Starting phenix.real_space_refine on Tue May 5 02:21:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzs_48767/05_2026/9mzs_48767.cif" } resolution = 3.9 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= 0.004 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 140 5.16 5 C 16017 2.51 5 N 4100 2.21 5 O 4743 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25004 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6136 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 774, 6129 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 30, 'TRANS': 743} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 774, 6129 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 30, 'TRANS': 743} Chain breaks: 1 bond proxies already assigned to first conformer: 6257 Chain: "B" Number of atoms: 6097 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6094 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 28, 'TRANS': 741} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 770, 6094 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 28, 'TRANS': 741} Chain breaks: 1 bond proxies already assigned to first conformer: 6224 Chain: "C" Number of atoms: 6139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 775, 6132 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 775, 6132 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain breaks: 1 bond proxies already assigned to first conformer: 6259 Chain: "D" Number of atoms: 6090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6090 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 29, 'TRANS': 740} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'2J9': 1, 'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'2J9': 1, 'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'2J9': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 9.62, per 1000 atoms: 0.38 Number of scatterers: 25004 At special positions: 0 Unit cell: (115.54, 157.94, 201.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 F 4 9.00 O 4743 8.00 N 4100 7.00 C 16017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS B 802 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS D 802 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 BETA1-3 " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1001 " - " ASN A 275 " " NAG B1001 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG E 1 " - " ASN A 67 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 67 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN B 275 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN D 378 " " NAG M 1 " - " ASN D 275 " " NAG N 1 " - " ASN D 67 " " NAG O 1 " - " ASN D 412 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5772 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 32 sheets defined 46.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.600A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.577A pdb=" N LEU A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.832A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.795A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.138A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.798A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.799A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.836A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 Processing helix chain 'A' and resid 630 through 662 removed outlier: 3.516A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.870A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 4.362A pdb=" N LYS A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.573A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.747A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 removed outlier: 3.708A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 845 removed outlier: 6.528A pdb=" N GLY A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 88 through 101 removed outlier: 3.500A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 152 through 168 removed outlier: 3.590A pdb=" N LEU B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.759A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.518A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.010A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.585A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.616A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.563A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.643A pdb=" N MET B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 418 removed outlier: 3.627A pdb=" N LYS B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 418' Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 462 through 475 removed outlier: 3.607A pdb=" N SER B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.965A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 633 through 659 removed outlier: 3.683A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 4.152A pdb=" N CYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 677' Processing helix chain 'B' and resid 689 through 697 removed outlier: 3.607A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.670A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.635A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.619A pdb=" N GLU B 743 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 789 removed outlier: 3.516A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 800 removed outlier: 3.653A pdb=" N GLU B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 846 removed outlier: 3.589A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.720A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.628A pdb=" N LEU C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.540A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.566A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.855A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.726A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.426A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.624A pdb=" N ARG C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.722A pdb=" N PHE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 364 removed outlier: 3.710A pdb=" N PHE C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 454 through 457 removed outlier: 4.037A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.296A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 562 through 585 Processing helix chain 'C' and resid 630 through 660 Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.641A pdb=" N THR C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 712 removed outlier: 3.525A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 747 Processing helix chain 'C' and resid 772 through 788 removed outlier: 4.320A pdb=" N ASP C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 Processing helix chain 'C' and resid 821 through 848 removed outlier: 3.576A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.861A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.654A pdb=" N TYR D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.627A pdb=" N SER D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.755A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 4.064A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 363 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.586A pdb=" N ARG D 503 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.738A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 581 Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.767A pdb=" N ALA D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 Processing helix chain 'D' and resid 689 through 697 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.565A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.521A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.823A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 806 through 810 Processing helix chain 'D' and resid 820 through 845 removed outlier: 4.190A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 83 removed outlier: 8.573A pdb=" N PHE A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 203 removed outlier: 5.012A pdb=" N HIS A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 256 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 393 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 400 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA4, first strand: chain 'A' and resid 432 through 435 Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.493A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.614A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.094A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 384 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 150 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.932A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 171 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 227 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 390 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 403 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 395 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.547A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 433 through 437 removed outlier: 6.232A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 444 through 446 Processing sheet with id=AB4, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB5, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 684 removed outlier: 6.425A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 755 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 542 " --> pdb=" O THR B 753 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 74 through 83 removed outlier: 6.011A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 198 through 203 removed outlier: 3.531A pdb=" N LYS C 200 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N HIS C 225 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 404 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 412 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 435 through 437 removed outlier: 6.049A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC2, first strand: chain 'C' and resid 513 through 514 Processing sheet with id=AC3, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.602A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 684 through 685 removed outlier: 7.012A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.839A pdb=" N THR D 75 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 41 through 43 Processing sheet with id=AC7, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.965A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 198 through 203 removed outlier: 4.791A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 369 through 370 removed outlier: 3.580A pdb=" N GLY D 373 " --> pdb=" O GLY D 370 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 433 through 437 removed outlier: 6.341A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD3, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD4, first strand: chain 'D' and resid 735 through 738 removed outlier: 4.000A pdb=" N TYR D 542 " --> pdb=" O THR D 753 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR D 753 " --> pdb=" O TYR D 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.500A pdb=" N LYS D 762 " --> pdb=" O LEU D 536 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4901 1.33 - 1.45: 6295 1.45 - 1.57: 14118 1.57 - 1.70: 4 1.70 - 1.82: 236 Bond restraints: 25554 Sorted by residual: bond pdb=" C PRO C 561 " pdb=" O PRO C 561 " ideal model delta sigma weight residual 1.238 1.206 0.031 1.42e-02 4.96e+03 4.91e+00 bond pdb=" N ILE C 563 " pdb=" CA ILE C 563 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.26e-02 6.30e+03 4.45e+00 bond pdb=" N ASP C 562 " pdb=" CA ASP C 562 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.24e-02 6.50e+03 3.46e+00 bond pdb=" C SER C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.85e+00 bond pdb=" C ASP C 562 " pdb=" N ILE C 563 " ideal model delta sigma weight residual 1.335 1.316 0.019 1.21e-02 6.83e+03 2.58e+00 ... (remaining 25549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 34416 3.60 - 7.21: 164 7.21 - 10.81: 30 10.81 - 14.41: 0 14.41 - 18.01: 1 Bond angle restraints: 34611 Sorted by residual: angle pdb=" C MET A 50 " pdb=" CA MET A 50 " pdb=" CB MET A 50 " ideal model delta sigma weight residual 111.48 129.49 -18.01 1.91e+00 2.74e-01 8.90e+01 angle pdb=" N MET A 50 " pdb=" CA MET A 50 " pdb=" C MET A 50 " ideal model delta sigma weight residual 109.95 101.22 8.73 1.44e+00 4.82e-01 3.68e+01 angle pdb=" N ALA A 52 " pdb=" CA ALA A 52 " pdb=" C ALA A 52 " ideal model delta sigma weight residual 112.54 118.51 -5.97 1.22e+00 6.72e-01 2.39e+01 angle pdb=" N ILE A 820 " pdb=" CA ILE A 820 " pdb=" C ILE A 820 " ideal model delta sigma weight residual 113.47 108.67 4.80 1.01e+00 9.80e-01 2.26e+01 angle pdb=" CA GLU B 743 " pdb=" CB GLU B 743 " pdb=" CG GLU B 743 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.69e+01 ... (remaining 34606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.16: 14731 28.16 - 56.32: 897 56.32 - 84.49: 64 84.49 - 112.65: 5 112.65 - 140.81: 2 Dihedral angle restraints: 15699 sinusoidal: 6719 harmonic: 8980 Sorted by residual: dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 347 " pdb=" CB CYS B 347 " ideal model delta sinusoidal sigma weight residual 93.00 7.95 85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS D 96 " pdb=" SG CYS D 96 " pdb=" SG CYS D 347 " pdb=" CB CYS D 347 " ideal model delta sinusoidal sigma weight residual 93.00 10.59 82.41 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -164.26 78.26 1 1.00e+01 1.00e-02 7.65e+01 ... (remaining 15696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3737 0.084 - 0.168: 235 0.168 - 0.253: 3 0.253 - 0.337: 1 0.337 - 0.421: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" CA MET A 50 " pdb=" N MET A 50 " pdb=" C MET A 50 " pdb=" CB MET A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA PRO C 561 " pdb=" N PRO C 561 " pdb=" C PRO C 561 " pdb=" CB PRO C 561 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 3974 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 304 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO D 305 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 305 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 305 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 658 " 0.007 2.00e-02 2.50e+03 1.65e-02 4.78e+00 pdb=" CG PHE B 658 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 658 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 658 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 658 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 658 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 658 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 686 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" CD GLU B 686 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 686 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 686 " 0.011 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 9187 2.86 - 3.37: 26035 3.37 - 3.88: 42543 3.88 - 4.39: 47175 4.39 - 4.90: 76633 Nonbonded interactions: 201573 Sorted by model distance: nonbonded pdb=" O3 NAG K 2 " pdb=" O2 BMA K 3 " model vdw 2.356 2.432 nonbonded pdb=" O2 BMA K 3 " pdb=" O3 BMA K 3 " model vdw 2.431 2.432 nonbonded pdb=" N MET A 50 " pdb=" O MET A 50 " model vdw 2.486 2.496 nonbonded pdb=" N GLU B 743 " pdb=" OE1 GLU B 743 " model vdw 2.512 3.120 nonbonded pdb=" O ASN A 141 " pdb=" OD1 ASN A 141 " model vdw 2.524 3.040 ... (remaining 201568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 583 or resid 629 through 845 or resid 1002)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 583 or resid 629 through 845 or resid 1003)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 583 or resid 629 through 845 or resid 1003)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 583 or resid 629 through 845 or resid 1003)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 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: 1.870 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.420 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.002 0.034 25597 Z= 0.117 Angle : 0.670 18.014 34730 Z= 0.319 Chirality : 0.042 0.421 3977 Planarity : 0.003 0.055 4318 Dihedral : 16.254 140.812 9897 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.19 % Allowed : 20.51 % Favored : 78.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 3078 helix: 0.42 (0.15), residues: 1243 sheet: -0.68 (0.31), residues: 305 loop : -1.41 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 354 TYR 0.016 0.001 TYR D 651 PHE 0.036 0.001 PHE B 658 TRP 0.015 0.001 TRP A 706 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00248 (25554) covalent geometry : angle 0.65505 (34611) SS BOND : bond 0.00148 ( 10) SS BOND : angle 0.85645 ( 20) hydrogen bonds : bond 0.20841 ( 1032) hydrogen bonds : angle 7.43873 ( 3019) link_BETA1-3 : bond 0.00852 ( 2) link_BETA1-3 : angle 3.20290 ( 6) link_BETA1-4 : bond 0.00776 ( 17) link_BETA1-4 : angle 3.01404 ( 51) link_NAG-ASN : bond 0.00233 ( 14) link_NAG-ASN : angle 2.16670 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 370 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7089 (t80) REVERT: A 168 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9075 (mmmt) REVERT: A 170 LYS cc_start: 0.6923 (tptt) cc_final: 0.6574 (tptt) REVERT: A 234 MET cc_start: 0.9199 (tpt) cc_final: 0.8854 (tpt) REVERT: A 245 MET cc_start: 0.8554 (mmp) cc_final: 0.8061 (mmm) REVERT: A 276 MET cc_start: 0.8011 (tpp) cc_final: 0.7364 (tpp) REVERT: A 315 PHE cc_start: 0.8447 (m-80) cc_final: 0.8209 (m-80) REVERT: A 695 LYS cc_start: 0.8852 (tppt) cc_final: 0.8583 (mmmm) REVERT: A 722 GLU cc_start: 0.8331 (tp30) cc_final: 0.7851 (tp30) REVERT: A 793 MET cc_start: 0.8261 (tpp) cc_final: 0.7766 (tpp) REVERT: B 170 LYS cc_start: 0.9054 (mptt) cc_final: 0.8852 (mmtm) REVERT: B 245 MET cc_start: 0.9244 (tpp) cc_final: 0.8966 (tpp) REVERT: B 248 MET cc_start: 0.9136 (mmm) cc_final: 0.8627 (mmm) REVERT: B 250 GLU cc_start: 0.8346 (tp30) cc_final: 0.8084 (tp30) REVERT: B 441 GLU cc_start: 0.7848 (mp0) cc_final: 0.7433 (tt0) REVERT: B 478 TYR cc_start: 0.7072 (p90) cc_final: 0.6850 (p90) REVERT: B 770 MET cc_start: 0.8260 (mmm) cc_final: 0.7905 (mmm) REVERT: B 790 LYS cc_start: 0.9297 (tppt) cc_final: 0.8827 (tptm) REVERT: B 793 MET cc_start: 0.9007 (tmm) cc_final: 0.8768 (ppp) REVERT: C 62 ASN cc_start: 0.9582 (m110) cc_final: 0.9309 (p0) REVERT: C 220 ARG cc_start: 0.9345 (mmm160) cc_final: 0.8966 (tpp-160) REVERT: C 222 LYS cc_start: 0.9426 (pttm) cc_final: 0.9211 (ptpp) REVERT: C 228 PHE cc_start: 0.9129 (m-10) cc_final: 0.8738 (m-10) REVERT: C 234 MET cc_start: 0.9360 (tpt) cc_final: 0.9088 (tpt) REVERT: C 340 MET cc_start: 0.5775 (mmp) cc_final: 0.4691 (mmp) REVERT: C 538 ILE cc_start: 0.9093 (mm) cc_final: 0.8723 (mm) REVERT: C 565 MET cc_start: 0.8680 (mmt) cc_final: 0.8441 (mmp) REVERT: C 650 SER cc_start: 0.9668 (m) cc_final: 0.9393 (t) REVERT: C 662 GLU cc_start: 0.7887 (pp20) cc_final: 0.7524 (pp20) REVERT: C 705 MET cc_start: 0.8743 (tpt) cc_final: 0.8537 (tpt) REVERT: C 783 LEU cc_start: 0.9104 (mm) cc_final: 0.8749 (mm) REVERT: D 122 CYS cc_start: 0.9253 (m) cc_final: 0.8805 (m) REVERT: D 413 MET cc_start: 0.6307 (ptt) cc_final: 0.5909 (ptt) REVERT: D 441 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6781 (tm-30) REVERT: D 501 MET cc_start: 0.8750 (mpp) cc_final: 0.7923 (mtm) REVERT: D 664 MET cc_start: 0.6965 (pmm) cc_final: 0.6326 (pmm) REVERT: D 705 MET cc_start: 0.8910 (mmt) cc_final: 0.8562 (mmt) REVERT: D 709 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8788 (pmm) REVERT: B 1003 GLU cc_start: 0.5997 (tp30) cc_final: 0.4789 (tp30) outliers start: 26 outliers final: 21 residues processed: 380 average time/residue: 0.1440 time to fit residues: 92.5472 Evaluate side-chains 380 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 357 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 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 = 0.3779 r_free = 0.3779 target = 0.102380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075618 restraints weight = 127239.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078776 restraints weight = 59947.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080775 restraints weight = 39419.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082019 restraints weight = 30866.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082788 restraints weight = 26674.096| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25597 Z= 0.134 Angle : 0.628 9.828 34730 Z= 0.302 Chirality : 0.042 0.190 3977 Planarity : 0.004 0.056 4318 Dihedral : 8.072 141.030 4098 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.20 % Allowed : 19.81 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3078 helix: 1.08 (0.15), residues: 1295 sheet: -0.64 (0.31), residues: 323 loop : -1.46 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 354 TYR 0.016 0.001 TYR D 651 PHE 0.021 0.001 PHE B 459 TRP 0.022 0.001 TRP A 706 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00297 (25554) covalent geometry : angle 0.61264 (34611) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.77763 ( 20) hydrogen bonds : bond 0.04517 ( 1032) hydrogen bonds : angle 5.00914 ( 3019) link_BETA1-3 : bond 0.00773 ( 2) link_BETA1-3 : angle 3.30418 ( 6) link_BETA1-4 : bond 0.00757 ( 17) link_BETA1-4 : angle 2.98921 ( 51) link_NAG-ASN : bond 0.00238 ( 14) link_NAG-ASN : angle 2.14723 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 370 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 153 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 170 LYS cc_start: 0.6786 (tptt) cc_final: 0.6379 (tptt) REVERT: A 234 MET cc_start: 0.8933 (tpt) cc_final: 0.8705 (tpp) REVERT: A 722 GLU cc_start: 0.7894 (tp30) cc_final: 0.7525 (tp30) REVERT: A 793 MET cc_start: 0.7507 (tpp) cc_final: 0.7190 (tpp) REVERT: B 316 MET cc_start: 0.8380 (tpp) cc_final: 0.8105 (tpp) REVERT: B 441 GLU cc_start: 0.7653 (mp0) cc_final: 0.7419 (tt0) REVERT: B 794 MET cc_start: 0.8088 (mtp) cc_final: 0.7669 (mtp) REVERT: C 184 ARG cc_start: 0.8525 (mpp80) cc_final: 0.7935 (mpp80) REVERT: C 220 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8782 (tpp-160) REVERT: C 316 MET cc_start: 0.7094 (mmp) cc_final: 0.6553 (mmp) REVERT: C 328 HIS cc_start: 0.9254 (m-70) cc_final: 0.9001 (m170) REVERT: C 340 MET cc_start: 0.5676 (mmp) cc_final: 0.4686 (mmp) REVERT: C 538 ILE cc_start: 0.9050 (mm) cc_final: 0.8679 (mm) REVERT: C 565 MET cc_start: 0.8395 (mmt) cc_final: 0.7982 (mmp) REVERT: C 650 SER cc_start: 0.9661 (m) cc_final: 0.9248 (t) REVERT: C 662 GLU cc_start: 0.7087 (pp20) cc_final: 0.6835 (pp20) REVERT: D 122 CYS cc_start: 0.9172 (m) cc_final: 0.8777 (m) REVERT: D 190 LYS cc_start: 0.9213 (pttt) cc_final: 0.8787 (pttt) REVERT: D 394 LEU cc_start: 0.9175 (tp) cc_final: 0.8879 (tt) REVERT: D 413 MET cc_start: 0.6777 (ptt) cc_final: 0.6378 (ptt) REVERT: D 441 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6852 (tm-30) REVERT: D 501 MET cc_start: 0.8706 (mpp) cc_final: 0.7695 (mtm) REVERT: D 651 TYR cc_start: 0.9070 (t80) cc_final: 0.8550 (t80) REVERT: D 664 MET cc_start: 0.7041 (pmm) cc_final: 0.6460 (pmm) REVERT: D 705 MET cc_start: 0.8862 (mmt) cc_final: 0.8612 (mmt) REVERT: B 1003 GLU cc_start: 0.5365 (tp30) cc_final: 0.4674 (tp30) outliers start: 53 outliers final: 34 residues processed: 397 average time/residue: 0.1435 time to fit residues: 96.3345 Evaluate side-chains 379 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 47 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 295 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 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 = 0.3703 r_free = 0.3703 target = 0.098786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071267 restraints weight = 98584.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074148 restraints weight = 49446.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075970 restraints weight = 33606.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077081 restraints weight = 26854.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077752 restraints weight = 23552.652| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25597 Z= 0.168 Angle : 0.642 10.045 34730 Z= 0.307 Chirality : 0.042 0.212 3977 Planarity : 0.003 0.056 4318 Dihedral : 7.774 141.173 4083 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.05 % Allowed : 20.33 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3078 helix: 1.17 (0.15), residues: 1307 sheet: -0.61 (0.30), residues: 329 loop : -1.49 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 354 TYR 0.019 0.001 TYR C 764 PHE 0.023 0.001 PHE B 459 TRP 0.017 0.001 TRP A 169 HIS 0.004 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00374 (25554) covalent geometry : angle 0.62588 (34611) SS BOND : bond 0.00173 ( 10) SS BOND : angle 0.81912 ( 20) hydrogen bonds : bond 0.03772 ( 1032) hydrogen bonds : angle 4.69235 ( 3019) link_BETA1-3 : bond 0.00720 ( 2) link_BETA1-3 : angle 3.42353 ( 6) link_BETA1-4 : bond 0.00743 ( 17) link_BETA1-4 : angle 2.98585 ( 51) link_NAG-ASN : bond 0.00233 ( 14) link_NAG-ASN : angle 2.23304 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 364 time to evaluate : 1.014 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: A 55 LEU cc_start: 0.9391 (tp) cc_final: 0.9101 (mt) REVERT: A 170 LYS cc_start: 0.6949 (tptt) cc_final: 0.6472 (tptt) REVERT: A 234 MET cc_start: 0.9035 (tpt) cc_final: 0.8749 (tpp) REVERT: A 528 ASP cc_start: 0.6852 (m-30) cc_final: 0.6482 (m-30) REVERT: A 722 GLU cc_start: 0.8152 (tp30) cc_final: 0.7724 (tp30) REVERT: A 793 MET cc_start: 0.7825 (tpp) cc_final: 0.7413 (tpp) REVERT: B 259 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8725 (pp) REVERT: B 441 GLU cc_start: 0.7692 (mp0) cc_final: 0.7427 (tt0) REVERT: B 478 TYR cc_start: 0.6945 (p90) cc_final: 0.6707 (p90) REVERT: B 790 LYS cc_start: 0.9068 (tptm) cc_final: 0.8816 (tppt) REVERT: B 793 MET cc_start: 0.8762 (ppp) cc_final: 0.8377 (tmm) REVERT: B 794 MET cc_start: 0.8343 (mtp) cc_final: 0.8015 (mtp) REVERT: C 62 ASN cc_start: 0.9580 (m-40) cc_final: 0.9207 (p0) REVERT: C 137 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8337 (mp10) REVERT: C 184 ARG cc_start: 0.8586 (mpp80) cc_final: 0.8216 (mpp80) REVERT: C 328 HIS cc_start: 0.9388 (m-70) cc_final: 0.9107 (m170) REVERT: C 340 MET cc_start: 0.6115 (mmp) cc_final: 0.5236 (mmp) REVERT: C 538 ILE cc_start: 0.9184 (mm) cc_final: 0.8853 (mm) REVERT: C 650 SER cc_start: 0.9667 (m) cc_final: 0.9333 (t) REVERT: C 662 GLU cc_start: 0.7545 (pp20) cc_final: 0.7117 (pp20) REVERT: D 122 CYS cc_start: 0.9205 (m) cc_final: 0.8755 (m) REVERT: D 190 LYS cc_start: 0.9263 (pttt) cc_final: 0.9053 (pttt) REVERT: D 245 MET cc_start: 0.8554 (mtt) cc_final: 0.8184 (mtt) REVERT: D 394 LEU cc_start: 0.9353 (tp) cc_final: 0.9076 (tt) REVERT: D 413 MET cc_start: 0.6881 (ptt) cc_final: 0.6622 (ptt) REVERT: D 441 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6801 (tm-30) REVERT: D 501 MET cc_start: 0.8781 (mpp) cc_final: 0.7861 (mtm) REVERT: D 664 MET cc_start: 0.7146 (pmm) cc_final: 0.6503 (pmm) REVERT: D 705 MET cc_start: 0.8952 (mmt) cc_final: 0.8467 (mmt) REVERT: B 1003 GLU cc_start: 0.5604 (tp30) cc_final: 0.4883 (tp30) outliers start: 76 outliers final: 48 residues processed: 412 average time/residue: 0.1426 time to fit residues: 99.4573 Evaluate side-chains 392 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 343 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 248 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 298 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN B 557 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071685 restraints weight = 111929.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074843 restraints weight = 52064.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076841 restraints weight = 34186.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.078080 restraints weight = 26852.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078838 restraints weight = 23309.187| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25597 Z= 0.128 Angle : 0.629 10.326 34730 Z= 0.297 Chirality : 0.042 0.261 3977 Planarity : 0.003 0.055 4318 Dihedral : 7.510 141.088 4074 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.76 % Allowed : 21.22 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3078 helix: 1.19 (0.15), residues: 1301 sheet: -0.67 (0.31), residues: 314 loop : -1.45 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 354 TYR 0.015 0.001 TYR D 252 PHE 0.021 0.001 PHE B 315 TRP 0.016 0.001 TRP A 706 HIS 0.003 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00288 (25554) covalent geometry : angle 0.61247 (34611) SS BOND : bond 0.00155 ( 10) SS BOND : angle 1.60509 ( 20) hydrogen bonds : bond 0.03379 ( 1032) hydrogen bonds : angle 4.51806 ( 3019) link_BETA1-3 : bond 0.00695 ( 2) link_BETA1-3 : angle 3.51447 ( 6) link_BETA1-4 : bond 0.00774 ( 17) link_BETA1-4 : angle 2.95863 ( 51) link_NAG-ASN : bond 0.00248 ( 14) link_NAG-ASN : angle 2.20386 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 0.901 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: symmetry clash REVERT: A 55 LEU cc_start: 0.9406 (tp) cc_final: 0.9118 (mt) REVERT: A 116 ASN cc_start: 0.9296 (m110) cc_final: 0.8898 (p0) REVERT: A 170 LYS cc_start: 0.7104 (tptt) cc_final: 0.6639 (tptt) REVERT: A 234 MET cc_start: 0.8998 (tpt) cc_final: 0.8712 (tpp) REVERT: A 432 SER cc_start: 0.7994 (m) cc_final: 0.7452 (t) REVERT: A 528 ASP cc_start: 0.6737 (m-30) cc_final: 0.6371 (m-30) REVERT: A 722 GLU cc_start: 0.8194 (tp30) cc_final: 0.7767 (tp30) REVERT: A 793 MET cc_start: 0.7890 (tpp) cc_final: 0.7456 (tpp) REVERT: B 259 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8705 (pp) REVERT: B 441 GLU cc_start: 0.7662 (mp0) cc_final: 0.7420 (tt0) REVERT: B 446 PHE cc_start: 0.8217 (m-80) cc_final: 0.7976 (m-80) REVERT: B 460 GLU cc_start: 0.8297 (pp20) cc_final: 0.7672 (pm20) REVERT: C 184 ARG cc_start: 0.8522 (mpp80) cc_final: 0.8116 (mpp80) REVERT: C 328 HIS cc_start: 0.9412 (m-70) cc_final: 0.9126 (m170) REVERT: C 340 MET cc_start: 0.6025 (mmp) cc_final: 0.5395 (mmp) REVERT: C 538 ILE cc_start: 0.9242 (mm) cc_final: 0.8888 (mm) REVERT: C 565 MET cc_start: 0.8502 (mmt) cc_final: 0.8190 (mmp) REVERT: C 650 SER cc_start: 0.9682 (m) cc_final: 0.9343 (t) REVERT: C 709 MET cc_start: 0.8379 (mtt) cc_final: 0.8042 (mmm) REVERT: D 122 CYS cc_start: 0.9198 (m) cc_final: 0.8743 (m) REVERT: D 190 LYS cc_start: 0.9242 (pttt) cc_final: 0.8972 (pttt) REVERT: D 245 MET cc_start: 0.8484 (mtt) cc_final: 0.8227 (mtt) REVERT: D 394 LEU cc_start: 0.9347 (tp) cc_final: 0.9084 (tt) REVERT: D 413 MET cc_start: 0.7022 (ptt) cc_final: 0.6813 (ptt) REVERT: D 441 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6696 (tm-30) REVERT: D 501 MET cc_start: 0.8761 (mpp) cc_final: 0.7890 (mtm) REVERT: D 651 TYR cc_start: 0.9253 (t80) cc_final: 0.8738 (t80) REVERT: D 664 MET cc_start: 0.7144 (pmm) cc_final: 0.6519 (pmm) REVERT: D 705 MET cc_start: 0.8929 (mmt) cc_final: 0.8087 (mmt) REVERT: B 1003 GLU cc_start: 0.5642 (tp30) cc_final: 0.4758 (tp30) outliers start: 68 outliers final: 47 residues processed: 411 average time/residue: 0.1398 time to fit residues: 97.7923 Evaluate side-chains 400 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 41 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 chunk 288 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 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 = 0.3704 r_free = 0.3704 target = 0.098860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071047 restraints weight = 112025.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074116 restraints weight = 52819.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076046 restraints weight = 34722.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077240 restraints weight = 27263.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077974 restraints weight = 23673.094| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25597 Z= 0.157 Angle : 0.644 10.713 34730 Z= 0.304 Chirality : 0.042 0.254 3977 Planarity : 0.003 0.056 4318 Dihedral : 7.419 141.191 4074 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.79 % Allowed : 21.63 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 3078 helix: 1.19 (0.15), residues: 1306 sheet: -0.75 (0.31), residues: 316 loop : -1.45 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 58 TYR 0.016 0.001 TYR C 764 PHE 0.021 0.001 PHE B 315 TRP 0.014 0.001 TRP A 706 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00352 (25554) covalent geometry : angle 0.62783 (34611) SS BOND : bond 0.00197 ( 10) SS BOND : angle 1.26463 ( 20) hydrogen bonds : bond 0.03325 ( 1032) hydrogen bonds : angle 4.47049 ( 3019) link_BETA1-3 : bond 0.00598 ( 2) link_BETA1-3 : angle 3.59297 ( 6) link_BETA1-4 : bond 0.00730 ( 17) link_BETA1-4 : angle 2.93132 ( 51) link_NAG-ASN : bond 0.00214 ( 14) link_NAG-ASN : angle 2.25778 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 0.966 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: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9459 (tp) cc_final: 0.9144 (mt) REVERT: A 170 LYS cc_start: 0.7157 (tptt) cc_final: 0.6757 (tptt) REVERT: A 234 MET cc_start: 0.8987 (tpt) cc_final: 0.8690 (tpp) REVERT: A 528 ASP cc_start: 0.6880 (m-30) cc_final: 0.6471 (m-30) REVERT: A 691 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 722 GLU cc_start: 0.8199 (tp30) cc_final: 0.7765 (tp30) REVERT: A 793 MET cc_start: 0.7870 (tpp) cc_final: 0.7406 (tpp) REVERT: B 259 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 441 GLU cc_start: 0.7644 (mp0) cc_final: 0.7412 (tt0) REVERT: B 446 PHE cc_start: 0.8223 (m-80) cc_final: 0.7979 (m-80) REVERT: B 460 GLU cc_start: 0.8243 (pp20) cc_final: 0.7704 (pm20) REVERT: B 793 MET cc_start: 0.8676 (tmm) cc_final: 0.8391 (tmm) REVERT: C 62 ASN cc_start: 0.9599 (m-40) cc_final: 0.9198 (p0) REVERT: C 184 ARG cc_start: 0.8599 (mpp80) cc_final: 0.8180 (mpp80) REVERT: C 328 HIS cc_start: 0.9382 (m-70) cc_final: 0.9118 (m170) REVERT: C 538 ILE cc_start: 0.9241 (mm) cc_final: 0.8885 (mm) REVERT: C 565 MET cc_start: 0.8589 (mmt) cc_final: 0.8283 (mmp) REVERT: C 650 SER cc_start: 0.9672 (m) cc_final: 0.9384 (t) REVERT: C 783 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 122 CYS cc_start: 0.9207 (m) cc_final: 0.8756 (m) REVERT: D 190 LYS cc_start: 0.9221 (pttt) cc_final: 0.8988 (pttt) REVERT: D 245 MET cc_start: 0.8673 (mtt) cc_final: 0.8360 (mtt) REVERT: D 247 MET cc_start: 0.8333 (mmm) cc_final: 0.8073 (tpp) REVERT: D 250 GLU cc_start: 0.8478 (pm20) cc_final: 0.8217 (pm20) REVERT: D 394 LEU cc_start: 0.9365 (tp) cc_final: 0.9101 (tt) REVERT: D 413 MET cc_start: 0.7335 (ptt) cc_final: 0.6982 (ptt) REVERT: D 441 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6636 (tm-30) REVERT: D 445 LEU cc_start: 0.7871 (mm) cc_final: 0.7639 (mm) REVERT: D 501 MET cc_start: 0.8816 (mpp) cc_final: 0.7928 (mtm) REVERT: D 664 MET cc_start: 0.7151 (pmm) cc_final: 0.6547 (pmm) REVERT: D 705 MET cc_start: 0.8869 (mmt) cc_final: 0.8460 (mmp) REVERT: B 1003 GLU cc_start: 0.5621 (tp30) cc_final: 0.4885 (tp30) outliers start: 69 outliers final: 54 residues processed: 407 average time/residue: 0.1452 time to fit residues: 100.4164 Evaluate side-chains 408 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 47 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN D 288 GLN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 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 = 0.3718 r_free = 0.3718 target = 0.099810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072480 restraints weight = 96098.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075362 restraints weight = 48581.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077187 restraints weight = 33120.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078349 restraints weight = 26513.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.079041 restraints weight = 23195.582| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25597 Z= 0.126 Angle : 0.638 11.227 34730 Z= 0.299 Chirality : 0.042 0.281 3977 Planarity : 0.003 0.055 4318 Dihedral : 7.309 141.063 4074 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.05 % Allowed : 22.41 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3078 helix: 1.20 (0.15), residues: 1306 sheet: -0.76 (0.31), residues: 316 loop : -1.44 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 358 TYR 0.019 0.001 TYR D 651 PHE 0.022 0.001 PHE B 315 TRP 0.015 0.001 TRP A 706 HIS 0.002 0.000 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00286 (25554) covalent geometry : angle 0.62251 (34611) SS BOND : bond 0.00168 ( 10) SS BOND : angle 1.14217 ( 20) hydrogen bonds : bond 0.03164 ( 1032) hydrogen bonds : angle 4.34419 ( 3019) link_BETA1-3 : bond 0.00620 ( 2) link_BETA1-3 : angle 3.58435 ( 6) link_BETA1-4 : bond 0.00771 ( 17) link_BETA1-4 : angle 2.89018 ( 51) link_NAG-ASN : bond 0.00219 ( 14) link_NAG-ASN : angle 2.20042 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 370 time to evaluate : 0.979 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: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9477 (tp) cc_final: 0.9165 (mt) REVERT: A 170 LYS cc_start: 0.7200 (tptt) cc_final: 0.6747 (tptt) REVERT: A 234 MET cc_start: 0.8946 (tpt) cc_final: 0.8715 (tpp) REVERT: A 528 ASP cc_start: 0.6716 (m-30) cc_final: 0.6357 (m-30) REVERT: A 691 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: A 722 GLU cc_start: 0.8190 (tp30) cc_final: 0.7733 (tp30) REVERT: A 793 MET cc_start: 0.7860 (tpp) cc_final: 0.7410 (tpp) REVERT: B 441 GLU cc_start: 0.7497 (mp0) cc_final: 0.7251 (tt0) REVERT: B 446 PHE cc_start: 0.8312 (m-80) cc_final: 0.8044 (m-80) REVERT: B 460 GLU cc_start: 0.8186 (pp20) cc_final: 0.7645 (pm20) REVERT: B 793 MET cc_start: 0.8695 (tmm) cc_final: 0.8429 (tmm) REVERT: C 62 ASN cc_start: 0.9602 (m-40) cc_final: 0.9173 (p0) REVERT: C 184 ARG cc_start: 0.8520 (mpp80) cc_final: 0.8067 (mpp80) REVERT: C 247 MET cc_start: 0.6992 (mmt) cc_final: 0.6754 (mmt) REVERT: C 328 HIS cc_start: 0.9393 (m-70) cc_final: 0.9109 (m170) REVERT: C 538 ILE cc_start: 0.9208 (mm) cc_final: 0.8861 (mm) REVERT: C 565 MET cc_start: 0.8566 (mmt) cc_final: 0.8161 (mmp) REVERT: C 650 SER cc_start: 0.9676 (m) cc_final: 0.9370 (t) REVERT: C 696 LYS cc_start: 0.9192 (mptt) cc_final: 0.8833 (mptt) REVERT: C 783 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8839 (mm) REVERT: D 122 CYS cc_start: 0.9185 (m) cc_final: 0.8708 (m) REVERT: D 187 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8378 (mm-30) REVERT: D 190 LYS cc_start: 0.9163 (pttt) cc_final: 0.8636 (pttt) REVERT: D 245 MET cc_start: 0.8600 (mtt) cc_final: 0.8300 (mtt) REVERT: D 250 GLU cc_start: 0.8466 (pm20) cc_final: 0.8239 (pm20) REVERT: D 337 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8455 (t80) REVERT: D 394 LEU cc_start: 0.9345 (tp) cc_final: 0.9096 (tt) REVERT: D 413 MET cc_start: 0.7294 (ptt) cc_final: 0.7091 (ptt) REVERT: D 441 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6646 (tm-30) REVERT: D 445 LEU cc_start: 0.7865 (mm) cc_final: 0.7622 (mm) REVERT: D 501 MET cc_start: 0.8865 (mpp) cc_final: 0.7899 (mtm) REVERT: D 664 MET cc_start: 0.7014 (pmm) cc_final: 0.6450 (pmm) REVERT: D 705 MET cc_start: 0.8855 (mmt) cc_final: 0.8624 (tpp) REVERT: B 1003 GLU cc_start: 0.5633 (tp30) cc_final: 0.4690 (tp30) outliers start: 76 outliers final: 58 residues processed: 417 average time/residue: 0.1372 time to fit residues: 97.4343 Evaluate side-chains 414 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 277 optimal weight: 0.0980 chunk 170 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.100987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.073836 restraints weight = 92761.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076793 restraints weight = 46259.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078671 restraints weight = 31251.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079857 restraints weight = 24872.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080588 restraints weight = 21712.885| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25597 Z= 0.110 Angle : 0.656 11.852 34730 Z= 0.304 Chirality : 0.043 0.328 3977 Planarity : 0.003 0.055 4318 Dihedral : 7.172 140.596 4074 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.53 % Allowed : 23.38 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 3078 helix: 1.19 (0.15), residues: 1310 sheet: -0.70 (0.31), residues: 316 loop : -1.45 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 354 TYR 0.016 0.001 TYR D 443 PHE 0.024 0.001 PHE B 315 TRP 0.016 0.001 TRP A 706 HIS 0.003 0.000 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00248 (25554) covalent geometry : angle 0.64059 (34611) SS BOND : bond 0.00563 ( 10) SS BOND : angle 1.55545 ( 20) hydrogen bonds : bond 0.03111 ( 1032) hydrogen bonds : angle 4.28978 ( 3019) link_BETA1-3 : bond 0.00650 ( 2) link_BETA1-3 : angle 3.59684 ( 6) link_BETA1-4 : bond 0.00771 ( 17) link_BETA1-4 : angle 2.85453 ( 51) link_NAG-ASN : bond 0.00229 ( 14) link_NAG-ASN : angle 2.15987 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 382 time to evaluate : 1.023 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: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9497 (tp) cc_final: 0.9274 (mt) REVERT: A 153 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7468 (t80) REVERT: A 168 LYS cc_start: 0.9245 (mmmt) cc_final: 0.9024 (mmmt) REVERT: A 170 LYS cc_start: 0.7246 (tptt) cc_final: 0.6846 (tptt) REVERT: A 234 MET cc_start: 0.8943 (tpt) cc_final: 0.8709 (tpp) REVERT: A 276 MET cc_start: 0.8852 (tpp) cc_final: 0.8306 (tpp) REVERT: A 528 ASP cc_start: 0.6688 (m-30) cc_final: 0.6326 (m-30) REVERT: A 722 GLU cc_start: 0.8221 (tp30) cc_final: 0.7813 (tp30) REVERT: A 793 MET cc_start: 0.7927 (tpp) cc_final: 0.7453 (tpp) REVERT: B 441 GLU cc_start: 0.7444 (mp0) cc_final: 0.7159 (tt0) REVERT: B 446 PHE cc_start: 0.8317 (m-80) cc_final: 0.8047 (m-80) REVERT: B 460 GLU cc_start: 0.8226 (pp20) cc_final: 0.7677 (pm20) REVERT: B 654 ASN cc_start: 0.9128 (m110) cc_final: 0.8759 (m-40) REVERT: B 793 MET cc_start: 0.8752 (tmm) cc_final: 0.8459 (tmm) REVERT: C 184 ARG cc_start: 0.8429 (mpp80) cc_final: 0.7932 (mpp80) REVERT: C 220 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8793 (tpp-160) REVERT: C 247 MET cc_start: 0.6972 (mmt) cc_final: 0.6718 (mmt) REVERT: C 328 HIS cc_start: 0.9377 (m-70) cc_final: 0.9082 (m170) REVERT: C 538 ILE cc_start: 0.9156 (mm) cc_final: 0.8778 (mm) REVERT: C 650 SER cc_start: 0.9718 (m) cc_final: 0.9371 (t) REVERT: C 696 LYS cc_start: 0.9174 (mptt) cc_final: 0.8852 (mptt) REVERT: D 122 CYS cc_start: 0.9174 (m) cc_final: 0.8696 (m) REVERT: D 187 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8344 (mm-30) REVERT: D 190 LYS cc_start: 0.9117 (pttt) cc_final: 0.8584 (pttt) REVERT: D 250 GLU cc_start: 0.8503 (pm20) cc_final: 0.8208 (pm20) REVERT: D 337 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (t80) REVERT: D 394 LEU cc_start: 0.9317 (tp) cc_final: 0.9099 (tt) REVERT: D 413 MET cc_start: 0.7094 (ptt) cc_final: 0.6887 (ptt) REVERT: D 441 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 501 MET cc_start: 0.8782 (mpp) cc_final: 0.7915 (mtm) REVERT: D 651 TYR cc_start: 0.9242 (t80) cc_final: 0.8668 (t80) REVERT: D 664 MET cc_start: 0.6982 (pmm) cc_final: 0.6428 (pmm) REVERT: D 705 MET cc_start: 0.8856 (mmt) cc_final: 0.8327 (mmt) REVERT: B 1003 GLU cc_start: 0.5910 (tp30) cc_final: 0.4909 (tp30) outliers start: 62 outliers final: 47 residues processed: 422 average time/residue: 0.1453 time to fit residues: 103.8160 Evaluate side-chains 410 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 337 PHE Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 158 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 292 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 200 optimal weight: 0.0870 chunk 144 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 260 optimal weight: 3.9990 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073685 restraints weight = 86688.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076473 restraints weight = 45846.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078201 restraints weight = 31942.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079285 restraints weight = 25921.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079942 restraints weight = 22884.237| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25597 Z= 0.124 Angle : 0.662 11.668 34730 Z= 0.306 Chirality : 0.043 0.297 3977 Planarity : 0.003 0.055 4318 Dihedral : 7.025 140.767 4070 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.53 % Allowed : 23.79 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.31 (0.15), residues: 3078 helix: 1.20 (0.15), residues: 1314 sheet: -0.69 (0.31), residues: 316 loop : -1.45 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 358 TYR 0.025 0.001 TYR B 764 PHE 0.047 0.001 PHE B 658 TRP 0.015 0.001 TRP A 706 HIS 0.002 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00283 (25554) covalent geometry : angle 0.64636 (34611) SS BOND : bond 0.00216 ( 10) SS BOND : angle 1.26648 ( 20) hydrogen bonds : bond 0.03057 ( 1032) hydrogen bonds : angle 4.29918 ( 3019) link_BETA1-3 : bond 0.00546 ( 2) link_BETA1-3 : angle 3.65887 ( 6) link_BETA1-4 : bond 0.00743 ( 17) link_BETA1-4 : angle 2.83379 ( 51) link_NAG-ASN : bond 0.00233 ( 14) link_NAG-ASN : angle 2.30297 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 369 time to evaluate : 0.952 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: symmetry clash REVERT: A 55 LEU cc_start: 0.9487 (tp) cc_final: 0.9277 (mt) REVERT: A 153 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 170 LYS cc_start: 0.7255 (tptt) cc_final: 0.6853 (tptt) REVERT: A 234 MET cc_start: 0.8992 (tpt) cc_final: 0.8741 (tpp) REVERT: A 528 ASP cc_start: 0.6664 (m-30) cc_final: 0.6326 (m-30) REVERT: A 722 GLU cc_start: 0.8173 (tp30) cc_final: 0.7780 (tp30) REVERT: A 793 MET cc_start: 0.7846 (tpp) cc_final: 0.7395 (tpp) REVERT: B 441 GLU cc_start: 0.7469 (mp0) cc_final: 0.7204 (tt0) REVERT: B 446 PHE cc_start: 0.8247 (m-80) cc_final: 0.7988 (m-80) REVERT: B 460 GLU cc_start: 0.8214 (pp20) cc_final: 0.7636 (pm20) REVERT: B 654 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8712 (m-40) REVERT: B 793 MET cc_start: 0.8693 (tmm) cc_final: 0.8429 (tmm) REVERT: C 184 ARG cc_start: 0.8482 (mpp80) cc_final: 0.8000 (mpp80) REVERT: C 228 PHE cc_start: 0.9114 (m-10) cc_final: 0.8769 (m-10) REVERT: C 247 MET cc_start: 0.6964 (mmt) cc_final: 0.6671 (mmt) REVERT: C 328 HIS cc_start: 0.9380 (m-70) cc_final: 0.9112 (m170) REVERT: C 538 ILE cc_start: 0.9189 (mm) cc_final: 0.8810 (mm) REVERT: C 565 MET cc_start: 0.8518 (mmt) cc_final: 0.8114 (mmp) REVERT: C 650 SER cc_start: 0.9707 (m) cc_final: 0.9401 (t) REVERT: C 696 LYS cc_start: 0.9195 (mptt) cc_final: 0.8865 (mptt) REVERT: C 709 MET cc_start: 0.8217 (mtt) cc_final: 0.7961 (mmm) REVERT: C 783 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8901 (mm) REVERT: D 122 CYS cc_start: 0.9185 (m) cc_final: 0.8702 (m) REVERT: D 187 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 190 LYS cc_start: 0.9134 (pttt) cc_final: 0.8527 (pttt) REVERT: D 247 MET cc_start: 0.8121 (tpp) cc_final: 0.7893 (tpp) REVERT: D 250 GLU cc_start: 0.8539 (pm20) cc_final: 0.8242 (pm20) REVERT: D 394 LEU cc_start: 0.9325 (tp) cc_final: 0.9105 (tt) REVERT: D 413 MET cc_start: 0.7185 (ptt) cc_final: 0.6831 (ptt) REVERT: D 441 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6678 (tm-30) REVERT: D 501 MET cc_start: 0.8779 (mpp) cc_final: 0.7889 (mtm) REVERT: D 651 TYR cc_start: 0.9249 (t80) cc_final: 0.8691 (t80) REVERT: D 664 MET cc_start: 0.7008 (pmm) cc_final: 0.6457 (pmm) REVERT: D 705 MET cc_start: 0.8916 (mmt) cc_final: 0.8375 (mmt) REVERT: B 1003 GLU cc_start: 0.5650 (tp30) cc_final: 0.4614 (tp30) outliers start: 62 outliers final: 57 residues processed: 408 average time/residue: 0.1429 time to fit residues: 98.4308 Evaluate side-chains 415 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 355 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 572 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 103 optimal weight: 0.1980 chunk 291 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 overall best weight: 2.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 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 = 0.3681 r_free = 0.3681 target = 0.097511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069421 restraints weight = 110766.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072429 restraints weight = 51998.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074325 restraints weight = 34187.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075493 restraints weight = 26908.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076196 restraints weight = 23427.631| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25597 Z= 0.210 Angle : 0.718 12.768 34730 Z= 0.339 Chirality : 0.044 0.295 3977 Planarity : 0.004 0.056 4318 Dihedral : 7.077 141.483 4070 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.79 % Allowed : 23.86 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3078 helix: 1.15 (0.15), residues: 1313 sheet: -0.55 (0.31), residues: 303 loop : -1.50 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 358 TYR 0.021 0.002 TYR C 764 PHE 0.038 0.002 PHE B 658 TRP 0.023 0.002 TRP A 169 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00469 (25554) covalent geometry : angle 0.70313 (34611) SS BOND : bond 0.00260 ( 10) SS BOND : angle 1.26046 ( 20) hydrogen bonds : bond 0.03333 ( 1032) hydrogen bonds : angle 4.51266 ( 3019) link_BETA1-3 : bond 0.00291 ( 2) link_BETA1-3 : angle 3.73908 ( 6) link_BETA1-4 : bond 0.00728 ( 17) link_BETA1-4 : angle 2.82299 ( 51) link_NAG-ASN : bond 0.00273 ( 14) link_NAG-ASN : angle 2.46275 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9315 (m110) cc_final: 0.8980 (p0) REVERT: A 153 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7480 (t80) REVERT: A 170 LYS cc_start: 0.7406 (tptt) cc_final: 0.6954 (tptt) REVERT: A 276 MET cc_start: 0.8792 (tpp) cc_final: 0.8402 (tpp) REVERT: A 528 ASP cc_start: 0.6922 (m-30) cc_final: 0.6481 (m-30) REVERT: A 695 LYS cc_start: 0.9128 (tppt) cc_final: 0.8729 (mtpp) REVERT: A 722 GLU cc_start: 0.8284 (tp30) cc_final: 0.7853 (tp30) REVERT: A 793 MET cc_start: 0.7978 (tpp) cc_final: 0.7488 (tpp) REVERT: B 441 GLU cc_start: 0.7553 (mp0) cc_final: 0.7208 (tt0) REVERT: B 443 TYR cc_start: 0.7560 (m-10) cc_final: 0.7285 (m-10) REVERT: B 446 PHE cc_start: 0.8272 (m-80) cc_final: 0.8008 (m-80) REVERT: B 460 GLU cc_start: 0.8371 (pp20) cc_final: 0.7717 (pm20) REVERT: B 770 MET cc_start: 0.8323 (mmm) cc_final: 0.7961 (mmm) REVERT: C 184 ARG cc_start: 0.8622 (mpp80) cc_final: 0.8153 (mpp80) REVERT: C 328 HIS cc_start: 0.9438 (m-70) cc_final: 0.9190 (m170) REVERT: C 538 ILE cc_start: 0.9290 (mm) cc_final: 0.8958 (mm) REVERT: C 565 MET cc_start: 0.8565 (mmt) cc_final: 0.8151 (mmp) REVERT: C 650 SER cc_start: 0.9666 (m) cc_final: 0.9436 (t) REVERT: C 662 GLU cc_start: 0.7681 (pp20) cc_final: 0.7202 (pp20) REVERT: C 696 LYS cc_start: 0.9292 (mptt) cc_final: 0.8918 (mptt) REVERT: C 709 MET cc_start: 0.8403 (mtt) cc_final: 0.7968 (mmm) REVERT: C 783 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8830 (mm) REVERT: D 122 CYS cc_start: 0.9201 (m) cc_final: 0.8727 (m) REVERT: D 187 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8339 (mm-30) REVERT: D 190 LYS cc_start: 0.9140 (pttt) cc_final: 0.8558 (pttt) REVERT: D 250 GLU cc_start: 0.8673 (pm20) cc_final: 0.8424 (pm20) REVERT: D 316 MET cc_start: 0.8810 (mmm) cc_final: 0.8462 (mmm) REVERT: D 394 LEU cc_start: 0.9429 (tp) cc_final: 0.9195 (tt) REVERT: D 413 MET cc_start: 0.7469 (ptt) cc_final: 0.7059 (ptt) REVERT: D 441 GLU cc_start: 0.7673 (tm-30) cc_final: 0.6764 (tm-30) REVERT: D 501 MET cc_start: 0.8740 (mpp) cc_final: 0.7816 (mtm) REVERT: D 664 MET cc_start: 0.7178 (pmm) cc_final: 0.6557 (pmm) REVERT: D 740 THR cc_start: 0.9123 (p) cc_final: 0.8858 (p) REVERT: B 1003 GLU cc_start: 0.5779 (tp30) cc_final: 0.4977 (tp30) outliers start: 69 outliers final: 59 residues processed: 392 average time/residue: 0.1401 time to fit residues: 93.6296 Evaluate side-chains 402 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE Chi-restraints excluded: chain D residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 161 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 0.0010 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 0.0470 chunk 183 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.100505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072380 restraints weight = 124142.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076378 restraints weight = 55327.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078759 restraints weight = 30812.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078684 restraints weight = 24284.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078808 restraints weight = 23903.286| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25597 Z= 0.116 Angle : 0.693 12.479 34730 Z= 0.320 Chirality : 0.043 0.321 3977 Planarity : 0.003 0.055 4318 Dihedral : 6.988 140.794 4070 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.12 % Allowed : 24.68 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3078 helix: 1.16 (0.15), residues: 1304 sheet: -0.54 (0.31), residues: 303 loop : -1.48 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.020 0.001 TYR D 443 PHE 0.038 0.001 PHE B 658 TRP 0.020 0.001 TRP A 706 HIS 0.010 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00263 (25554) covalent geometry : angle 0.67892 (34611) SS BOND : bond 0.00191 ( 10) SS BOND : angle 1.25705 ( 20) hydrogen bonds : bond 0.03118 ( 1032) hydrogen bonds : angle 4.33842 ( 3019) link_BETA1-3 : bond 0.00548 ( 2) link_BETA1-3 : angle 3.52602 ( 6) link_BETA1-4 : bond 0.00785 ( 17) link_BETA1-4 : angle 2.80841 ( 51) link_NAG-ASN : bond 0.00260 ( 14) link_NAG-ASN : angle 2.23443 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 0.928 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: A 116 ASN cc_start: 0.9222 (m110) cc_final: 0.8798 (p0) REVERT: A 153 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 276 MET cc_start: 0.8785 (tpp) cc_final: 0.8447 (tpp) REVERT: A 528 ASP cc_start: 0.6724 (m-30) cc_final: 0.6291 (m-30) REVERT: A 691 MET cc_start: 0.8461 (mtm) cc_final: 0.8012 (pmm) REVERT: A 695 LYS cc_start: 0.9049 (tppt) cc_final: 0.8645 (mtpp) REVERT: A 722 GLU cc_start: 0.8216 (tp30) cc_final: 0.7796 (tp30) REVERT: A 793 MET cc_start: 0.7881 (tpp) cc_final: 0.7427 (tpp) REVERT: B 441 GLU cc_start: 0.7505 (mp0) cc_final: 0.7203 (tt0) REVERT: B 460 GLU cc_start: 0.8205 (pp20) cc_final: 0.7587 (pm20) REVERT: B 770 MET cc_start: 0.8109 (mmm) cc_final: 0.7739 (mmm) REVERT: C 184 ARG cc_start: 0.8428 (mpp80) cc_final: 0.7940 (mpp80) REVERT: C 228 PHE cc_start: 0.9133 (m-10) cc_final: 0.8756 (m-10) REVERT: C 247 MET cc_start: 0.7013 (mmt) cc_final: 0.6704 (mmt) REVERT: C 328 HIS cc_start: 0.9440 (m-70) cc_final: 0.9183 (m170) REVERT: C 538 ILE cc_start: 0.9217 (mm) cc_final: 0.8869 (mm) REVERT: C 565 MET cc_start: 0.8545 (mmt) cc_final: 0.8130 (mmp) REVERT: C 650 SER cc_start: 0.9675 (m) cc_final: 0.9371 (t) REVERT: C 696 LYS cc_start: 0.9249 (mptt) cc_final: 0.8914 (mptt) REVERT: C 709 MET cc_start: 0.8344 (mtt) cc_final: 0.7946 (mmm) REVERT: C 770 MET cc_start: 0.7980 (mmp) cc_final: 0.7764 (mmp) REVERT: C 783 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8936 (mm) REVERT: D 122 CYS cc_start: 0.9138 (m) cc_final: 0.8670 (m) REVERT: D 187 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8331 (mm-30) REVERT: D 190 LYS cc_start: 0.9124 (pttt) cc_final: 0.8516 (pttt) REVERT: D 250 GLU cc_start: 0.8536 (pm20) cc_final: 0.8212 (pm20) REVERT: D 316 MET cc_start: 0.8756 (mmm) cc_final: 0.8133 (mmm) REVERT: D 394 LEU cc_start: 0.9339 (tp) cc_final: 0.9115 (tt) REVERT: D 413 MET cc_start: 0.7382 (ptt) cc_final: 0.6991 (ptt) REVERT: D 441 GLU cc_start: 0.7634 (tm-30) cc_final: 0.6741 (tm-30) REVERT: D 501 MET cc_start: 0.8776 (mpp) cc_final: 0.7838 (mtm) REVERT: D 651 TYR cc_start: 0.9229 (t80) cc_final: 0.8547 (t80) REVERT: D 664 MET cc_start: 0.7052 (pmm) cc_final: 0.6447 (pmm) REVERT: D 705 MET cc_start: 0.8624 (tpp) cc_final: 0.8072 (mmt) REVERT: B 1003 GLU cc_start: 0.5612 (tp30) cc_final: 0.4725 (tp30) outliers start: 51 outliers final: 48 residues processed: 400 average time/residue: 0.1387 time to fit residues: 94.3537 Evaluate side-chains 406 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 356 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 690 THR Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 755 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 chunk 257 optimal weight: 0.0870 chunk 174 optimal weight: 7.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070628 restraints weight = 149135.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074637 restraints weight = 60443.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077161 restraints weight = 33387.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077314 restraints weight = 25169.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077463 restraints weight = 24917.376| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25597 Z= 0.144 Angle : 0.702 11.687 34730 Z= 0.325 Chirality : 0.043 0.293 3977 Planarity : 0.003 0.056 4318 Dihedral : 6.931 140.922 4070 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.31 % Allowed : 24.87 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.15), residues: 3078 helix: 1.16 (0.15), residues: 1309 sheet: -0.53 (0.31), residues: 303 loop : -1.52 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.017 0.001 TYR A 571 PHE 0.038 0.001 PHE B 658 TRP 0.021 0.001 TRP A 169 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00331 (25554) covalent geometry : angle 0.68797 (34611) SS BOND : bond 0.00200 ( 10) SS BOND : angle 1.21586 ( 20) hydrogen bonds : bond 0.03129 ( 1032) hydrogen bonds : angle 4.34995 ( 3019) link_BETA1-3 : bond 0.00387 ( 2) link_BETA1-3 : angle 3.41051 ( 6) link_BETA1-4 : bond 0.00739 ( 17) link_BETA1-4 : angle 2.77799 ( 51) link_NAG-ASN : bond 0.00221 ( 14) link_NAG-ASN : angle 2.30198 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5173.13 seconds wall clock time: 90 minutes 7.56 seconds (5407.56 seconds total)