % Allowed : 12.66 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3096 helix: 1.29 (0.15), residues: 1287 sheet: -1.02 (0.26), residues: 370 loop : -1.12 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.017 0.001 TYR B 683 PHE 0.027 0.001 PHE E 462 TRP 0.021 0.001 TRP A 740 HIS 0.021 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (25387) covalent geometry : angle 0.57217 / 0.29 (34327) SS BOND : bond 0.00383 / 0.20 ( 44) SS BOND : angle 1.45910 / 1.00 ( 88) hydrogen bonds : bond 0.04509 / 2.91 ( 1057) hydrogen bonds : angle 4.47993 / 3.14 ( 3156) glycosidic custom : bond 0.00677 / 0.36 ( 1) glycosidic custom : angle 1.61367 / 0.85 ( 2) link_BETA1-4 : bond 0.00764 / 0.46 ( 5) link_BETA1-4 : angle 1.62699 / 0.98 ( 15) link_NAG-ASN : bond 0.00364 / 0.21 ( 10) link_NAG-ASN : angle 2.96294 / 1.89 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8021 (pt) REVERT: A 603 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8034 (p-80) REVERT: B 384 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9147 (pt) REVERT: B 565 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6987 (p90) REVERT: B 671 MET cc_start: 0.8559 (mmm) cc_final: 0.8248 (tpt) REVERT: C 225 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7968 (pp) REVERT: C 389 MET cc_start: 0.8773 (ttt) cc_final: 0.8480 (ttt) REVERT: C 421 THR cc_start: 0.8475 (m) cc_final: 0.8054 (p) REVERT: D 192 PHE cc_start: 0.8220 (t80) cc_final: 0.7973 (t80) REVERT: D 323 ILE cc_start: 0.9262 (tt) cc_final: 0.8823 (tt) REVERT: D 361 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8862 (t160) REVERT: D 564 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6471 (mt) REVERT: E 211 TYR cc_start: 0.6723 (m-10) cc_final: 0.6463 (m-10) REVERT: E 220 ASP cc_start: 0.7526 (t0) cc_final: 0.7280 (p0) REVERT: E 321 TYR cc_start: 0.6684 (t80) cc_final: 0.6441 (t80) REVERT: E 607 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6761 (mp0) outliers start: 71 outliers final: 49 residues processed: 208 average time/residue: 0.1447 time to fit residues: 49.7120 Evaluate side-chains 188 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 601 MET Chi-restraints excluded: chain E residue 607 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 250 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 383 ASN E 185 ASN E 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106690 restraints weight = 38986.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106719 restraints weight = 39119.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107643 restraints weight = 34871.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108267 restraints weight = 25979.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108346 restraints weight = 23676.531| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25447 Z= 0.177 Angle : 0.625 15.181 34462 Z= 0.320 Chirality : 0.059 2.400 3772 Planarity : 0.004 0.045 4426 Dihedral : 5.385 58.703 3368 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 2.83 % Allowed : 13.07 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3096 helix: 1.31 (0.15), residues: 1288 sheet: -1.02 (0.26), residues: 374 loop : -1.11 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 632 TYR 0.019 0.002 TYR B 683 PHE 0.019 0.001 PHE E 462 TRP 0.022 0.001 TRP A 740 HIS 0.006 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (25387) covalent geometry : angle 0.61278 / 0.32 (34327) SS BOND : bond 0.00389 / 0.22 ( 44) SS BOND : angle 1.53188 / 1.05 ( 88) hydrogen bonds : bond 0.04897 / 3.17 ( 1057) hydrogen bonds : angle 4.56495 / 3.20 ( 3156) glycosidic custom : bond 0.00693 / 0.36 ( 1) glycosidic custom : angle 1.58984 / 0.84 ( 2) link_BETA1-4 : bond 0.00813 / 0.49 ( 5) link_BETA1-4 : angle 1.77766 / 1.08 ( 15) link_NAG-ASN : bond 0.00381 / 0.20 ( 10) link_NAG-ASN : angle 3.13395 / 2.03 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8054 (pt) REVERT: B 364 ARG cc_start: 0.8091 (mmp80) cc_final: 0.7707 (mmt90) REVERT: B 384 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9152 (pt) REVERT: B 565 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7412 (p90) REVERT: C 104 ASP cc_start: 0.8080 (m-30) cc_final: 0.7880 (m-30) REVERT: C 225 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7933 (pp) REVERT: C 271 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: C 421 THR cc_start: 0.8489 (m) cc_final: 0.8000 (p) REVERT: D 192 PHE cc_start: 0.8277 (t80) cc_final: 0.8040 (t80) REVERT: D 323 ILE cc_start: 0.9266 (tt) cc_final: 0.8816 (tt) REVERT: D 354 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8917 (tttt) REVERT: D 361 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8917 (t160) REVERT: D 564 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6516 (mt) REVERT: E 211 TYR cc_start: 0.6827 (m-10) cc_final: 0.6568 (m-10) REVERT: E 220 ASP cc_start: 0.7644 (t0) cc_final: 0.7305 (p0) REVERT: E 321 TYR cc_start: 0.6683 (t80) cc_final: 0.6434 (t80) REVERT: E 517 GLU cc_start: 0.2412 (OUTLIER) cc_final: 0.2192 (pt0) REVERT: E 607 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: E 631 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7041 (mt-10) outliers start: 76 outliers final: 53 residues processed: 209 average time/residue: 0.1474 time to fit residues: 51.1897 Evaluate side-chains 193 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 456 ASN Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 517 GLU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 601 MET Chi-restraints excluded: chain E residue 607 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 127 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 251 optimal weight: 0.0070 chunk 281 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 383 ASN E 185 ASN ** E 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110353 restraints weight = 38749.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110339 restraints weight = 38266.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111150 restraints weight = 34619.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111787 restraints weight = 25940.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111859 restraints weight = 23011.263| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 25447 Z= 0.110 Angle : 0.573 13.994 34462 Z= 0.292 Chirality : 0.057 2.400 3772 Planarity : 0.003 0.044 4426 Dihedral : 5.216 56.783 3368 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.38 % Allowed : 13.70 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3096 helix: 1.57 (0.15), residues: 1283 sheet: -0.81 (0.26), residues: 370 loop : -1.06 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 475 TYR 0.023 0.001 TYR B 683 PHE 0.020 0.001 PHE E 462 TRP 0.019 0.001 TRP A 740 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (25387) covalent geometry : angle 0.56261 / 0.29 (34327) SS BOND : bond 0.00284 / 0.16 ( 44) SS BOND : angle 1.31058 / 0.90 ( 88) hydrogen bonds : bond 0.04242 / 2.73 ( 1057) hydrogen bonds : angle 4.32052 / 3.04 ( 3156) glycosidic custom : bond 0.00657 / 0.35 ( 1) glycosidic custom : angle 1.57553 / 0.83 ( 2) link_BETA1-4 : bond 0.00787 / 0.48 ( 5) link_BETA1-4 : angle 1.58108 / 0.94 ( 15) link_NAG-ASN : bond 0.00387 / 0.22 ( 10) link_NAG-ASN : angle 2.84067 / 1.81 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: B 384 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9124 (pt) REVERT: B 565 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7121 (p90) REVERT: C 225 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7959 (pp) REVERT: C 271 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: C 382 MET cc_start: 0.7465 (mtt) cc_final: 0.7225 (mtt) REVERT: C 421 THR cc_start: 0.8411 (m) cc_final: 0.7972 (p) REVERT: D 323 ILE cc_start: 0.9240 (tt) cc_final: 0.8801 (tt) REVERT: D 345 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7531 (m) REVERT: D 361 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8857 (t160) REVERT: D 564 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6452 (mt) REVERT: D 630 LEU cc_start: 0.8990 (mt) cc_final: 0.8761 (mt) REVERT: E 211 TYR cc_start: 0.6627 (m-10) cc_final: 0.6425 (m-10) REVERT: E 284 CYS cc_start: 0.5613 (t) cc_final: 0.5239 (t) REVERT: E 321 TYR cc_start: 0.6468 (t80) cc_final: 0.6263 (t80) REVERT: E 607 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: E 631 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6844 (mt-10) outliers start: 64 outliers final: 43 residues processed: 215 average time/residue: 0.1461 time to fit residues: 52.7613 Evaluate side-chains 188 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 601 MET Chi-restraints excluded: chain E residue 607 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 56 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 172 GLN E 185 ASN ** E 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106050 restraints weight = 39088.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106502 restraints weight = 36880.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106944 restraints weight = 31941.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107716 restraints weight = 27938.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107712 restraints weight = 23816.680| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25447 Z= 0.186 Angle : 0.626 13.949 34462 Z= 0.320 Chirality : 0.059 2.400 3772 Planarity : 0.004 0.044 4426 Dihedral : 5.193 57.725 3366 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 2.42 % Allowed : 14.04 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3096 helix: 1.45 (0.15), residues: 1292 sheet: -0.93 (0.26), residues: 372 loop : -1.06 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 632 TYR 0.023 0.002 TYR B 683 PHE 0.045 0.002 PHE A 298 TRP 0.036 0.002 TRP C 550 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (25387) covalent geometry : angle 0.61538 / 0.32 (34327) SS BOND : bond 0.00366 / 0.21 ( 44) SS BOND : angle 1.43614 / 0.98 ( 88) hydrogen bonds : bond 0.04806 / 3.11 ( 1057) hydrogen bonds : angle 4.47341 / 3.14 ( 3156) glycosidic custom : bond 0.00682 / 0.36 ( 1) glycosidic custom : angle 1.52567 / 0.80 ( 2) link_BETA1-4 : bond 0.00766 / 0.46 ( 5) link_BETA1-4 : angle 1.77949 / 1.08 ( 15) link_NAG-ASN : bond 0.00377 / 0.20 ( 10) link_NAG-ASN : angle 3.07322 / 2.00 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 130 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8095 (pt) REVERT: B 384 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9184 (pt) REVERT: B 565 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7409 (p90) REVERT: C 225 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7916 (pp) REVERT: C 271 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: C 421 THR cc_start: 0.8427 (m) cc_final: 0.7965 (p) REVERT: D 26 MET cc_start: 0.8617 (tpt) cc_final: 0.8243 (mpp) REVERT: D 323 ILE cc_start: 0.9283 (tt) cc_final: 0.8841 (tt) REVERT: D 361 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8863 (t160) REVERT: D 464 MET cc_start: 0.8887 (mmp) cc_final: 0.8684 (mmm) REVERT: D 564 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6491 (mt) REVERT: E 211 TYR cc_start: 0.6735 (m-10) cc_final: 0.6512 (m-10) REVERT: E 284 CYS cc_start: 0.5608 (t) cc_final: 0.5253 (t) REVERT: E 335 MET cc_start: 0.6500 (tpp) cc_final: 0.6183 (tpp) REVERT: E 525 TYR cc_start: 0.7897 (t80) cc_final: 0.7542 (t80) REVERT: E 607 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: E 631 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6463 (mt-10) outliers start: 65 outliers final: 52 residues processed: 186 average time/residue: 0.1456 time to fit residues: 45.2431 Evaluate side-chains 186 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 381 MET Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 601 MET Chi-restraints excluded: chain E residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 35 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 GLN E 185 ASN ** E 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109292 restraints weight = 38988.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109698 restraints weight = 38551.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110333 restraints weight = 32700.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110875 restraints weight = 28019.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110924 restraints weight = 23406.091| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25447 Z= 0.119 Angle : 0.574 13.367 34462 Z= 0.293 Chirality : 0.057 2.400 3772 Planarity : 0.003 0.043 4426 Dihedral : 5.066 59.870 3366 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.31 % Allowed : 14.07 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3096 helix: 1.63 (0.15), residues: 1296 sheet: -0.81 (0.26), residues: 370 loop : -1.01 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 475 TYR 0.018 0.001 TYR B 683 PHE 0.033 0.001 PHE A 298 TRP 0.036 0.001 TRP C 550 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25387) covalent geometry : angle 0.56392 / 0.29 (34327) SS BOND : bond 0.00293 / 0.17 ( 44) SS BOND : angle 1.29876 / 0.88 ( 88) hydrogen bonds : bond 0.04251 / 2.75 ( 1057) hydrogen bonds : angle 4.28215 / 3.01 ( 3156) glycosidic custom : bond 0.00649 / 0.34 ( 1) glycosidic custom : angle 1.55900 / 0.82 ( 2) link_BETA1-4 : bond 0.00798 / 0.49 ( 5) link_BETA1-4 : angle 1.59992 / 0.96 ( 15) link_NAG-ASN : bond 0.00373 / 0.21 ( 10) link_NAG-ASN : angle 2.87975 / 1.84 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 565 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7180 (p90) REVERT: C 271 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: C 382 MET cc_start: 0.7598 (mtt) cc_final: 0.7316 (mtt) REVERT: C 421 THR cc_start: 0.8370 (m) cc_final: 0.7910 (p) REVERT: D 323 ILE cc_start: 0.9252 (tt) cc_final: 0.8818 (tt) REVERT: D 345 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7766 (m) REVERT: D 354 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8945 (tttt) REVERT: D 361 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8803 (t160) REVERT: D 464 MET cc_start: 0.8830 (mmp) cc_final: 0.8629 (mmm) REVERT: D 564 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6466 (mt) REVERT: E 335 MET cc_start: 0.6530 (tpp) cc_final: 0.6187 (tpp) REVERT: E 607 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.6615 (mp0) outliers start: 62 outliers final: 49 residues processed: 189 average time/residue: 0.1562 time to fit residues: 49.0305 Evaluate side-chains 180 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 601 MET Chi-restraints excluded: chain E residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 132 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 185 ASN ** E 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110005 restraints weight = 38949.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.110208 restraints weight = 38033.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111225 restraints weight = 32232.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111636 restraints weight = 25450.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.111695 restraints weight = 22840.891| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25447 Z= 0.114 Angle : 0.572 13.068 34462 Z= 0.291 Chirality : 0.057 2.400 3772 Planarity : 0.003 0.042 4426 Dihedral : 4.916 57.716 3364 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.38 % Allowed : 14.18 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3096 helix: 1.72 (0.15), residues: 1295 sheet: -0.64 (0.27), residues: 350 loop : -1.00 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 475 TYR 0.026 0.001 TYR E 525 PHE 0.030 0.001 PHE A 298 TRP 0.035 0.001 TRP C 550 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25387) covalent geometry : angle 0.56278 / 0.29 (34327) SS BOND : bond 0.00285 / 0.16 ( 44) SS BOND : angle 1.24621 / 0.85 ( 88) hydrogen bonds : bond 0.04158 / 2.69 ( 1057) hydrogen bonds : angle 4.23241 / 2.97 ( 3156) glycosidic custom : bond 0.00640 / 0.34 ( 1) glycosidic custom : angle 1.50279 / 0.79 ( 2) link_BETA1-4 : bond 0.00778 / 0.48 ( 5) link_BETA1-4 : angle 1.56354 / 0.94 ( 15) link_NAG-ASN : bond 0.00360 / 0.20 ( 10) link_NAG-ASN : angle 2.77736 / 1.79 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.56 seconds wall clock time: 55 minutes 30.44 seconds (3330.44 seconds total)