Starting phenix.real_space_refine on Sat Aug 8 05:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymj_73108/08_2026/9ymj_73108.map" } resolution = 3.4 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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 16005 2.51 5 N 4251 2.21 5 O 5091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25476 Number of models: 1 Model: "" Number of chains: 11 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 991 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "H" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 978 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "A" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4442 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 23, 'TRANS': 541} Chain breaks: 4 Chain: "P" 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" 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: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Restraints were copied for chains: F, J, G, K, I, N, M, O, B, C, U, Z, V, a, W, b, X, c, Y, d Time building chain proxies: 7.02, per 1000 atoms: 0.28 Number of scatterers: 25476 At special positions: 0 Unit cell: (166.458, 172.661, 132.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5091 8.00 N 4251 7.00 C 16005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN V 4 " - " MAN V 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN a 4 " - " MAN a 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 8 " " MAN T 4 " - " MAN T 7 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 7 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 8 " " MAN d 4 " - " MAN d 7 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 5 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA a 3 " - " MAN a 6 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 701 " - " ASN A 88 " " NAG A 703 " - " ASN A 130 " " NAG A 704 " - " ASN A 137 " " NAG A 705 " - " ASN A 156 " " NAG A 706 " - " ASN A 160 " " NAG A 707 " - " ASN A 197 " " NAG A 708 " - " ASN A 230 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 301 " " NAG A 711 " - " ASN A 392 " " NAG A 712 " - " ASN A 442 " " NAG A 713 " - " ASN A 448 " " NAG A 714 " - " ASN A 611 " " NAG B 701 " - " ASN B 88 " " NAG B 703 " - " ASN B 130 " " NAG B 704 " - " ASN B 137 " " NAG B 705 " - " ASN B 156 " " NAG B 706 " - " ASN B 160 " " NAG B 707 " - " ASN B 197 " " NAG B 708 " - " ASN B 230 " " NAG B 709 " - " ASN B 241 " " NAG B 710 " - " ASN B 301 " " NAG B 711 " - " ASN B 392 " " NAG B 712 " - " ASN B 442 " " NAG B 713 " - " ASN B 448 " " NAG B 714 " - " ASN B 611 " " NAG C 701 " - " ASN C 88 " " NAG C 703 " - " ASN C 130 " " NAG C 704 " - " ASN C 137 " " NAG C 705 " - " ASN C 156 " " NAG C 706 " - " ASN C 160 " " NAG C 707 " - " ASN C 197 " " NAG C 708 " - " ASN C 230 " " NAG C 709 " - " ASN C 241 " " NAG C 710 " - " ASN C 301 " " NAG C 711 " - " ASN C 392 " " NAG C 712 " - " ASN C 442 " " NAG C 713 " - " ASN C 448 " " NAG C 714 " - " ASN C 611 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 289 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 262 " " NAG W 1 " - " ASN B 276 " " NAG X 1 " - " ASN B 289 " " NAG Y 1 " - " ASN B 332 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN C 276 " " NAG c 1 " - " ASN C 289 " " NAG d 1 " - " ASN C 332 " Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5586 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 60 sheets defined 16.1% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.288A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.324A pdb=" N LYS A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.216A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 545 removed outlier: 3.816A pdb=" N GLN A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 596 Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.856A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 659 removed outlier: 4.009A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.288A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 353 removed outlier: 4.324A pdb=" N LYS B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.216A pdb=" N ASN B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 545 removed outlier: 3.816A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.856A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 4.009A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 651 " --> pdb=" O PHE B 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.288A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.324A pdb=" N LYS C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.216A pdb=" N ASN C 478 " --> pdb=" O ASN C 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 545 removed outlier: 3.817A pdb=" N GLN C 540 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 543 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.856A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 659 removed outlier: 4.008A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE C 651 " --> pdb=" O PHE C 647 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.960A pdb=" N PHE D 33 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.501A pdb=" N THR E 5 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP H 33 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 95 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP H 33 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 95 " --> pdb=" O TRP H 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 5.965A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.870A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.926A pdb=" N ILE A 225 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.218A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AB9, first strand: chain 'A' and resid 260 through 261 removed outlier: 10.313A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.749A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 3.671A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.664A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.960A pdb=" N PHE F 33 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.501A pdb=" N THR G 5 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE G 87 " --> pdb=" O TYR G 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.756A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP I 33 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL I 95 " --> pdb=" O TRP I 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 101 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.756A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP I 33 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL I 95 " --> pdb=" O TRP I 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 12 removed outlier: 5.965A pdb=" N GLN M 37 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 9 through 12 Processing sheet with id=AD4, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AD5, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.870A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.926A pdb=" N ILE B 225 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 75 through 76 removed outlier: 7.218A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AE1, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AE2, first strand: chain 'B' and resid 260 through 261 removed outlier: 10.313A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL B 292 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 298 current: chain 'B' and resid 358 through 361 Processing sheet with id=AE3, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.750A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL B 292 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 443 through 456 current: chain 'B' and resid 413 through 421 removed outlier: 3.670A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.664A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.960A pdb=" N PHE J 33 " --> pdb=" O GLN J 95 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.501A pdb=" N THR K 5 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.757A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 34 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP N 33 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 95 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU N 101 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.757A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 34 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP N 33 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 95 " --> pdb=" O TRP N 33 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 9 through 12 removed outlier: 5.965A pdb=" N GLN O 37 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.870A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.926A pdb=" N ILE C 225 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.218A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AG2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AG3, first strand: chain 'C' and resid 200 through 203 Processing sheet with id=AG4, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.313A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AG5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.749A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 421 removed outlier: 3.671A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.664A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2349 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: 7.15 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7875 1.34 - 1.47: 7006 1.47 - 1.59: 11006 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 26055 Sorted by residual: bond pdb=" N ASN C 137 " pdb=" CA ASN C 137 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.23e-02 6.61e+03 4.52e+00 bond pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.23e-02 6.61e+03 4.41e+00 bond pdb=" N ASN B 137 " pdb=" CA ASN B 137 " ideal model delta sigma weight residual 1.462 1.488 -0.025 1.23e-02 6.61e+03 4.26e+00 bond pdb=" C SER K 7 " pdb=" N PRO K 8 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.14e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.10e+00 ... (remaining 26050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 33572 2.18 - 4.36: 1545 4.36 - 6.54: 292 6.54 - 8.72: 36 8.72 - 10.90: 3 Bond angle restraints: 35448 Sorted by residual: angle pdb=" CA CYS B 196 " pdb=" CB CYS B 196 " pdb=" SG CYS B 196 " ideal model delta sigma weight residual 114.40 123.10 -8.70 2.30e+00 1.89e-01 1.43e+01 angle pdb=" CA CYS A 196 " pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " ideal model delta sigma weight residual 114.40 123.10 -8.70 2.30e+00 1.89e-01 1.43e+01 angle pdb=" CA CYS C 196 " pdb=" CB CYS C 196 " pdb=" SG CYS C 196 " ideal model delta sigma weight residual 114.40 123.08 -8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CA ASN B 137 " pdb=" C ASN B 137 " pdb=" O ASN B 137 " ideal model delta sigma weight residual 122.44 118.10 4.34 1.34e+00 5.57e-01 1.05e+01 angle pdb=" CA ASN C 137 " pdb=" C ASN C 137 " pdb=" O ASN C 137 " ideal model delta sigma weight residual 122.44 118.12 4.32 1.34e+00 5.57e-01 1.04e+01 ... (remaining 35443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 14753 21.09 - 42.18: 1549 42.18 - 63.27: 385 63.27 - 84.36: 143 84.36 - 105.46: 36 Dihedral angle restraints: 16866 sinusoidal: 8142 harmonic: 8724 Sorted by residual: dihedral pdb=" CA THR B 529 " pdb=" C THR B 529 " pdb=" N MET B 530 " pdb=" CA MET B 530 " ideal model delta harmonic sigma weight residual -180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA THR A 529 " pdb=" C THR A 529 " pdb=" N MET A 530 " pdb=" CA MET A 530 " ideal model delta harmonic sigma weight residual 180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA THR C 529 " pdb=" C THR C 529 " pdb=" N MET C 530 " pdb=" CA MET C 530 " ideal model delta harmonic sigma weight residual -180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 16863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3982 0.117 - 0.234: 251 0.234 - 0.351: 12 0.351 - 0.468: 6 0.468 - 0.585: 3 Chirality restraints: 4254 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 130 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 130 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.52e+00 ... (remaining 4251 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 522 " 0.025 2.00e-02 2.50e+03 3.73e-02 2.43e+01 pdb=" CG PHE A 522 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE A 522 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 522 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 522 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 522 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 522 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 522 " 0.025 2.00e-02 2.50e+03 3.73e-02 2.43e+01 pdb=" CG PHE C 522 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE C 522 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 522 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE C 522 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 522 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 522 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 522 " 0.025 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE B 522 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE B 522 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE B 522 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE B 522 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 522 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 522 " -0.010 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 39 2.34 - 2.98: 12924 2.98 - 3.62: 35690 3.62 - 4.26: 58091 4.26 - 4.90: 97800 Nonbonded interactions: 204544 Sorted by model distance: nonbonded pdb=" OE2 GLU H 101 " pdb=" C1 MAN T 6 " model vdw 1.696 3.470 nonbonded pdb=" OE2 GLU N 101 " pdb=" C1 MAN d 6 " model vdw 1.696 3.470 nonbonded pdb=" OE2 GLU I 101 " pdb=" C1 MAN Y 6 " model vdw 1.696 3.470 nonbonded pdb=" OE2 GLU I 101 " pdb=" O5 MAN Y 6 " model vdw 1.999 3.040 nonbonded pdb=" OE2 GLU N 101 " pdb=" O5 MAN d 6 " model vdw 1.999 3.040 ... (remaining 204539 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: 0.07 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'W' selection = chain 'b' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'c' } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.400 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.006 0.049 26214 Z= 0.245 Angle : 1.117 14.208 35880 Z= 0.537 Chirality : 0.062 0.585 4254 Planarity : 0.007 0.125 4362 Dihedral : 19.042 105.456 11145 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.95 % Allowed : 28.88 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.49 (0.14), residues: 2991 helix: 0.40 (0.26), residues: 399 sheet: -0.18 (0.16), residues: 951 loop : -0.52 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG D 66 TYR 0.032 0.002 TYR A 484 PHE 0.085 0.003 PHE A 522 TRP 0.026 0.002 TRP I 36 HIS 0.018 0.001 HIS N 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (26055) covalent geometry : angle 1.04725 / 0.52 (35448) SS BOND : bond 0.00488 / 0.30 ( 45) SS BOND : angle 2.78687 / 1.83 ( 90) hydrogen bonds : bond 0.14240 / 9.69 ( 849) hydrogen bonds : angle 7.61542 / 5.30 ( 2349) link_ALPHA1-2 : bond 0.01119 / 0.53 ( 9) link_ALPHA1-2 : angle 4.03087 / 2.69 ( 27) link_ALPHA1-3 : bond 0.01562 / 0.90 ( 12) link_ALPHA1-3 : angle 5.46149 / 3.62 ( 36) link_ALPHA1-6 : bond 0.00806 / 0.47 ( 12) link_ALPHA1-6 : angle 2.45054 / 1.56 ( 36) link_BETA1-4 : bond 0.01069 / 0.68 ( 27) link_BETA1-4 : angle 4.60515 / 3.38 ( 81) link_NAG-ASN : bond 0.00610 / 0.40 ( 54) link_NAG-ASN : angle 3.30352 / 2.47 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 645 time to evaluate : 1.163 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8267 (ttm170) REVERT: E 9 SER cc_start: 0.7784 (p) cc_final: 0.7230 (p) REVERT: E 42 LYS cc_start: 0.7975 (mttt) cc_final: 0.7704 (mttp) REVERT: E 86 TYR cc_start: 0.8231 (m-80) cc_final: 0.8007 (m-80) REVERT: L 27 ASN cc_start: 0.8006 (m-40) cc_final: 0.7735 (m110) REVERT: L 52 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6556 (p90) REVERT: L 54 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7916 (ptp90) REVERT: L 61 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7231 (ttp-110) REVERT: A 213 ILE cc_start: 0.8916 (mm) cc_final: 0.8697 (mm) REVERT: A 588 GLU cc_start: 0.8759 (tt0) cc_final: 0.8403 (tp30) REVERT: A 633 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7784 (ptp-170) REVERT: F 19 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8300 (ttm170) REVERT: F 67 VAL cc_start: 0.9142 (t) cc_final: 0.8912 (p) REVERT: F 94 ARG cc_start: 0.8170 (ttp-170) cc_final: 0.7915 (ttp80) REVERT: G 42 LYS cc_start: 0.7987 (mttt) cc_final: 0.7540 (mttp) REVERT: G 96 GLU cc_start: 0.8019 (pm20) cc_final: 0.7689 (pm20) REVERT: I 107 VAL cc_start: 0.7766 (p) cc_final: 0.7510 (m) REVERT: M 27 ASN cc_start: 0.7916 (m-40) cc_final: 0.7628 (m110) REVERT: M 52 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6482 (p90) REVERT: M 54 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7218 (mtm-85) REVERT: M 61 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7266 (ttp-110) REVERT: M 87 TYR cc_start: 0.6719 (m-80) cc_final: 0.6510 (m-80) REVERT: B 213 ILE cc_start: 0.8857 (mm) cc_final: 0.8580 (mm) REVERT: B 633 ARG cc_start: 0.8272 (ptp-170) cc_final: 0.7888 (ptp-170) REVERT: J 19 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8279 (ttm170) REVERT: K 9 SER cc_start: 0.7685 (p) cc_final: 0.6947 (p) REVERT: K 36 TYR cc_start: 0.8172 (m-80) cc_final: 0.7964 (m-80) REVERT: K 42 LYS cc_start: 0.7823 (mttt) cc_final: 0.7569 (mttp) REVERT: K 86 TYR cc_start: 0.8263 (m-80) cc_final: 0.7984 (m-80) REVERT: K 96 GLU cc_start: 0.8150 (pm20) cc_final: 0.7846 (pm20) REVERT: N 4 LEU cc_start: 0.8827 (mm) cc_final: 0.8478 (mm) REVERT: O 27 ASN cc_start: 0.8074 (m-40) cc_final: 0.7779 (m110) REVERT: C 496 ILE cc_start: 0.8152 (mp) cc_final: 0.7727 (mt) REVERT: C 584 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8344 (mt-10) REVERT: C 628 TRP cc_start: 0.7992 (m100) cc_final: 0.7736 (m100) REVERT: C 631 TRP cc_start: 0.7857 (t-100) cc_final: 0.7602 (t-100) REVERT: C 633 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.8008 (ptp-170) outliers start: 25 outliers final: 9 residues processed: 666 average time/residue: 0.1901 time to fit residues: 195.7193 Evaluate side-chains 536 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 525 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain C residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 GLN A 195 ASN A 229 ASN B 195 ASN B 229 ASN O 89 GLN C 195 ASN C 229 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.154531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124787 restraints weight = 44295.249| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.07 r_work: 0.3439 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26214 Z= 0.152 Angle : 0.786 11.413 35880 Z= 0.364 Chirality : 0.051 0.379 4254 Planarity : 0.005 0.057 4362 Dihedral : 13.812 91.463 5677 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.87 % Allowed : 25.53 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2991 helix: 0.50 (0.25), residues: 426 sheet: 0.10 (0.16), residues: 948 loop : -0.52 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 469 TYR 0.022 0.001 TYR N 90 PHE 0.017 0.002 PHE B 651 TRP 0.021 0.002 TRP O 35 HIS 0.010 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (26055) covalent geometry : angle 0.73892 / 0.35 (35448) SS BOND : bond 0.00291 / 0.19 ( 45) SS BOND : angle 1.20280 / 0.81 ( 90) hydrogen bonds : bond 0.03806 / 2.60 ( 849) hydrogen bonds : angle 6.12128 / 4.27 ( 2349) link_ALPHA1-2 : bond 0.01561 / 0.76 ( 9) link_ALPHA1-2 : angle 2.98452 / 1.93 ( 27) link_ALPHA1-3 : bond 0.01655 / 0.94 ( 12) link_ALPHA1-3 : angle 3.41662 / 2.25 ( 36) link_ALPHA1-6 : bond 0.00700 / 0.43 ( 12) link_ALPHA1-6 : angle 1.88238 / 1.28 ( 36) link_BETA1-4 : bond 0.00575 / 0.35 ( 27) link_BETA1-4 : angle 2.68958 / 1.89 ( 81) link_NAG-ASN : bond 0.00417 / 0.26 ( 54) link_NAG-ASN : angle 2.82987 / 2.15 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 564 time to evaluate : 0.896 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6404 (mmp80) REVERT: E 42 LYS cc_start: 0.7987 (mttt) cc_final: 0.7702 (mttp) REVERT: E 49 TYR cc_start: 0.8136 (p90) cc_final: 0.7899 (p90) REVERT: E 105 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.6950 (t0) REVERT: H 32 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.8138 (m100) REVERT: L 52 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6480 (p90) REVERT: L 54 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7762 (ptp90) REVERT: L 61 ARG cc_start: 0.7656 (ptp-170) cc_final: 0.7193 (ttp-110) REVERT: A 325 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: A 588 GLU cc_start: 0.8765 (tt0) cc_final: 0.8382 (tp30) REVERT: F 67 VAL cc_start: 0.9088 (t) cc_final: 0.8854 (p) REVERT: F 94 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7880 (ttp80) REVERT: G 39 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6667 (mmp80) REVERT: G 96 GLU cc_start: 0.8035 (pm20) cc_final: 0.7684 (pm20) REVERT: G 105 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.6808 (t0) REVERT: G 106 LEU cc_start: 0.7328 (pt) cc_final: 0.7066 (pt) REVERT: I 20 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6880 (tt) REVERT: I 66 ARG cc_start: 0.7231 (mtm180) cc_final: 0.6865 (mtm180) REVERT: M 52 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6365 (p90) REVERT: M 54 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: M 61 ARG cc_start: 0.7548 (ptp-170) cc_final: 0.7308 (ttp-110) REVERT: B 104 MET cc_start: 0.9188 (ttt) cc_final: 0.8970 (ttt) REVERT: B 654 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: J 19 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8407 (ttm170) REVERT: K 33 LEU cc_start: 0.8472 (tt) cc_final: 0.8236 (tt) REVERT: K 39 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6706 (mmp80) REVERT: K 49 TYR cc_start: 0.8070 (p90) cc_final: 0.7849 (p90) REVERT: K 96 GLU cc_start: 0.8063 (pm20) cc_final: 0.7697 (pm20) REVERT: K 105 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.6905 (t0) REVERT: N 4 LEU cc_start: 0.8761 (mm) cc_final: 0.8388 (mm) REVERT: N 86 ASP cc_start: 0.6057 (m-30) cc_final: 0.5662 (m-30) REVERT: O 54 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7418 (mtm-85) REVERT: O 77 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7288 (mtm-85) REVERT: C 296 CYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7347 (m) REVERT: C 308 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8571 (ttm-80) REVERT: C 496 ILE cc_start: 0.8398 (mp) cc_final: 0.8059 (mt) REVERT: C 628 TRP cc_start: 0.7690 (m100) cc_final: 0.7388 (m100) REVERT: C 631 TRP cc_start: 0.7892 (t-100) cc_final: 0.7548 (t-100) REVERT: C 633 ARG cc_start: 0.8331 (ptp-170) cc_final: 0.8041 (ptp-170) REVERT: C 654 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8084 (tt0) outliers start: 128 outliers final: 66 residues processed: 644 average time/residue: 0.1749 time to fit residues: 175.9097 Evaluate side-chains 579 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 499 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 161 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 57 optimal weight: 0.0570 chunk 289 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 HIS L 89 GLN ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN M 89 GLN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 203 GLN C 203 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110961 restraints weight = 43636.273| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.98 r_work: 0.3236 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 26214 Z= 0.249 Angle : 0.830 12.403 35880 Z= 0.386 Chirality : 0.054 0.566 4254 Planarity : 0.005 0.056 4362 Dihedral : 13.107 87.036 5677 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.09 % Allowed : 25.53 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.44 (0.15), residues: 2991 helix: 0.56 (0.26), residues: 408 sheet: 0.05 (0.16), residues: 981 loop : -0.69 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 77 TYR 0.020 0.002 TYR I 99 PHE 0.019 0.002 PHE I 100C TRP 0.037 0.002 TRP O 35 HIS 0.009 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (26055) covalent geometry : angle 0.77152 / 0.37 (35448) SS BOND : bond 0.00534 / 0.35 ( 45) SS BOND : angle 1.14224 / 0.83 ( 90) hydrogen bonds : bond 0.03904 / 2.66 ( 849) hydrogen bonds : angle 6.05462 / 4.24 ( 2349) link_ALPHA1-2 : bond 0.01285 / 0.60 ( 9) link_ALPHA1-2 : angle 2.84782 / 1.86 ( 27) link_ALPHA1-3 : bond 0.01595 / 0.92 ( 12) link_ALPHA1-3 : angle 3.41088 / 2.25 ( 36) link_ALPHA1-6 : bond 0.00567 / 0.33 ( 12) link_ALPHA1-6 : angle 1.88601 / 1.30 ( 36) link_BETA1-4 : bond 0.01034 / 0.67 ( 27) link_BETA1-4 : angle 3.03401 / 2.13 ( 81) link_NAG-ASN : bond 0.00776 / 0.52 ( 54) link_NAG-ASN : angle 3.50281 / 2.61 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 509 time to evaluate : 0.945 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: symmetry clash revert: symmetry clash REVERT: E 39 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6322 (mmp80) REVERT: E 42 LYS cc_start: 0.8054 (mttt) cc_final: 0.7734 (mttp) REVERT: E 105 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.6791 (t0) REVERT: H 32 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8007 (m100) REVERT: L 52 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6494 (p90) REVERT: A 654 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: F 94 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7331 (ttp80) REVERT: G 39 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6794 (mmp80) REVERT: G 96 GLU cc_start: 0.8116 (pm20) cc_final: 0.7654 (pm20) REVERT: G 105 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.6845 (t0) REVERT: I 20 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6917 (tt) REVERT: M 52 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6490 (p90) REVERT: M 54 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7325 (mtm-85) REVERT: B 296 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7109 (m) REVERT: B 654 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: J 71 TRP cc_start: 0.7887 (p90) cc_final: 0.7452 (p90) REVERT: K 39 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6799 (mmp80) REVERT: K 105 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.6768 (t0) REVERT: N 4 LEU cc_start: 0.8854 (mm) cc_final: 0.8445 (mm) REVERT: N 12 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7705 (m) REVERT: N 20 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7179 (mt) REVERT: N 86 ASP cc_start: 0.6188 (m-30) cc_final: 0.5889 (m-30) REVERT: O 54 ARG cc_start: 0.8362 (mtm110) cc_final: 0.7487 (mtm-85) REVERT: C 475 MET cc_start: 0.8376 (mmt) cc_final: 0.8128 (mmt) REVERT: C 628 TRP cc_start: 0.7688 (m100) cc_final: 0.7338 (m100) REVERT: C 631 TRP cc_start: 0.7942 (t-100) cc_final: 0.7656 (t-100) REVERT: C 633 ARG cc_start: 0.8352 (ptp-170) cc_final: 0.8064 (ptp-170) REVERT: C 654 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7950 (tt0) outliers start: 160 outliers final: 96 residues processed: 599 average time/residue: 0.1714 time to fit residues: 160.3132 Evaluate side-chains 569 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 457 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 57 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 195 ASN B 535 ASN N 39 GLN O 38 GLN C 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118568 restraints weight = 44596.367| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.29 r_work: 0.3379 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26214 Z= 0.199 Angle : 0.791 10.989 35880 Z= 0.365 Chirality : 0.052 0.356 4254 Planarity : 0.004 0.057 4362 Dihedral : 12.427 84.383 5677 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.28 % Allowed : 25.76 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.52 (0.15), residues: 2991 helix: 0.45 (0.26), residues: 435 sheet: 0.12 (0.16), residues: 915 loop : -0.81 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 77 TYR 0.018 0.002 TYR O 87 PHE 0.018 0.002 PHE B 651 TRP 0.044 0.002 TRP O 35 HIS 0.006 0.001 HIS H 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (26055) covalent geometry : angle 0.73680 / 0.35 (35448) SS BOND : bond 0.00388 / 0.24 ( 45) SS BOND : angle 1.02701 / 0.73 ( 90) hydrogen bonds : bond 0.03550 / 2.40 ( 849) hydrogen bonds : angle 5.88644 / 4.14 ( 2349) link_ALPHA1-2 : bond 0.01465 / 0.68 ( 9) link_ALPHA1-2 : angle 2.62868 / 1.72 ( 27) link_ALPHA1-3 : bond 0.01449 / 0.82 ( 12) link_ALPHA1-3 : angle 3.24217 / 2.14 ( 36) link_ALPHA1-6 : bond 0.00643 / 0.38 ( 12) link_ALPHA1-6 : angle 1.80328 / 1.24 ( 36) link_BETA1-4 : bond 0.00660 / 0.39 ( 27) link_BETA1-4 : angle 3.02977 / 2.18 ( 81) link_NAG-ASN : bond 0.00467 / 0.30 ( 54) link_NAG-ASN : angle 3.22424 / 2.44 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 504 time to evaluate : 0.658 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: E 39 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6689 (mmp80) REVERT: E 42 LYS cc_start: 0.7949 (mttt) cc_final: 0.7592 (mttp) REVERT: E 86 TYR cc_start: 0.8106 (m-80) cc_final: 0.7819 (m-80) REVERT: E 105 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.6882 (t0) REVERT: H 20 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6888 (tt) REVERT: H 32 TRP cc_start: 0.8851 (OUTLIER) cc_final: 0.8028 (m100) REVERT: H 66 ARG cc_start: 0.7356 (mtp180) cc_final: 0.7129 (mtp180) REVERT: L 52 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6477 (p90) REVERT: A 51 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 129 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9027 (mt) REVERT: A 296 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7189 (m) REVERT: A 325 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: A 353 TYR cc_start: 0.7682 (m-80) cc_final: 0.7451 (m-80) REVERT: A 626 MET cc_start: 0.7042 (mtt) cc_final: 0.6554 (mtp) REVERT: A 654 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: F 94 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7149 (ttp80) REVERT: G 39 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6827 (mmp80) REVERT: I 20 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6924 (tt) REVERT: M 52 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6407 (p90) REVERT: M 54 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7263 (mtm-85) REVERT: B 99 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8464 (t0) REVERT: B 296 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7382 (m) REVERT: J 29 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8011 (mm) REVERT: J 71 TRP cc_start: 0.7847 (p90) cc_final: 0.7377 (p90) REVERT: K 39 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6640 (mmp80) REVERT: K 105 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.6871 (t0) REVERT: N 4 LEU cc_start: 0.8856 (mm) cc_final: 0.8532 (mm) REVERT: N 12 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7805 (m) REVERT: N 86 ASP cc_start: 0.5945 (m-30) cc_final: 0.5663 (m-30) REVERT: O 27 ASN cc_start: 0.7576 (m110) cc_final: 0.7334 (m110) REVERT: O 54 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7288 (mtm-85) REVERT: O 89 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 72 HIS cc_start: 0.7652 (t70) cc_final: 0.7403 (t70) REVERT: C 99 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8404 (t0) REVERT: C 296 CYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7153 (m) REVERT: C 325 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: C 654 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8049 (tt0) outliers start: 165 outliers final: 97 residues processed: 620 average time/residue: 0.1628 time to fit residues: 159.2205 Evaluate side-chains 581 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 461 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 146 optimal weight: 0.0970 chunk 179 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN L 38 GLN ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 6 GLN M 38 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.150240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.119036 restraints weight = 44619.999| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.33 r_work: 0.3378 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26214 Z= 0.173 Angle : 0.776 10.280 35880 Z= 0.358 Chirality : 0.051 0.358 4254 Planarity : 0.004 0.056 4362 Dihedral : 12.069 82.777 5677 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.71 % Allowed : 26.86 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.51 (0.15), residues: 2991 helix: 0.52 (0.27), residues: 432 sheet: 0.11 (0.17), residues: 918 loop : -0.81 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.021 0.002 TYR M 87 PHE 0.018 0.002 PHE C 651 TRP 0.033 0.002 TRP O 35 HIS 0.008 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (26055) covalent geometry : angle 0.72290 / 0.35 (35448) SS BOND : bond 0.00393 / 0.25 ( 45) SS BOND : angle 1.09384 / 0.77 ( 90) hydrogen bonds : bond 0.03397 / 2.30 ( 849) hydrogen bonds : angle 5.80245 / 4.09 ( 2349) link_ALPHA1-2 : bond 0.01494 / 0.69 ( 9) link_ALPHA1-2 : angle 2.54955 / 1.68 ( 27) link_ALPHA1-3 : bond 0.01549 / 0.86 ( 12) link_ALPHA1-3 : angle 3.21712 / 2.13 ( 36) link_ALPHA1-6 : bond 0.00633 / 0.37 ( 12) link_ALPHA1-6 : angle 1.76824 / 1.21 ( 36) link_BETA1-4 : bond 0.00668 / 0.39 ( 27) link_BETA1-4 : angle 2.99190 / 2.16 ( 81) link_NAG-ASN : bond 0.00474 / 0.30 ( 54) link_NAG-ASN : angle 3.11289 / 2.34 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 486 time to evaluate : 0.797 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: D 21 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7819 (m) REVERT: E 39 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6616 (mmp80) REVERT: E 42 LYS cc_start: 0.7919 (mttt) cc_final: 0.7573 (mttp) REVERT: E 105 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.6902 (t0) REVERT: H 32 TRP cc_start: 0.8832 (OUTLIER) cc_final: 0.8029 (m100) REVERT: H 66 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7164 (mtp180) REVERT: L 52 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6536 (p90) REVERT: L 89 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 114 GLN cc_start: 0.8653 (pt0) cc_final: 0.8203 (pt0) REVERT: A 129 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9016 (mt) REVERT: A 296 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7318 (m) REVERT: A 325 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: A 654 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: F 94 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7686 (ttp80) REVERT: G 39 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6657 (mmp80) REVERT: I 12 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7599 (m) REVERT: M 52 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6501 (p90) REVERT: B 99 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 277 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8505 (tpt) REVERT: B 296 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7463 (m) REVERT: B 530 MET cc_start: 0.7540 (mtm) cc_final: 0.7157 (mtm) REVERT: J 29 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8014 (mm) REVERT: J 71 TRP cc_start: 0.7845 (p90) cc_final: 0.7369 (p90) REVERT: K 39 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6585 (mmp80) REVERT: K 105 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.6877 (t0) REVERT: N 4 LEU cc_start: 0.8901 (mm) cc_final: 0.8589 (mm) REVERT: N 12 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7838 (m) REVERT: N 100 TYR cc_start: 0.8119 (m-80) cc_final: 0.7901 (m-80) REVERT: O 54 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7323 (mtm-85) REVERT: O 89 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 72 HIS cc_start: 0.7624 (t70) cc_final: 0.7293 (t70) REVERT: C 296 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7298 (m) REVERT: C 325 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: C 654 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8030 (tt0) outliers start: 150 outliers final: 101 residues processed: 592 average time/residue: 0.1599 time to fit residues: 149.1490 Evaluate side-chains 582 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 459 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 143 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117444 restraints weight = 44876.228| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.36 r_work: 0.3346 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26214 Z= 0.214 Angle : 0.805 13.301 35880 Z= 0.373 Chirality : 0.052 0.359 4254 Planarity : 0.004 0.057 4362 Dihedral : 11.786 80.149 5675 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.51 % Allowed : 26.75 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.59 (0.15), residues: 2991 helix: 0.49 (0.27), residues: 432 sheet: -0.01 (0.16), residues: 945 loop : -0.83 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 54 TYR 0.028 0.002 TYR I 99 PHE 0.018 0.002 PHE C 651 TRP 0.025 0.002 TRP A 628 HIS 0.007 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (26055) covalent geometry : angle 0.75098 / 0.36 (35448) SS BOND : bond 0.00744 / 0.42 ( 45) SS BOND : angle 1.86753 / 1.27 ( 90) hydrogen bonds : bond 0.03490 / 2.36 ( 849) hydrogen bonds : angle 5.79293 / 4.10 ( 2349) link_ALPHA1-2 : bond 0.01391 / 0.65 ( 9) link_ALPHA1-2 : angle 2.42908 / 1.60 ( 27) link_ALPHA1-3 : bond 0.01393 / 0.81 ( 12) link_ALPHA1-3 : angle 3.20009 / 2.11 ( 36) link_ALPHA1-6 : bond 0.00601 / 0.36 ( 12) link_ALPHA1-6 : angle 1.90292 / 1.31 ( 36) link_BETA1-4 : bond 0.00644 / 0.40 ( 27) link_BETA1-4 : angle 3.13673 / 2.27 ( 81) link_NAG-ASN : bond 0.00469 / 0.30 ( 54) link_NAG-ASN : angle 3.04815 / 2.30 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 466 time to evaluate : 1.031 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: symmetry clash REVERT: E 39 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6772 (mmp80) REVERT: E 105 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.6993 (t0) REVERT: H 32 TRP cc_start: 0.8863 (OUTLIER) cc_final: 0.8009 (m100) REVERT: H 66 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7216 (mtp180) REVERT: H 100 TYR cc_start: 0.8236 (m-80) cc_final: 0.7965 (m-80) REVERT: L 52 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6497 (p90) REVERT: A 129 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9056 (mt) REVERT: A 296 CYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 325 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 654 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: G 39 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6727 (mmp80) REVERT: G 105 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.6882 (t0) REVERT: M 52 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6546 (p90) REVERT: B 99 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8472 (t0) REVERT: B 296 CYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7528 (m) REVERT: B 325 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: J 29 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8046 (mm) REVERT: J 71 TRP cc_start: 0.7861 (p90) cc_final: 0.7370 (p90) REVERT: K 39 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6625 (mmp80) REVERT: K 105 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.6787 (t0) REVERT: N 4 LEU cc_start: 0.8930 (mm) cc_final: 0.8630 (mm) REVERT: N 12 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7865 (m) REVERT: N 100 TYR cc_start: 0.8136 (m-80) cc_final: 0.7842 (m-80) REVERT: O 54 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7665 (ptp90) REVERT: C 99 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8400 (t0) REVERT: C 296 CYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7420 (m) REVERT: C 325 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8421 (m-30) REVERT: C 654 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8059 (tt0) outliers start: 171 outliers final: 119 residues processed: 591 average time/residue: 0.1758 time to fit residues: 163.4903 Evaluate side-chains 587 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 446 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 268 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 244 optimal weight: 0.0020 chunk 21 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 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 = 0.4034 r_free = 0.4034 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118448 restraints weight = 44696.673| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.25 r_work: 0.3409 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26214 Z= 0.158 Angle : 0.771 10.741 35880 Z= 0.355 Chirality : 0.051 0.354 4254 Planarity : 0.004 0.057 4362 Dihedral : 11.376 78.341 5673 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 5.63 % Allowed : 27.66 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.46 (0.15), residues: 2991 helix: 0.85 (0.28), residues: 414 sheet: 0.05 (0.17), residues: 930 loop : -0.79 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.024 0.001 TYR I 99 PHE 0.019 0.002 PHE A 210 TRP 0.033 0.002 TRP O 35 HIS 0.008 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (26055) covalent geometry : angle 0.71982 / 0.34 (35448) SS BOND : bond 0.00450 / 0.29 ( 45) SS BOND : angle 1.64459 / 1.13 ( 90) hydrogen bonds : bond 0.03236 / 2.18 ( 849) hydrogen bonds : angle 5.65886 / 4.00 ( 2349) link_ALPHA1-2 : bond 0.01464 / 0.68 ( 9) link_ALPHA1-2 : angle 2.34786 / 1.55 ( 27) link_ALPHA1-3 : bond 0.01423 / 0.81 ( 12) link_ALPHA1-3 : angle 3.18770 / 2.10 ( 36) link_ALPHA1-6 : bond 0.00687 / 0.42 ( 12) link_ALPHA1-6 : angle 1.97560 / 1.32 ( 36) link_BETA1-4 : bond 0.00604 / 0.37 ( 27) link_BETA1-4 : angle 3.00536 / 2.20 ( 81) link_NAG-ASN : bond 0.00435 / 0.29 ( 54) link_NAG-ASN : angle 2.87782 / 2.18 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 476 time to evaluate : 0.994 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: symmetry clash REVERT: E 39 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6691 (mmp80) REVERT: E 105 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.6956 (t0) REVERT: H 32 TRP cc_start: 0.8764 (OUTLIER) cc_final: 0.8011 (m100) REVERT: H 66 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7204 (mtp180) REVERT: H 100 TYR cc_start: 0.8176 (m-80) cc_final: 0.7952 (m-80) REVERT: L 52 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6437 (p90) REVERT: L 89 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8174 (pp30) REVERT: A 95 MET cc_start: 0.7203 (ptp) cc_final: 0.6972 (ttp) REVERT: A 129 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9057 (mt) REVERT: A 296 CYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7305 (m) REVERT: A 325 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: A 626 MET cc_start: 0.7334 (mtt) cc_final: 0.6998 (mtp) REVERT: F 94 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7067 (ttp80) REVERT: G 105 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.6828 (t0) REVERT: M 52 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6472 (p90) REVERT: B 99 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 296 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7337 (m) REVERT: J 29 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7979 (mm) REVERT: J 71 TRP cc_start: 0.7903 (p90) cc_final: 0.7405 (p90) REVERT: K 39 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6526 (mmp80) REVERT: K 105 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.6763 (t0) REVERT: N 4 LEU cc_start: 0.8933 (mm) cc_final: 0.8638 (mm) REVERT: N 12 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7797 (m) REVERT: O 54 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7649 (ptp90) REVERT: O 77 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7039 (ptp-170) REVERT: O 103 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.7154 (tpp-160) REVERT: C 99 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (t0) REVERT: C 296 CYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7140 (m) REVERT: C 325 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: C 626 MET cc_start: 0.7593 (mtt) cc_final: 0.7106 (mtp) REVERT: C 654 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 148 outliers final: 104 residues processed: 589 average time/residue: 0.1683 time to fit residues: 156.3480 Evaluate side-chains 576 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 453 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 100 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 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 = 0.4030 r_free = 0.4030 target = 0.150064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118982 restraints weight = 44913.057| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.22 r_work: 0.3388 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26214 Z= 0.167 Angle : 0.768 10.409 35880 Z= 0.354 Chirality : 0.051 0.508 4254 Planarity : 0.004 0.058 4362 Dihedral : 11.181 74.943 5671 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.59 % Allowed : 27.55 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.48 (0.15), residues: 2991 helix: 0.81 (0.28), residues: 414 sheet: 0.03 (0.17), residues: 930 loop : -0.79 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.022 0.001 TYR M 87 PHE 0.017 0.002 PHE C 651 TRP 0.058 0.002 TRP O 35 HIS 0.006 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (26055) covalent geometry : angle 0.71600 / 0.34 (35448) SS BOND : bond 0.00362 / 0.24 ( 45) SS BOND : angle 1.46770 / 1.01 ( 90) hydrogen bonds : bond 0.03266 / 2.20 ( 849) hydrogen bonds : angle 5.61541 / 3.96 ( 2349) link_ALPHA1-2 : bond 0.01376 / 0.64 ( 9) link_ALPHA1-2 : angle 2.27587 / 1.50 ( 27) link_ALPHA1-3 : bond 0.01391 / 0.80 ( 12) link_ALPHA1-3 : angle 3.14677 / 2.07 ( 36) link_ALPHA1-6 : bond 0.00656 / 0.40 ( 12) link_ALPHA1-6 : angle 2.00058 / 1.34 ( 36) link_BETA1-4 : bond 0.00570 / 0.34 ( 27) link_BETA1-4 : angle 3.06013 / 2.24 ( 81) link_NAG-ASN : bond 0.00433 / 0.29 ( 54) link_NAG-ASN : angle 2.95223 / 2.21 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 479 time to evaluate : 0.910 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: symmetry clash REVERT: D 96 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7445 (ttm-80) REVERT: E 39 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6587 (mmp80) REVERT: E 105 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.6993 (t0) REVERT: H 32 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.8022 (m100) REVERT: H 66 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7300 (mtp180) REVERT: H 100 TYR cc_start: 0.8196 (m-80) cc_final: 0.7926 (m-80) REVERT: L 42 GLN cc_start: 0.7688 (mp10) cc_final: 0.7429 (pm20) REVERT: L 52 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6427 (p90) REVERT: A 56 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 69 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.7575 (m-90) REVERT: A 95 MET cc_start: 0.7230 (ptp) cc_final: 0.6946 (ttp) REVERT: A 129 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 296 CYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7418 (m) REVERT: A 325 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: A 626 MET cc_start: 0.7361 (mtt) cc_final: 0.7066 (mtp) REVERT: F 71 TRP cc_start: 0.7732 (p90) cc_final: 0.7233 (p90) REVERT: F 94 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7106 (ttp80) REVERT: G 86 TYR cc_start: 0.8044 (m-80) cc_final: 0.7693 (m-80) REVERT: G 105 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.6947 (t0) REVERT: I 12 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7597 (m) REVERT: M 52 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6484 (p90) REVERT: M 103 ARG cc_start: 0.7156 (tpp-160) cc_final: 0.6598 (tpm170) REVERT: B 99 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8446 (t0) REVERT: B 325 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: B 626 MET cc_start: 0.7145 (ttt) cc_final: 0.6564 (ttt) REVERT: J 29 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7957 (mm) REVERT: J 71 TRP cc_start: 0.7901 (p90) cc_final: 0.7341 (p90) REVERT: K 39 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6603 (mmp80) REVERT: K 105 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.6686 (t0) REVERT: N 4 LEU cc_start: 0.8841 (mm) cc_final: 0.8552 (mm) REVERT: N 12 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7803 (m) REVERT: N 91 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.5454 (m-80) REVERT: O 54 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7668 (ptp90) REVERT: O 77 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7097 (ptp-170) REVERT: C 99 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8351 (t0) REVERT: C 325 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (m-30) REVERT: C 626 MET cc_start: 0.7498 (mtt) cc_final: 0.7155 (mtp) REVERT: C 654 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8070 (tt0) outliers start: 147 outliers final: 100 residues processed: 582 average time/residue: 0.1613 time to fit residues: 148.2212 Evaluate side-chains 572 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 450 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 199 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 146 optimal weight: 0.0060 chunk 60 optimal weight: 0.1980 chunk 198 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN I 3 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120267 restraints weight = 45093.705| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.19 r_work: 0.3374 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26214 Z= 0.160 Angle : 0.778 10.729 35880 Z= 0.358 Chirality : 0.052 0.486 4254 Planarity : 0.004 0.057 4362 Dihedral : 11.032 71.828 5671 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.21 % Allowed : 28.39 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.43 (0.15), residues: 2991 helix: 0.91 (0.28), residues: 414 sheet: 0.04 (0.17), residues: 936 loop : -0.76 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.023 0.001 TYR O 87 PHE 0.020 0.002 PHE A 538 TRP 0.062 0.002 TRP O 35 HIS 0.006 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (26055) covalent geometry : angle 0.72418 / 0.35 (35448) SS BOND : bond 0.00445 / 0.26 ( 45) SS BOND : angle 1.48748 / 1.02 ( 90) hydrogen bonds : bond 0.03214 / 2.15 ( 849) hydrogen bonds : angle 5.57947 / 3.94 ( 2349) link_ALPHA1-2 : bond 0.01379 / 0.64 ( 9) link_ALPHA1-2 : angle 2.23418 / 1.48 ( 27) link_ALPHA1-3 : bond 0.01363 / 0.78 ( 12) link_ALPHA1-3 : angle 3.10730 / 2.04 ( 36) link_ALPHA1-6 : bond 0.00685 / 0.42 ( 12) link_ALPHA1-6 : angle 1.95751 / 1.31 ( 36) link_BETA1-4 : bond 0.00541 / 0.34 ( 27) link_BETA1-4 : angle 3.02813 / 2.22 ( 81) link_NAG-ASN : bond 0.00474 / 0.31 ( 54) link_NAG-ASN : angle 3.09326 / 2.37 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 472 time to evaluate : 0.875 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: symmetry clash revert: symmetry clash REVERT: E 39 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6593 (mmp80) REVERT: E 105 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.6998 (t0) REVERT: H 32 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.8097 (m100) REVERT: H 100 TYR cc_start: 0.8170 (m-80) cc_final: 0.7932 (m-80) REVERT: L 42 GLN cc_start: 0.7694 (mp10) cc_final: 0.7441 (pm20) REVERT: L 52 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6437 (p90) REVERT: A 53 PHE cc_start: 0.7932 (t80) cc_final: 0.7669 (t80) REVERT: A 56 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8214 (p) REVERT: A 69 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.7550 (m-90) REVERT: A 95 MET cc_start: 0.7263 (ptp) cc_final: 0.6968 (ttp) REVERT: A 129 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9076 (mt) REVERT: A 296 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7466 (m) REVERT: A 325 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: F 13 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8210 (mmtm) REVERT: F 71 TRP cc_start: 0.7771 (p90) cc_final: 0.7283 (p90) REVERT: F 94 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7869 (ttp80) REVERT: G 86 TYR cc_start: 0.7956 (m-80) cc_final: 0.7623 (m-80) REVERT: G 105 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7039 (t0) REVERT: I 12 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7608 (m) REVERT: M 52 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6485 (p90) REVERT: B 99 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8438 (t0) REVERT: B 325 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: B 626 MET cc_start: 0.7306 (ttt) cc_final: 0.6761 (ttt) REVERT: J 29 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7926 (mm) REVERT: J 71 TRP cc_start: 0.7914 (p90) cc_final: 0.7345 (p90) REVERT: K 39 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6573 (mmp80) REVERT: K 105 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.6760 (t0) REVERT: N 4 LEU cc_start: 0.8884 (mm) cc_final: 0.8584 (mm) REVERT: N 12 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7853 (m) REVERT: N 91 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: O 54 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7634 (ptp90) REVERT: O 77 ARG cc_start: 0.7761 (ptp90) cc_final: 0.7141 (ptp-170) REVERT: C 51 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8774 (p) REVERT: C 99 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8394 (t0) REVERT: C 325 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: C 626 MET cc_start: 0.7360 (mtt) cc_final: 0.6852 (mtp) REVERT: C 654 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8040 (tt0) outliers start: 137 outliers final: 102 residues processed: 573 average time/residue: 0.1829 time to fit residues: 164.1678 Evaluate side-chains 579 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 454 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 286 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN I 3 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118662 restraints weight = 45069.574| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.43 r_work: 0.3371 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26214 Z= 0.181 Angle : 0.791 10.650 35880 Z= 0.365 Chirality : 0.052 0.481 4254 Planarity : 0.004 0.057 4362 Dihedral : 10.882 67.721 5671 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.02 % Allowed : 29.03 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.45 (0.15), residues: 2991 helix: 0.86 (0.28), residues: 414 sheet: 0.03 (0.17), residues: 951 loop : -0.77 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.022 0.002 TYR O 87 PHE 0.026 0.002 PHE A 538 TRP 0.060 0.002 TRP O 35 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (26055) covalent geometry : angle 0.73748 / 0.35 (35448) SS BOND : bond 0.00432 / 0.26 ( 45) SS BOND : angle 1.51058 / 1.05 ( 90) hydrogen bonds : bond 0.03259 / 2.19 ( 849) hydrogen bonds : angle 5.56831 / 3.93 ( 2349) link_ALPHA1-2 : bond 0.01321 / 0.62 ( 9) link_ALPHA1-2 : angle 2.18304 / 1.44 ( 27) link_ALPHA1-3 : bond 0.01320 / 0.75 ( 12) link_ALPHA1-3 : angle 3.06278 / 2.01 ( 36) link_ALPHA1-6 : bond 0.00662 / 0.41 ( 12) link_ALPHA1-6 : angle 2.00162 / 1.35 ( 36) link_BETA1-4 : bond 0.00517 / 0.33 ( 27) link_BETA1-4 : angle 3.14596 / 2.29 ( 81) link_NAG-ASN : bond 0.00479 / 0.31 ( 54) link_NAG-ASN : angle 3.10116 / 2.37 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 464 time to evaluate : 1.047 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: symmetry clash revert: symmetry clash REVERT: D 96 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7644 (ttm-80) REVERT: E 5 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7074 (p) REVERT: E 39 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6578 (mmp80) REVERT: E 105 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7010 (t0) REVERT: H 32 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.8042 (m100) REVERT: L 42 GLN cc_start: 0.7723 (mp10) cc_final: 0.7475 (pm20) REVERT: L 52 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6433 (p90) REVERT: L 89 GLN cc_start: 0.8323 (pp30) cc_final: 0.8055 (pp30) REVERT: A 53 PHE cc_start: 0.8052 (t80) cc_final: 0.7107 (t80) REVERT: A 56 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 69 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7528 (m-90) REVERT: A 95 MET cc_start: 0.7281 (ptp) cc_final: 0.6976 (ttp) REVERT: A 129 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9080 (mt) REVERT: A 296 CYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7339 (m) REVERT: F 13 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8195 (mmtm) REVERT: F 71 TRP cc_start: 0.7753 (p90) cc_final: 0.7265 (p90) REVERT: G 86 TYR cc_start: 0.7905 (m-80) cc_final: 0.7690 (m-80) REVERT: G 105 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.6949 (t0) REVERT: I 12 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7635 (m) REVERT: M 52 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6538 (p90) REVERT: B 99 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8423 (t0) REVERT: B 626 MET cc_start: 0.7429 (ttt) cc_final: 0.6914 (ttt) REVERT: J 29 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7950 (mm) REVERT: J 71 TRP cc_start: 0.7953 (p90) cc_final: 0.7346 (p90) REVERT: K 39 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6557 (mmp80) REVERT: K 105 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.6790 (t0) REVERT: N 4 LEU cc_start: 0.8878 (mm) cc_final: 0.8599 (mm) REVERT: N 91 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5595 (m-80) REVERT: O 42 GLN cc_start: 0.7737 (pm20) cc_final: 0.7437 (pm20) REVERT: O 54 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7679 (ptp90) REVERT: C 99 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8371 (t0) REVERT: C 325 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: C 626 MET cc_start: 0.7428 (mtt) cc_final: 0.6952 (mtp) REVERT: C 654 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8015 (tt0) outliers start: 132 outliers final: 103 residues processed: 558 average time/residue: 0.1610 time to fit residues: 141.6358 Evaluate side-chains 582 residues out of total 2628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 459 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TRP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 TYR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 TYR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 620 GLN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 91 PHE Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 620 GLN Chi-restraints excluded: chain C residue 654 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 272 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN I 3 HIS I 105 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.119991 restraints weight = 44715.049| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.22 r_work: 0.3404 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26214 Z= 0.153 Angle : 0.787 16.879 35880 Z= 0.363 Chirality : 0.052 0.429 4254 Planarity : 0.004 0.056 4362 Dihedral : 10.591 65.847 5671 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.02 % Allowed : 29.00 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.38 (0.15), residues: 2991 helix: 0.96 (0.28), residues: 414 sheet: 0.08 (0.17), residues: 903 loop : -0.72 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 54 TYR 0.021 0.001 TYR M 87 PHE 0.022 0.002 PHE A 538 TRP 0.048 0.002 TRP O 35 HIS 0.005 0.001 HIS O 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26055) covalent geometry : angle 0.73287 / 0.35 (35448) SS BOND : bond 0.00414 / 0.24 ( 45) SS BOND : angle 2.00484 / 1.35 ( 90) hydrogen bonds : bond 0.03155 / 2.12 ( 849) hydrogen bonds : angle 5.48850 / 3.88 ( 2349) link_ALPHA1-2 : bond 0.01349 / 0.63 ( 9) link_ALPHA1-2 : angle 2.14934 / 1.42 ( 27) link_ALPHA1-3 : bond 0.01211 / 0.70 ( 12) link_ALPHA1-3 : angle 2.95744 / 1.93 ( 36) link_ALPHA1-6 : bond 0.00720 / 0.44 ( 12) link_ALPHA1-6 : angle 1.93082 / 1.30 ( 36) link_BETA1-4 : bond 0.00499 / 0.32 ( 27) link_BETA1-4 : angle 3.13383 / 2.27 ( 81) link_NAG-ASN : bond 0.00465 / 0.31 ( 54) link_NAG-ASN : angle 3.01642 / 2.31 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.91 seconds wall clock time: 112 minutes 8.52 seconds (6728.52 seconds total)