Starting phenix.real_space_refine on Thu Mar 5 10:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.map" model { file = "/net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly9_23589/03_2026/7ly9_23589.cif" } resolution = 3.91 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= 0.010 sd= 0.061 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 126 5.16 5 C 13467 2.51 5 N 3572 2.21 5 O 4299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21464 Number of models: 1 Model: "" Number of chains: 35 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3449 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "C" 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: "F" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 899 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3440 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" 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: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 924 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "K" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3442 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "A" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "N" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "O" 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: "P" 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: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.88, per 1000 atoms: 0.23 Number of scatterers: 21464 At special positions: 0 Unit cell: (149.07, 139.205, 146.877, 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 126 16.00 O 4299 8.00 N 3572 7.00 C 13467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.04 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS N 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 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 ALPHA1-3 " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " 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 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG C 301 " - " ASN C 72 " " NAG D 601 " - " ASN D 130 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 241 " " NAG D 605 " - " ASN D 301 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 442 " " NAG D 608 " - " ASN D 448 " " NAG D 609 " - " ASN D 393 " " NAG D 610 " - " ASN D 197 " " NAG D 611 " - " ASN D 88 " " NAG D 612 " - " ASN D 234 " " NAG D 613 " - " ASN D 502 " " NAG D 614 " - " ASN D 461 " " NAG D 615 " - " ASN D 356 " " NAG D 616 " - " ASN D 386 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 230 " " NAG G 602 " - " ASN G 241 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 356 " " NAG G 605 " - " ASN G 362 " " NAG G 606 " - " ASN G 386 " " NAG G 607 " - " ASN G 442 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 502 " " NAG G 610 " - " ASN G 393 " " NAG G 611 " - " ASN G 197 " " NAG G 612 " - " ASN G 130 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 234 " " NAG G 615 " - " ASN G 88 " " NAG I 301 " - " ASN I 72 " " NAG J 701 " - " ASN J 637 " " NAG J 702 " - " ASN J 611 " " NAG K 601 " - " ASN K 130 " " NAG K 602 " - " ASN K 156 " " NAG K 603 " - " ASN K 230 " " NAG K 604 " - " ASN K 234 " " NAG K 605 " - " ASN K 241 " " NAG K 606 " - " ASN K 301 " " NAG K 607 " - " ASN K 362 " " NAG K 608 " - " ASN K 386 " " NAG K 609 " - " ASN K 442 " " NAG K 610 " - " ASN K 448 " " NAG K 611 " - " ASN K 393 " " NAG K 612 " - " ASN K 197 " " NAG K 613 " - " ASN K 502 " " NAG K 614 " - " ASN K 88 " " NAG M 301 " - " ASN M 72 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG O 1 " - " ASN G 289 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN D 289 " " NAG T 1 " - " ASN D 332 " " NAG U 1 " - " ASN D 276 " " NAG V 1 " - " ASN D 262 " " NAG W 1 " - " ASN K 262 " " NAG X 1 " - " ASN K 289 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 276 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 822.3 milliseconds 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 58 sheets defined 17.7% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.888A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 99 through 116 Processing helix chain 'G' and resid 335 through 356 removed outlier: 3.716A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.650A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 392 removed outlier: 4.198A pdb=" N PHE G 392 " --> pdb=" O ASP G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.743A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.806A pdb=" N PHE F 522 " --> pdb=" O VAL F 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.994A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 6.262A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 587 " --> pdb=" O ILE F 583 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.643A pdb=" N ILE F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 637 removed outlier: 3.666A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN F 637 " --> pdb=" O ARG F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 3.633A pdb=" N VAL F 648 " --> pdb=" O LYS F 644 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.322A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.553A pdb=" N GLN D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 4.088A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.190A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 523 removed outlier: 4.353A pdb=" N PHE J 519 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE J 522 " --> pdb=" O VAL J 518 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 523 " --> pdb=" O PHE J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 536 removed outlier: 3.518A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 removed outlier: 6.396A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 626 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.520A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP J 632 " --> pdb=" O TRP J 628 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG J 633 " --> pdb=" O MET J 629 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.508A pdb=" N VAL J 648 " --> pdb=" O LYS J 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 117 removed outlier: 3.538A pdb=" N LYS K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 356 removed outlier: 3.688A pdb=" N LYS K 348 " --> pdb=" O ARG K 344 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU K 351 " --> pdb=" O GLU K 347 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS K 352 " --> pdb=" O LYS K 348 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 388 through 392 removed outlier: 4.147A pdb=" N PHE K 392 " --> pdb=" O ASP K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 481 removed outlier: 4.161A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 removed outlier: 4.041A pdb=" N THR A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 517 through 523 removed outlier: 3.828A pdb=" N LEU N 523 " --> pdb=" O PHE N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 536 Processing helix chain 'N' and resid 569 through 596 removed outlier: 3.560A pdb=" N PHE N 573 " --> pdb=" O GLY N 569 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU N 576 " --> pdb=" O GLY N 572 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 636 removed outlier: 3.717A pdb=" N TRP N 631 " --> pdb=" O THR N 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP N 632 " --> pdb=" O TRP N 628 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG N 633 " --> pdb=" O MET N 629 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 659 removed outlier: 3.615A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA2, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.632A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.540A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.191A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AA6, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.844A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AA8, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.586A pdb=" N THR G 499 " --> pdb=" O TRP G 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.508A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.612A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.538A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 169 through 177 removed outlier: 4.281A pdb=" N SER G 158 " --> pdb=" O ASN G 130 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.674A pdb=" N VAL G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR G 435 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.825A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AB7, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.657A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.861A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR G 384 " --> pdb=" O ARG G 419 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 419 " --> pdb=" O TYR G 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.579A pdb=" N GLU B 23 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 18 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 82 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 20 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 70 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.507A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 33 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 35 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.532A pdb=" N CYS C 23 " --> pdb=" O TYR C 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'C' and resid 53 through 54 removed outlier: 7.039A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 87 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.664A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AC9, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.510A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.970A pdb=" N ASN D 130 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER D 158 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 170 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'D' and resid 394 through 395 removed outlier: 3.500A pdb=" N PHE D 361 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 292 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN D 332 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 419 " --> pdb=" O TYR D 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 384 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 259 through 261 removed outlier: 3.998A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 271 through 274 Processing sheet with id=AD6, first strand: chain 'D' and resid 444 through 445 Processing sheet with id=AD7, first strand: chain 'D' and resid 305 through 312 removed outlier: 3.773A pdb=" N LYS D 305 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.998A pdb=" N THR E 110 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 90 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP E 37 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 18 through 24 removed outlier: 3.857A pdb=" N VAL E 18 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 82 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.988A pdb=" N GLN I 24 " --> pdb=" O THR I 5 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.882A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 53 through 54 removed outlier: 7.060A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 53 through 54 removed outlier: 7.060A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR I 86 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 35 through 36 Processing sheet with id=AE6, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AE7, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AE8, first strand: chain 'K' and resid 75 through 76 removed outlier: 3.900A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE K 53 " --> pdb=" O CYS K 218 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.173A pdb=" N PHE K 93 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 130 through 131 removed outlier: 3.883A pdb=" N ASN K 130 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER K 158 " --> pdb=" O ASN K 130 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 161 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG K 170 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 181 through 183 Processing sheet with id=AF3, first strand: chain 'K' and resid 200 through 203 removed outlier: 6.691A pdb=" N VAL K 200 " --> pdb=" O ALA K 433 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR K 435 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET K 434 " --> pdb=" O ILE K 424 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.784A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS K 445 " --> pdb=" O CYS K 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.829A pdb=" N ILE K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS K 394 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AF7, first strand: chain 'K' and resid 332 through 334 Processing sheet with id=AF8, first strand: chain 'K' and resid 377 through 378 removed outlier: 4.423A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR K 384 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG K 419 " --> pdb=" O TYR K 384 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.103A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 82 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 77 " --> pdb=" O HIS A 71A" (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 81 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.503A pdb=" N ALA A 10 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 110 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 107 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 90 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.503A pdb=" N ALA A 10 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 110 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 107 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 90 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.525A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP M 67 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN M 72 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG M 65 " --> pdb=" O ASN M 72 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.949A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1527 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: 3.30 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3520 1.32 - 1.45: 6391 1.45 - 1.58: 11851 1.58 - 1.70: 2 1.70 - 1.83: 166 Bond restraints: 21930 Sorted by residual: bond pdb=" OH TYS H 100A" pdb=" S TYS H 100A" ideal model delta sigma weight residual 1.679 1.564 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CA TYR C 91 " pdb=" C TYR C 91 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.34e-02 5.57e+03 2.29e+01 bond pdb=" OH TYS H 100C" pdb=" S TYS H 100C" ideal model delta sigma weight residual 1.679 1.600 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" N THR D 358 " pdb=" CA THR D 358 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" N GLU G 190 " pdb=" CA GLU G 190 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.25e-02 6.40e+03 1.23e+01 ... (remaining 21925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 28989 2.06 - 4.12: 667 4.12 - 6.18: 119 6.18 - 8.24: 7 8.24 - 10.30: 4 Bond angle restraints: 29786 Sorted by residual: angle pdb=" C ASN D 262 " pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " ideal model delta sigma weight residual 115.89 105.59 10.30 1.32e+00 5.74e-01 6.09e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" O TYR C 91 " ideal model delta sigma weight residual 120.51 111.88 8.63 1.43e+00 4.89e-01 3.64e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLU C 96 " ideal model delta sigma weight residual 116.84 125.45 -8.61 1.71e+00 3.42e-01 2.54e+01 angle pdb=" CA PRO G 214 " pdb=" C PRO G 214 " pdb=" O PRO G 214 " ideal model delta sigma weight residual 121.36 115.89 5.47 1.13e+00 7.83e-01 2.34e+01 angle pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " pdb=" CG ASN D 262 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 29781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 13077 21.73 - 43.47: 917 43.47 - 65.20: 178 65.20 - 86.93: 55 86.93 - 108.67: 24 Dihedral angle restraints: 14251 sinusoidal: 6948 harmonic: 7303 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.44 -73.44 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual -86.00 -141.05 55.05 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS D 218 " pdb=" SG CYS D 218 " pdb=" SG CYS D 247 " pdb=" CB CYS D 247 " ideal model delta sinusoidal sigma weight residual -86.00 -136.25 50.25 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 14248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3468 0.134 - 0.267: 58 0.267 - 0.401: 10 0.401 - 0.535: 1 0.535 - 0.669: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA THR G 209 " pdb=" N THR G 209 " pdb=" C THR G 209 " pdb=" CB THR G 209 " both_signs ideal model delta sigma weight residual False 2.53 2.94 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA LEU D 261 " pdb=" N LEU D 261 " pdb=" C LEU D 261 " pdb=" CB LEU D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 3535 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 262 " 0.041 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN D 262 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 262 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 262 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 252 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 253 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 208 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL G 208 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL G 208 " 0.023 2.00e-02 2.50e+03 pdb=" N THR G 209 " 0.020 2.00e-02 2.50e+03 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 232 2.58 - 3.16: 18061 3.16 - 3.74: 29802 3.74 - 4.32: 41891 4.32 - 4.90: 70675 Nonbonded interactions: 160661 Sorted by model distance: nonbonded pdb=" OD2 ASP G 457 " pdb=" OG1 THR G 467 " model vdw 2.003 3.040 nonbonded pdb=" O THR G 209 " pdb=" OG1 THR G 209 " model vdw 2.160 3.040 nonbonded pdb=" O PRO C 8 " pdb=" OG SER C 9 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG I 66 " pdb=" O7 NAG U 2 " model vdw 2.233 3.120 nonbonded pdb=" O SER N 612 " pdb=" ND2 ASN N 616 " model vdw 2.245 3.120 ... (remaining 160656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 104 or resid 301)) selection = (chain 'I' and (resid 1 through 104 or resid 301)) selection = chain 'M' } ncs_group { reference = (chain 'D' and (resid 33 through 503 or resid 603 through 615)) selection = (chain 'G' and (resid 33 through 397 or resid 410 through 503 or resid 603 throu \ gh 615)) selection = (chain 'K' and (resid 33 through 397 or resid 410 through 613)) } ncs_group { reference = (chain 'F' and resid 516 through 702) selection = (chain 'J' and (resid 516 through 657 or resid 701 through 702)) selection = (chain 'N' and (resid 516 through 657 or resid 701 through 702)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.260 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.005 0.115 22066 Z= 0.250 Angle : 0.739 18.253 30154 Z= 0.373 Chirality : 0.054 0.669 3538 Planarity : 0.003 0.094 3686 Dihedral : 15.508 108.667 9435 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 0.76 % Allowed : 0.45 % Favored : 98.79 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.18), residues: 2475 helix: 1.78 (0.32), residues: 318 sheet: 0.17 (0.22), residues: 609 loop : -0.71 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 308 TYR 0.028 0.001 TYR C 91 PHE 0.010 0.001 PHE A 73 TRP 0.015 0.001 TRP D 479 HIS 0.003 0.000 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00465 (21930) covalent geometry : angle 0.71826 (29786) SS BOND : bond 0.00246 ( 40) SS BOND : angle 1.23470 ( 80) hydrogen bonds : bond 0.29540 ( 579) hydrogen bonds : angle 9.69905 ( 1527) link_ALPHA1-3 : bond 0.00410 ( 7) link_ALPHA1-3 : angle 1.62043 ( 21) link_ALPHA1-6 : bond 0.00392 ( 6) link_ALPHA1-6 : angle 1.64341 ( 18) link_BETA1-4 : bond 0.00316 ( 17) link_BETA1-4 : angle 1.24510 ( 51) link_NAG-ASN : bond 0.00858 ( 66) link_NAG-ASN : angle 2.03077 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.705 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: H 82 LEU cc_start: 0.8135 (mp) cc_final: 0.7769 (tt) REVERT: F 612 SER cc_start: 0.8393 (m) cc_final: 0.8123 (p) REVERT: F 629 MET cc_start: 0.6769 (mmt) cc_final: 0.6160 (mmp) REVERT: E 4 LEU cc_start: 0.8323 (tp) cc_final: 0.7917 (tp) REVERT: N 595 MET cc_start: 0.7342 (ptm) cc_final: 0.6995 (ttp) REVERT: N 639 THR cc_start: 0.8111 (p) cc_final: 0.7733 (t) outliers start: 17 outliers final: 4 residues processed: 210 average time/residue: 0.1805 time to fit residues: 55.8758 Evaluate side-chains 103 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 ASN H 82AASN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN B 6 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 653 GLN D 105 HIS D 287 HIS D 330 HIS ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN K 377 ASN A 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.036137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029065 restraints weight = 187353.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.030003 restraints weight = 101906.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.030655 restraints weight = 68669.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031089 restraints weight = 52261.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.031376 restraints weight = 43187.039| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 22066 Z= 0.322 Angle : 0.826 11.609 30154 Z= 0.417 Chirality : 0.049 0.321 3538 Planarity : 0.005 0.059 3686 Dihedral : 10.318 79.159 4724 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.03 % Allowed : 8.37 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2475 helix: 1.13 (0.28), residues: 347 sheet: -0.09 (0.20), residues: 648 loop : -1.01 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 61 TYR 0.030 0.003 TYR N 643 PHE 0.022 0.002 PHE D 382 TRP 0.020 0.002 TRP N 631 HIS 0.007 0.001 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00680 (21930) covalent geometry : angle 0.79222 (29786) SS BOND : bond 0.00779 ( 40) SS BOND : angle 1.64518 ( 80) hydrogen bonds : bond 0.05821 ( 579) hydrogen bonds : angle 6.69486 ( 1527) link_ALPHA1-3 : bond 0.00589 ( 7) link_ALPHA1-3 : angle 2.52921 ( 21) link_ALPHA1-6 : bond 0.00600 ( 6) link_ALPHA1-6 : angle 2.24812 ( 18) link_BETA1-4 : bond 0.00586 ( 17) link_BETA1-4 : angle 2.05636 ( 51) link_NAG-ASN : bond 0.00528 ( 66) link_NAG-ASN : angle 2.47109 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.9032 (m-10) cc_final: 0.8810 (m-80) REVERT: H 96 LYS cc_start: 0.9595 (mtpt) cc_final: 0.9263 (mtpt) REVERT: G 100 MET cc_start: 0.8975 (mtm) cc_final: 0.8774 (mtm) REVERT: G 104 MET cc_start: 0.9026 (ttt) cc_final: 0.8589 (tmm) REVERT: G 434 MET cc_start: 0.8509 (mtt) cc_final: 0.8170 (mtt) REVERT: F 530 MET cc_start: 0.8496 (tpp) cc_final: 0.8030 (mmm) REVERT: D 377 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8711 (t0) REVERT: E 4 LEU cc_start: 0.7764 (tp) cc_final: 0.7131 (tp) REVERT: K 95 MET cc_start: 0.9313 (ppp) cc_final: 0.8903 (ppp) outliers start: 23 outliers final: 9 residues processed: 115 average time/residue: 0.1538 time to fit residues: 28.2809 Evaluate side-chains 93 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain M residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.028959 restraints weight = 185061.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.029913 restraints weight = 100155.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.030569 restraints weight = 67153.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.031032 restraints weight = 50916.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.031335 restraints weight = 41798.244| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22066 Z= 0.160 Angle : 0.633 8.846 30154 Z= 0.316 Chirality : 0.046 0.346 3538 Planarity : 0.004 0.043 3686 Dihedral : 9.248 73.276 4720 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.17 % Allowed : 10.71 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2475 helix: 1.47 (0.29), residues: 341 sheet: -0.00 (0.20), residues: 655 loop : -0.99 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.023 0.001 TYR E 99 PHE 0.019 0.001 PHE F 522 TRP 0.016 0.001 TRP F 631 HIS 0.003 0.001 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00355 (21930) covalent geometry : angle 0.60448 (29786) SS BOND : bond 0.00425 ( 40) SS BOND : angle 1.25852 ( 80) hydrogen bonds : bond 0.05057 ( 579) hydrogen bonds : angle 5.88091 ( 1527) link_ALPHA1-3 : bond 0.00945 ( 7) link_ALPHA1-3 : angle 1.93811 ( 21) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 2.15187 ( 18) link_BETA1-4 : bond 0.00430 ( 17) link_BETA1-4 : angle 1.62475 ( 51) link_NAG-ASN : bond 0.00324 ( 66) link_NAG-ASN : angle 1.99024 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 LYS cc_start: 0.9614 (mtpt) cc_final: 0.9218 (mtpt) REVERT: G 104 MET cc_start: 0.8968 (ttt) cc_final: 0.8541 (tmm) REVERT: G 302 MET cc_start: 0.8558 (mmp) cc_final: 0.8300 (mmp) REVERT: F 595 MET cc_start: 0.9175 (ttp) cc_final: 0.8647 (tmm) REVERT: E 80 MET cc_start: 0.9166 (tmm) cc_final: 0.8859 (tmm) REVERT: K 104 MET cc_start: 0.9634 (ttt) cc_final: 0.9108 (ttt) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.1324 time to fit residues: 24.9955 Evaluate side-chains 97 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 198 optimal weight: 0.0010 chunk 107 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.036354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029309 restraints weight = 182552.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.030292 restraints weight = 97096.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.030950 restraints weight = 64280.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031352 restraints weight = 48643.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031717 restraints weight = 40836.687| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 22066 Z= 0.114 Angle : 0.599 9.208 30154 Z= 0.298 Chirality : 0.045 0.353 3538 Planarity : 0.003 0.042 3686 Dihedral : 8.457 68.598 4720 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.94 % Allowed : 12.60 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2475 helix: 1.62 (0.29), residues: 335 sheet: 0.05 (0.20), residues: 656 loop : -0.92 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 61 TYR 0.018 0.001 TYR E 27 PHE 0.031 0.001 PHE F 522 TRP 0.015 0.001 TRP G 427 HIS 0.003 0.001 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00246 (21930) covalent geometry : angle 0.57068 (29786) SS BOND : bond 0.00489 ( 40) SS BOND : angle 1.31146 ( 80) hydrogen bonds : bond 0.04038 ( 579) hydrogen bonds : angle 5.52163 ( 1527) link_ALPHA1-3 : bond 0.01031 ( 7) link_ALPHA1-3 : angle 2.12459 ( 21) link_ALPHA1-6 : bond 0.00862 ( 6) link_ALPHA1-6 : angle 2.04467 ( 18) link_BETA1-4 : bond 0.00441 ( 17) link_BETA1-4 : angle 1.58360 ( 51) link_NAG-ASN : bond 0.00344 ( 66) link_NAG-ASN : angle 1.85179 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 LYS cc_start: 0.9605 (mtpt) cc_final: 0.9248 (mtpt) REVERT: G 104 MET cc_start: 0.8930 (ttt) cc_final: 0.8676 (tmt) REVERT: G 302 MET cc_start: 0.8542 (mmp) cc_final: 0.8297 (mmp) REVERT: F 595 MET cc_start: 0.9145 (ttp) cc_final: 0.7458 (tmm) REVERT: E 80 MET cc_start: 0.9180 (tmm) cc_final: 0.8928 (tmm) REVERT: K 95 MET cc_start: 0.9265 (ppp) cc_final: 0.8863 (ppp) REVERT: K 104 MET cc_start: 0.9571 (ttt) cc_final: 0.9090 (ttt) REVERT: K 499 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7688 (p) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.1399 time to fit residues: 25.1456 Evaluate side-chains 98 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 449 ILE Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain M residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.034712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.027803 restraints weight = 186267.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.028717 restraints weight = 101194.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.029328 restraints weight = 68003.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.029781 restraints weight = 51900.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.030095 restraints weight = 42615.591| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22066 Z= 0.195 Angle : 0.652 10.341 30154 Z= 0.322 Chirality : 0.046 0.329 3538 Planarity : 0.004 0.034 3686 Dihedral : 8.071 64.119 4718 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.07 % Allowed : 13.45 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2475 helix: 1.56 (0.29), residues: 343 sheet: -0.12 (0.19), residues: 714 loop : -1.00 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 61 TYR 0.023 0.002 TYR H 58 PHE 0.025 0.002 PHE F 522 TRP 0.040 0.002 TRP D 427 HIS 0.003 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00426 (21930) covalent geometry : angle 0.62409 (29786) SS BOND : bond 0.00384 ( 40) SS BOND : angle 1.46447 ( 80) hydrogen bonds : bond 0.03958 ( 579) hydrogen bonds : angle 5.33168 ( 1527) link_ALPHA1-3 : bond 0.00771 ( 7) link_ALPHA1-3 : angle 2.04817 ( 21) link_ALPHA1-6 : bond 0.00769 ( 6) link_ALPHA1-6 : angle 2.20942 ( 18) link_BETA1-4 : bond 0.00447 ( 17) link_BETA1-4 : angle 1.51588 ( 51) link_NAG-ASN : bond 0.00283 ( 66) link_NAG-ASN : angle 1.95189 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 LYS cc_start: 0.9615 (mtpt) cc_final: 0.9398 (mtpt) REVERT: G 302 MET cc_start: 0.8564 (mmp) cc_final: 0.8284 (mmp) REVERT: F 595 MET cc_start: 0.9034 (ttp) cc_final: 0.8511 (ttp) REVERT: F 647 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8805 (tp30) REVERT: D 358 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8174 (p) REVERT: D 377 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8874 (t0) REVERT: E 4 LEU cc_start: 0.8811 (tp) cc_final: 0.8586 (tp) REVERT: E 80 MET cc_start: 0.9220 (tmm) cc_final: 0.8914 (tmm) REVERT: I 45 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8763 (ttmt) REVERT: K 95 MET cc_start: 0.9378 (ppp) cc_final: 0.8915 (ppp) REVERT: K 104 MET cc_start: 0.9593 (ttt) cc_final: 0.9059 (ttt) REVERT: A 101 ASP cc_start: 0.9089 (t0) cc_final: 0.8767 (m-30) outliers start: 46 outliers final: 23 residues processed: 118 average time/residue: 0.1283 time to fit residues: 25.3161 Evaluate side-chains 103 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 449 ILE Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN F 616 ASN D 397 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.026118 restraints weight = 190771.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026982 restraints weight = 102514.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027571 restraints weight = 68831.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.027994 restraints weight = 52428.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.028271 restraints weight = 43239.024| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 22066 Z= 0.316 Angle : 0.788 8.456 30154 Z= 0.389 Chirality : 0.048 0.323 3538 Planarity : 0.005 0.044 3686 Dihedral : 8.320 59.301 4718 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.74 % Allowed : 13.95 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.98 (0.17), residues: 2475 helix: 1.23 (0.28), residues: 341 sheet: -0.56 (0.19), residues: 737 loop : -1.17 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.021 0.002 TYR K 217 PHE 0.032 0.002 PHE K 53 TRP 0.058 0.002 TRP G 479 HIS 0.013 0.002 HIS K 216 Details of bonding type rmsd covalent geometry : bond 0.00689 (21930) covalent geometry : angle 0.75462 (29786) SS BOND : bond 0.00550 ( 40) SS BOND : angle 1.99112 ( 80) hydrogen bonds : bond 0.04415 ( 579) hydrogen bonds : angle 5.64487 ( 1527) link_ALPHA1-3 : bond 0.00684 ( 7) link_ALPHA1-3 : angle 2.34829 ( 21) link_ALPHA1-6 : bond 0.00829 ( 6) link_ALPHA1-6 : angle 2.51274 ( 18) link_BETA1-4 : bond 0.00526 ( 17) link_BETA1-4 : angle 1.68186 ( 51) link_NAG-ASN : bond 0.00412 ( 66) link_NAG-ASN : angle 2.33477 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 78 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.9672 (OUTLIER) cc_final: 0.9034 (p0) REVERT: G 100 MET cc_start: 0.9174 (mtm) cc_final: 0.8965 (mtm) REVERT: G 104 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8386 (tmm) REVERT: G 297 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (p) REVERT: F 595 MET cc_start: 0.8989 (ttp) cc_final: 0.8326 (tmm) REVERT: E 4 LEU cc_start: 0.8724 (tp) cc_final: 0.8461 (tp) REVERT: E 80 MET cc_start: 0.9260 (tmm) cc_final: 0.9003 (tmm) REVERT: K 95 MET cc_start: 0.9398 (ppp) cc_final: 0.8278 (ppp) REVERT: K 104 MET cc_start: 0.9631 (ttt) cc_final: 0.9047 (ttt) REVERT: K 480 ARG cc_start: 0.9474 (OUTLIER) cc_final: 0.8586 (mtm-85) outliers start: 61 outliers final: 38 residues processed: 132 average time/residue: 0.1279 time to fit residues: 28.6642 Evaluate side-chains 110 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 68 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 229 ASN Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 255 VAL Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 475 MET Chi-restraints excluded: chain K residue 480 ARG Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 47 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 ASN E 56 GLN I 77 ASN I 79 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.033637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.026883 restraints weight = 186556.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027766 restraints weight = 100022.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.028374 restraints weight = 66985.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.028807 restraints weight = 50887.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.029094 restraints weight = 41873.083| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22066 Z= 0.144 Angle : 0.651 8.778 30154 Z= 0.320 Chirality : 0.046 0.333 3538 Planarity : 0.003 0.039 3686 Dihedral : 7.806 59.416 4717 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.53 % Allowed : 15.79 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.75 (0.17), residues: 2475 helix: 1.61 (0.29), residues: 334 sheet: -0.42 (0.19), residues: 744 loop : -1.07 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 61 TYR 0.021 0.001 TYR E 27 PHE 0.026 0.001 PHE F 522 TRP 0.021 0.001 TRP D 427 HIS 0.002 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00320 (21930) covalent geometry : angle 0.62088 (29786) SS BOND : bond 0.00483 ( 40) SS BOND : angle 1.63319 ( 80) hydrogen bonds : bond 0.03750 ( 579) hydrogen bonds : angle 5.26117 ( 1527) link_ALPHA1-3 : bond 0.00814 ( 7) link_ALPHA1-3 : angle 2.00629 ( 21) link_ALPHA1-6 : bond 0.00968 ( 6) link_ALPHA1-6 : angle 2.14163 ( 18) link_BETA1-4 : bond 0.00404 ( 17) link_BETA1-4 : angle 1.45895 ( 51) link_NAG-ASN : bond 0.00273 ( 66) link_NAG-ASN : angle 2.02735 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.792 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: H 34 MET cc_start: 0.8739 (mmp) cc_final: 0.8491 (mmp) REVERT: H 82 MET cc_start: 0.9090 (mpp) cc_final: 0.8450 (mpp) REVERT: G 100 MET cc_start: 0.9103 (mtm) cc_final: 0.8885 (mtm) REVERT: G 104 MET cc_start: 0.8891 (ttt) cc_final: 0.8444 (tmm) REVERT: G 302 MET cc_start: 0.8690 (mmp) cc_final: 0.8093 (mmp) REVERT: E 80 MET cc_start: 0.9227 (tmm) cc_final: 0.8880 (tmm) REVERT: K 95 MET cc_start: 0.9390 (ppp) cc_final: 0.8903 (ppp) REVERT: K 104 MET cc_start: 0.9602 (ttt) cc_final: 0.9101 (ttt) REVERT: K 302 MET cc_start: 0.8926 (mmm) cc_final: 0.8723 (mmp) REVERT: A 101 ASP cc_start: 0.9093 (t0) cc_final: 0.8799 (m-30) REVERT: N 629 MET cc_start: 0.9279 (tpp) cc_final: 0.8875 (tpp) outliers start: 34 outliers final: 27 residues processed: 109 average time/residue: 0.1350 time to fit residues: 24.6662 Evaluate side-chains 100 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 478 ASN C 6 GLN E 56 GLN K 72 HIS ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.032368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.025669 restraints weight = 193201.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.026513 restraints weight = 103495.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.027096 restraints weight = 69386.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.027503 restraints weight = 53039.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.027726 restraints weight = 43913.158| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 22066 Z= 0.317 Angle : 0.785 8.385 30154 Z= 0.384 Chirality : 0.048 0.300 3538 Planarity : 0.004 0.040 3686 Dihedral : 8.070 59.555 4717 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.02 % Allowed : 15.61 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 2475 helix: 1.24 (0.28), residues: 341 sheet: -0.56 (0.19), residues: 746 loop : -1.21 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.015 0.002 TYR C 91 PHE 0.024 0.002 PHE F 522 TRP 0.028 0.002 TRP D 427 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00693 (21930) covalent geometry : angle 0.75284 (29786) SS BOND : bond 0.00479 ( 40) SS BOND : angle 1.88701 ( 80) hydrogen bonds : bond 0.04251 ( 579) hydrogen bonds : angle 5.56638 ( 1527) link_ALPHA1-3 : bond 0.00649 ( 7) link_ALPHA1-3 : angle 2.31410 ( 21) link_ALPHA1-6 : bond 0.00812 ( 6) link_ALPHA1-6 : angle 2.30444 ( 18) link_BETA1-4 : bond 0.00551 ( 17) link_BETA1-4 : angle 1.71528 ( 51) link_NAG-ASN : bond 0.00436 ( 66) link_NAG-ASN : angle 2.31635 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 68 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9077 (mp) cc_final: 0.8774 (tp) REVERT: G 104 MET cc_start: 0.9016 (ttt) cc_final: 0.8526 (tmm) REVERT: G 297 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8257 (p) REVERT: G 302 MET cc_start: 0.8596 (mmp) cc_final: 0.8010 (mmp) REVERT: F 610 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8209 (m100) REVERT: E 4 LEU cc_start: 0.8519 (tp) cc_final: 0.7908 (tp) REVERT: K 95 MET cc_start: 0.9382 (ppp) cc_final: 0.8312 (ppp) REVERT: K 104 MET cc_start: 0.9626 (ttt) cc_final: 0.9035 (ttt) REVERT: K 467 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8571 (p) outliers start: 45 outliers final: 35 residues processed: 111 average time/residue: 0.1192 time to fit residues: 22.4526 Evaluate side-chains 103 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 491 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 69 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 236 optimal weight: 0.0050 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN E 56 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** 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 = 0.2985 r_free = 0.2985 target = 0.033781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.027014 restraints weight = 186565.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027905 restraints weight = 99786.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.028525 restraints weight = 66597.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.028910 restraints weight = 50599.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.029226 restraints weight = 42407.057| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22066 Z= 0.116 Angle : 0.649 10.588 30154 Z= 0.318 Chirality : 0.046 0.346 3538 Planarity : 0.003 0.043 3686 Dihedral : 7.328 57.993 4717 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.53 % Allowed : 16.46 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.74 (0.17), residues: 2475 helix: 1.63 (0.29), residues: 338 sheet: -0.44 (0.19), residues: 744 loop : -1.05 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 61 TYR 0.017 0.001 TYR E 27 PHE 0.027 0.001 PHE F 522 TRP 0.026 0.002 TRP D 427 HIS 0.003 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00256 (21930) covalent geometry : angle 0.62288 (29786) SS BOND : bond 0.00496 ( 40) SS BOND : angle 1.49733 ( 80) hydrogen bonds : bond 0.03535 ( 579) hydrogen bonds : angle 5.11441 ( 1527) link_ALPHA1-3 : bond 0.00806 ( 7) link_ALPHA1-3 : angle 1.82927 ( 21) link_ALPHA1-6 : bond 0.01129 ( 6) link_ALPHA1-6 : angle 1.61298 ( 18) link_BETA1-4 : bond 0.00405 ( 17) link_BETA1-4 : angle 1.41835 ( 51) link_NAG-ASN : bond 0.00382 ( 66) link_NAG-ASN : angle 1.93682 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9064 (mp) cc_final: 0.8796 (tp) REVERT: G 104 MET cc_start: 0.8910 (ttt) cc_final: 0.8432 (tmm) REVERT: G 297 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8016 (t) REVERT: G 302 MET cc_start: 0.8556 (mmp) cc_final: 0.7904 (mmp) REVERT: G 427 TRP cc_start: 0.7048 (m100) cc_final: 0.6667 (m100) REVERT: F 610 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.8200 (m100) REVERT: D 104 MET cc_start: 0.8488 (ttp) cc_final: 0.8121 (ttp) REVERT: D 302 MET cc_start: 0.8581 (mmp) cc_final: 0.7609 (mmm) REVERT: E 4 LEU cc_start: 0.8481 (tp) cc_final: 0.7907 (tp) REVERT: E 80 MET cc_start: 0.9235 (tmm) cc_final: 0.8829 (tmm) REVERT: K 95 MET cc_start: 0.9345 (ppp) cc_final: 0.8846 (ppp) REVERT: K 104 MET cc_start: 0.9605 (ttt) cc_final: 0.9102 (ttt) outliers start: 34 outliers final: 27 residues processed: 112 average time/residue: 0.1335 time to fit residues: 25.2403 Evaluate side-chains 103 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 TYR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 197 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN H 82AASN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** 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 = 0.2960 r_free = 0.2960 target = 0.033147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.026432 restraints weight = 188403.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.027301 restraints weight = 100787.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027905 restraints weight = 67371.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.028272 restraints weight = 51184.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.028581 restraints weight = 43055.642| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22066 Z= 0.176 Angle : 0.656 9.036 30154 Z= 0.322 Chirality : 0.045 0.323 3538 Planarity : 0.004 0.042 3686 Dihedral : 7.263 59.239 4717 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.66 % Allowed : 16.73 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.67 (0.17), residues: 2475 helix: 1.77 (0.29), residues: 334 sheet: -0.40 (0.19), residues: 746 loop : -1.01 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 633 TYR 0.013 0.001 TYR E 27 PHE 0.025 0.001 PHE F 522 TRP 0.035 0.001 TRP D 427 HIS 0.002 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00392 (21930) covalent geometry : angle 0.62916 (29786) SS BOND : bond 0.00459 ( 40) SS BOND : angle 1.60260 ( 80) hydrogen bonds : bond 0.03594 ( 579) hydrogen bonds : angle 5.11024 ( 1527) link_ALPHA1-3 : bond 0.00660 ( 7) link_ALPHA1-3 : angle 1.94206 ( 21) link_ALPHA1-6 : bond 0.01055 ( 6) link_ALPHA1-6 : angle 1.50211 ( 18) link_BETA1-4 : bond 0.00458 ( 17) link_BETA1-4 : angle 1.44498 ( 51) link_NAG-ASN : bond 0.00267 ( 66) link_NAG-ASN : angle 1.96918 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9106 (mp) cc_final: 0.8842 (tp) REVERT: G 104 MET cc_start: 0.8952 (ttt) cc_final: 0.8474 (tmm) REVERT: G 297 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8076 (p) REVERT: G 302 MET cc_start: 0.8555 (mmp) cc_final: 0.7988 (mmp) REVERT: F 610 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.8176 (m100) REVERT: D 104 MET cc_start: 0.8557 (ttp) cc_final: 0.8340 (ttp) REVERT: E 4 LEU cc_start: 0.8715 (tp) cc_final: 0.8194 (tp) REVERT: E 80 MET cc_start: 0.9267 (tmm) cc_final: 0.8867 (tmm) REVERT: K 95 MET cc_start: 0.9336 (ppp) cc_final: 0.8243 (ppp) REVERT: K 104 MET cc_start: 0.9630 (ttt) cc_final: 0.9055 (ttt) REVERT: K 467 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8636 (p) outliers start: 37 outliers final: 28 residues processed: 108 average time/residue: 0.1302 time to fit residues: 23.7028 Evaluate side-chains 105 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 230 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 296 CYS Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain K residue 467 THR Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain N residue 618 THR Chi-restraints excluded: chain N residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 26 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.027035 restraints weight = 185877.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.027946 restraints weight = 97354.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028578 restraints weight = 64287.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.028957 restraints weight = 48328.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.029273 restraints weight = 40464.480| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22066 Z= 0.114 Angle : 0.620 8.807 30154 Z= 0.304 Chirality : 0.045 0.337 3538 Planarity : 0.003 0.040 3686 Dihedral : 6.774 55.662 4717 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.30 % Allowed : 17.18 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2475 helix: 1.73 (0.29), residues: 338 sheet: -0.25 (0.19), residues: 735 loop : -1.01 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 633 TYR 0.018 0.001 TYR E 27 PHE 0.026 0.001 PHE F 522 TRP 0.037 0.001 TRP D 427 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00253 (21930) covalent geometry : angle 0.59544 (29786) SS BOND : bond 0.00463 ( 40) SS BOND : angle 1.42861 ( 80) hydrogen bonds : bond 0.03298 ( 579) hydrogen bonds : angle 4.94696 ( 1527) link_ALPHA1-3 : bond 0.00718 ( 7) link_ALPHA1-3 : angle 1.71749 ( 21) link_ALPHA1-6 : bond 0.01269 ( 6) link_ALPHA1-6 : angle 1.20294 ( 18) link_BETA1-4 : bond 0.00434 ( 17) link_BETA1-4 : angle 1.37238 ( 51) link_NAG-ASN : bond 0.00327 ( 66) link_NAG-ASN : angle 1.84314 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.24 seconds wall clock time: 49 minutes 49.57 seconds (2989.57 seconds total)