Starting phenix.real_space_refine on Sat Jul 4 21:37:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zlk_14783/07_2026/7zlk_14783.cif" } resolution = 3.99 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= 0.001 sd= 0.032 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 141 5.16 5 C 14758 2.51 5 N 3941 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23518 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 954 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "Q" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "T" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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 chiralities: 7 Chain: "K" 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 chiralities: 4 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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 chiralities: 7 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "a" 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 chiralities: 3 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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 chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.50, per 1000 atoms: 0.23 Number of scatterers: 23518 At special positions: 0 Unit cell: (151.8, 151.8, 170.2, 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 141 16.00 O 4678 8.00 N 3941 7.00 C 14758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.19 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 86 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 7 " " MAN J 4 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 7 " " MAN c 4 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " " BMA K 3 " - " MAN K 4 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 188 " " NAG A 605 " - " ASN A 362 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 188 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 88 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 241 " " NAG D 604 " - " ASN D 289 " " NAG D 605 " - " ASN D 189 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 386 " " NAG D 608 " - " ASN D 88 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 448 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 301 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 980.6 milliseconds 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 19.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.044A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.053A pdb=" N ARG A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.995A pdb=" N GLN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 545 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 569 through 596 removed outlier: 5.482A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 631 through 649 removed outlier: 4.014A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.566A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.293A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 535 Processing helix chain 'E' and resid 536 through 545 removed outlier: 3.614A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.611A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.889A pdb=" N LYS D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.516A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 543 through 550 removed outlier: 3.879A pdb=" N VAL F 549 " --> pdb=" O LEU F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 556 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 652 through 662 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.599A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.648A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 77 through 81 Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.503A pdb=" N HIS S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 5.733A pdb=" N SER S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.298A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.917A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.860A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.170A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 310 removed outlier: 6.929A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.760A pdb=" N ARG C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.350A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.876A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 416 Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 310 removed outlier: 6.724A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.251A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.801A pdb=" N ARG D 66 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.714A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.614A pdb=" N HIS D 374 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.762A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.951A pdb=" N TYR M 33 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.078A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 8 through 11 removed outlier: 6.559A pdb=" N TRP N 33 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AE3, first strand: chain 'N' and resid 17 through 22 Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 8 Processing sheet with id=AE5, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.948A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.755A pdb=" N TRP Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.581A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'S' and resid 57 through 59 removed outlier: 6.677A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR S 33 " --> pdb=" O GLU S 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.606A pdb=" N TRP T 33 " --> pdb=" O VAL T 45 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 8 through 11 Processing sheet with id=AF9, first strand: chain 'T' and resid 17 through 22 889 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4525 1.32 - 1.46: 8381 1.46 - 1.60: 10899 1.60 - 1.75: 41 1.75 - 1.89: 181 Bond restraints: 24027 Sorted by residual: bond pdb=" N PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" CB HIS D 308 " pdb=" CG HIS D 308 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.29e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" CB LEU T 107 " pdb=" CG LEU T 107 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PHE Q 29 " pdb=" CG PHE Q 29 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 ... (remaining 24022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.10: 32374 6.10 - 12.20: 285 12.20 - 18.30: 8 18.30 - 24.40: 0 24.40 - 30.51: 1 Bond angle restraints: 32668 Sorted by residual: angle pdb=" N ASP S 101 " pdb=" CA ASP S 101 " pdb=" C ASP S 101 " ideal model delta sigma weight residual 109.81 140.32 -30.51 2.21e+00 2.05e-01 1.91e+02 angle pdb=" N PHE Q 29 " pdb=" CA PHE Q 29 " pdb=" C PHE Q 29 " ideal model delta sigma weight residual 113.02 127.64 -14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" N PHE H 29 " pdb=" CA PHE H 29 " pdb=" C PHE H 29 " ideal model delta sigma weight residual 113.02 126.23 -13.21 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N THR P 92 " pdb=" CA THR P 92 " pdb=" C THR P 92 " ideal model delta sigma weight residual 111.36 122.50 -11.14 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N PRO S 102 " pdb=" CA PRO S 102 " pdb=" C PRO S 102 " ideal model delta sigma weight residual 113.40 100.56 12.84 1.34e+00 5.57e-01 9.18e+01 ... (remaining 32663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13124 17.91 - 35.81: 354 35.81 - 53.72: 108 53.72 - 71.62: 41 71.62 - 89.53: 28 Dihedral angle restraints: 13655 sinusoidal: 5485 harmonic: 8170 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -164.40 78.40 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -163.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -140.56 54.56 1 1.00e+01 1.00e-02 4.03e+01 ... (remaining 13652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3091 0.141 - 0.283: 659 0.283 - 0.424: 152 0.424 - 0.565: 42 0.565 - 0.707: 2 Chirality restraints: 3946 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 3943 not shown) Planarity restraints: 4037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.314 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG b 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 608 " 0.254 2.00e-02 2.50e+03 2.10e-01 5.53e+02 pdb=" C7 NAG D 608 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG D 608 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 608 " -0.347 2.00e-02 2.50e+03 pdb=" O7 NAG D 608 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 603 " 0.225 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG D 603 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 603 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG D 603 " -0.315 2.00e-02 2.50e+03 pdb=" O7 NAG D 603 " 0.176 2.00e-02 2.50e+03 ... (remaining 4034 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7414 2.86 - 3.37: 21544 3.37 - 3.88: 39653 3.88 - 4.39: 45561 4.39 - 4.90: 72660 Nonbonded interactions: 186832 Sorted by model distance: nonbonded pdb=" O PHE S 100H" pdb=" NE1 TRP S 103 " model vdw 2.348 3.120 nonbonded pdb=" N ALA F 541 " pdb=" O ALA F 541 " model vdw 2.357 2.496 nonbonded pdb=" N ALA B 533 " pdb=" N SER B 534 " model vdw 2.375 2.560 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 429 " model vdw 2.380 3.120 nonbonded pdb=" NZ LYS D 500 " pdb=" OD2 ASP N 51 " model vdw 2.394 3.120 ... (remaining 186827 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 'C' and resid 35 through 605) selection = (chain 'D' and resid 35 through 605) } ncs_group { reference = (chain 'B' and (resid 523 through 558 or resid 569 through 651)) selection = (chain 'E' and resid 523 through 651) selection = (chain 'F' and resid 523 through 651) } ncs_group { reference = chain 'G' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 7)) selection = (chain 'X' and (resid 1 or resid 4 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 7)) selection = (chain 'd' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'M' and resid 1 through 108) selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } 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: 1.890 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.670 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.022 0.155 24168 Z= 1.154 Angle : 1.889 30.506 33048 Z= 1.219 Chirality : 0.131 0.707 3946 Planarity : 0.011 0.273 4000 Dihedral : 10.605 89.531 8264 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.44 % Favored : 99.48 % 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: 0.34 (0.15), residues: 2780 helix: -0.23 (0.23), residues: 387 sheet: 0.75 (0.16), residues: 844 loop : 0.16 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 469 TYR 0.062 0.009 TYR T 48 PHE 0.050 0.007 PHE M 52 TRP 0.067 0.011 TRP O 47 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02141 / 1.13 (24027) covalent geometry : angle 1.84932 / 1.22 (32668) SS BOND : bond 0.02853 / 1.55 ( 43) SS BOND : angle 3.16760 / 2.13 ( 86) hydrogen bonds : bond 0.16644 / 11.04 ( 842) hydrogen bonds : angle 7.63685 / 5.31 ( 2214) link_ALPHA1-2 : bond 0.08518 / 4.48 ( 1) link_ALPHA1-2 : angle 7.57404 / 3.99 ( 3) link_ALPHA1-3 : bond 0.08828 / 4.90 ( 15) link_ALPHA1-3 : angle 5.33909 / 3.80 ( 45) link_ALPHA1-6 : bond 0.05772 / 3.18 ( 16) link_ALPHA1-6 : angle 3.21648 / 2.17 ( 48) link_BETA1-4 : bond 0.07357 / 4.77 ( 29) link_BETA1-4 : angle 5.36914 / 3.71 ( 87) link_NAG-ASN : bond 0.07577 / 4.74 ( 37) link_NAG-ASN : angle 2.84058 / 1.90 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 872 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8654 (t) cc_final: 0.8402 (p) REVERT: A 78 ASP cc_start: 0.8378 (m-30) cc_final: 0.7793 (t70) REVERT: A 95 MET cc_start: 0.8766 (ptt) cc_final: 0.8552 (ppp) REVERT: A 180 ASP cc_start: 0.8380 (m-30) cc_final: 0.8171 (m-30) REVERT: A 284 ILE cc_start: 0.8443 (mt) cc_final: 0.8047 (tt) REVERT: A 368 ASP cc_start: 0.8253 (t0) cc_final: 0.7971 (t0) REVERT: A 387 THR cc_start: 0.8315 (p) cc_final: 0.8027 (t) REVERT: A 426 MET cc_start: 0.6826 (mtp) cc_final: 0.6426 (mtm) REVERT: B 523 LEU cc_start: 0.8850 (mt) cc_final: 0.8550 (mt) REVERT: B 530 MET cc_start: 0.3290 (mmp) cc_final: 0.2890 (mmp) REVERT: B 624 ASN cc_start: 0.6565 (m-40) cc_final: 0.5289 (t0) REVERT: B 631 TRP cc_start: 0.6428 (m-10) cc_final: 0.6209 (m-10) REVERT: C 42 VAL cc_start: 0.9391 (t) cc_final: 0.9187 (p) REVERT: C 68 VAL cc_start: 0.9051 (p) cc_final: 0.8729 (p) REVERT: C 103 GLN cc_start: 0.8420 (tp40) cc_final: 0.7819 (tm-30) REVERT: C 165 ILE cc_start: 0.8294 (mt) cc_final: 0.8026 (mm) REVERT: C 370 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 419 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7883 (mtp180) REVERT: E 530 MET cc_start: 0.8202 (mtp) cc_final: 0.7730 (mtm) REVERT: E 601 LYS cc_start: 0.8309 (mttt) cc_final: 0.7624 (mtmt) REVERT: E 618 SER cc_start: 0.8218 (m) cc_final: 0.7983 (p) REVERT: E 639 THR cc_start: 0.8432 (m) cc_final: 0.7565 (t) REVERT: E 644 ASN cc_start: 0.8448 (m-40) cc_final: 0.8171 (t0) REVERT: E 648 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 92 ASN cc_start: 0.7693 (t0) cc_final: 0.7463 (t0) REVERT: D 198 THR cc_start: 0.8509 (m) cc_final: 0.8256 (p) REVERT: D 246 GLN cc_start: 0.7241 (mp10) cc_final: 0.5895 (tp40) REVERT: D 434 MET cc_start: 0.8221 (ttm) cc_final: 0.7993 (ttp) REVERT: D 468 PHE cc_start: 0.7609 (m-80) cc_final: 0.6957 (m-80) REVERT: F 540 GLN cc_start: 0.8985 (tp40) cc_final: 0.8490 (tp40) REVERT: F 545 LEU cc_start: 0.9009 (tp) cc_final: 0.8491 (tt) REVERT: F 601 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8716 (mmtp) REVERT: F 623 TRP cc_start: 0.9149 (m100) cc_final: 0.8679 (m100) REVERT: H 81 LYS cc_start: 0.8180 (tttt) cc_final: 0.7917 (mmtm) REVERT: H 82 MET cc_start: 0.6850 (tpp) cc_final: 0.6323 (tpp) REVERT: H 93 VAL cc_start: 0.8808 (t) cc_final: 0.8207 (m) REVERT: H 110 LEU cc_start: 0.8435 (tp) cc_final: 0.8227 (tp) REVERT: L 27 GLN cc_start: 0.7333 (tp-100) cc_final: 0.7044 (tm-30) REVERT: L 27 LEU cc_start: 0.8126 (mt) cc_final: 0.7793 (mt) REVERT: L 61 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: L 97 THR cc_start: 0.8924 (t) cc_final: 0.8682 (t) REVERT: M 72 ASP cc_start: 0.7924 (t0) cc_final: 0.7412 (t0) REVERT: M 86 ASP cc_start: 0.8215 (m-30) cc_final: 0.7948 (m-30) REVERT: M 91 TYR cc_start: 0.7775 (m-80) cc_final: 0.7539 (m-80) REVERT: M 100 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8374 (tt0) REVERT: N 44 LEU cc_start: 0.6950 (tp) cc_final: 0.6717 (tp) REVERT: N 49 ASP cc_start: 0.8065 (m-30) cc_final: 0.7801 (m-30) REVERT: N 52 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7201 (mtp-110) REVERT: N 60 PHE cc_start: 0.7893 (m-80) cc_final: 0.7236 (m-80) REVERT: N 70 THR cc_start: 0.8612 (m) cc_final: 0.8336 (t) REVERT: N 81 GLU cc_start: 0.8825 (tt0) cc_final: 0.8517 (mm-30) REVERT: N 83 ASP cc_start: 0.7982 (m-30) cc_final: 0.7403 (p0) REVERT: N 87 GLN cc_start: 0.8709 (tt0) cc_final: 0.8287 (tt0) REVERT: N 93 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8442 (ttp-110) REVERT: N 94 ASP cc_start: 0.8326 (m-30) cc_final: 0.7899 (m-30) REVERT: O 6 GLN cc_start: 0.7551 (pt0) cc_final: 0.6692 (pt0) REVERT: O 59 TYR cc_start: 0.6178 (m-80) cc_final: 0.5782 (m-80) REVERT: O 82 MET cc_start: 0.6546 (mtp) cc_final: 0.5871 (mmm) REVERT: O 100 MET cc_start: 0.8657 (mtp) cc_final: 0.7665 (ttm) REVERT: O 105 HIS cc_start: 0.7594 (p-80) cc_final: 0.7289 (m-70) REVERT: P 27 GLN cc_start: 0.6966 (mt0) cc_final: 0.6747 (mp10) REVERT: P 51 ILE cc_start: 0.7580 (mm) cc_final: 0.7349 (mm) REVERT: P 71 PHE cc_start: 0.8016 (m-80) cc_final: 0.7583 (m-10) REVERT: P 100 GLN cc_start: 0.7358 (pm20) cc_final: 0.7017 (pm20) REVERT: Q 36 TRP cc_start: 0.8691 (m100) cc_final: 0.7928 (m100) REVERT: Q 93 VAL cc_start: 0.9275 (t) cc_final: 0.9059 (m) REVERT: Q 100 MET cc_start: 0.8336 (mtp) cc_final: 0.7800 (mmt) REVERT: R 27 HIS cc_start: 0.8061 (t-90) cc_final: 0.7614 (t70) REVERT: R 38 GLN cc_start: 0.8105 (tt0) cc_final: 0.7692 (tm-30) REVERT: S 4 LEU cc_start: 0.8282 (mt) cc_final: 0.7907 (mp) REVERT: S 24 VAL cc_start: 0.8303 (t) cc_final: 0.7097 (t) REVERT: S 37 ILE cc_start: 0.7477 (mt) cc_final: 0.6989 (mm) REVERT: S 58 ASN cc_start: 0.7426 (t0) cc_final: 0.7120 (t0) REVERT: S 72 ASP cc_start: 0.7284 (t0) cc_final: 0.7042 (t0) REVERT: S 75 LYS cc_start: 0.8982 (mttt) cc_final: 0.8764 (mtmm) REVERT: S 78 PHE cc_start: 0.5581 (m-80) cc_final: 0.4675 (m-80) REVERT: S 107 THR cc_start: 0.8256 (t) cc_final: 0.7964 (p) REVERT: T 45 VAL cc_start: 0.8098 (t) cc_final: 0.7665 (t) outliers start: 2 outliers final: 1 residues processed: 874 average time/residue: 0.1797 time to fit residues: 232.0114 Evaluate side-chains 441 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN B 577 GLN C 195 ASN C 249 HIS C 425 ASN E 616 ASN E 653 GLN D 203 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 653 GLN H 6 GLN L 37 GLN N 25 ASN N 35 GLN O 100 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100CASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.114474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086526 restraints weight = 64437.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.089260 restraints weight = 38846.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089938 restraints weight = 25866.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090361 restraints weight = 24347.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090570 restraints weight = 22025.255| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24168 Z= 0.189 Angle : 0.862 19.836 33048 Z= 0.431 Chirality : 0.052 0.416 3946 Planarity : 0.005 0.057 4000 Dihedral : 5.870 46.512 3042 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.73 % Allowed : 11.81 % Favored : 85.46 % 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: 0.25 (0.15), residues: 2780 helix: 0.70 (0.26), residues: 391 sheet: 0.47 (0.16), residues: 896 loop : -0.06 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 100F TYR 0.031 0.002 TYR L 49 PHE 0.036 0.003 PHE C 277 TRP 0.022 0.002 TRP A 338 HIS 0.012 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (24027) covalent geometry : angle 0.81486 / 0.42 (32668) SS BOND : bond 0.00350 / 0.25 ( 43) SS BOND : angle 1.41145 / 1.00 ( 86) hydrogen bonds : bond 0.05729 / 3.83 ( 842) hydrogen bonds : angle 6.01196 / 4.15 ( 2214) link_ALPHA1-2 : bond 0.00509 / 0.27 ( 1) link_ALPHA1-2 : angle 5.79149 / 3.07 ( 3) link_ALPHA1-3 : bond 0.01195 / 0.64 ( 15) link_ALPHA1-3 : angle 2.61201 / 1.92 ( 45) link_ALPHA1-6 : bond 0.01080 / 0.58 ( 16) link_ALPHA1-6 : angle 1.64119 / 1.12 ( 48) link_BETA1-4 : bond 0.01547 / 0.86 ( 29) link_BETA1-4 : angle 3.91557 / 2.74 ( 87) link_NAG-ASN : bond 0.00777 / 0.47 ( 37) link_NAG-ASN : angle 2.74043 / 1.79 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 581 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8344 (m100) cc_final: 0.7660 (m100) REVERT: A 180 ASP cc_start: 0.8432 (m-30) cc_final: 0.8061 (m-30) REVERT: A 426 MET cc_start: 0.6126 (mtp) cc_final: 0.5346 (mtp) REVERT: B 530 MET cc_start: 0.2869 (mmp) cc_final: 0.2388 (mmt) REVERT: B 535 MET cc_start: 0.8398 (mmm) cc_final: 0.8167 (mmt) REVERT: B 588 ARG cc_start: 0.8933 (tmm-80) cc_final: 0.8648 (ttm-80) REVERT: B 601 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8251 (mmmm) REVERT: C 75 VAL cc_start: 0.8789 (p) cc_final: 0.8477 (m) REVERT: C 95 MET cc_start: 0.8603 (ptp) cc_final: 0.8363 (ptp) REVERT: C 112 TRP cc_start: 0.8111 (m100) cc_final: 0.7645 (m100) REVERT: C 180 ASP cc_start: 0.8825 (m-30) cc_final: 0.8544 (t0) REVERT: C 342 LEU cc_start: 0.9045 (mt) cc_final: 0.8827 (tp) REVERT: C 434 MET cc_start: 0.8892 (ttp) cc_final: 0.8611 (ttp) REVERT: E 601 LYS cc_start: 0.8396 (mttt) cc_final: 0.7902 (mtmt) REVERT: E 618 SER cc_start: 0.7641 (m) cc_final: 0.7163 (p) REVERT: E 620 ASP cc_start: 0.8678 (p0) cc_final: 0.8340 (p0) REVERT: E 627 THR cc_start: 0.8809 (p) cc_final: 0.8580 (p) REVERT: E 631 TRP cc_start: 0.8812 (t-100) cc_final: 0.8605 (t-100) REVERT: E 639 THR cc_start: 0.8580 (m) cc_final: 0.7687 (p) REVERT: E 644 ASN cc_start: 0.8318 (m-40) cc_final: 0.8021 (m-40) REVERT: E 646 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8386 (mm) REVERT: E 647 GLU cc_start: 0.7479 (pp20) cc_final: 0.7012 (pp20) REVERT: E 648 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8187 (mt-10) REVERT: D 116 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8805 (mp) REVERT: D 373 MET cc_start: 0.7537 (mtm) cc_final: 0.6898 (mtp) REVERT: D 425 ASN cc_start: 0.8485 (p0) cc_final: 0.7960 (p0) REVERT: D 468 PHE cc_start: 0.7584 (m-80) cc_final: 0.7251 (m-80) REVERT: F 601 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8630 (mmmm) REVERT: F 623 TRP cc_start: 0.8676 (m100) cc_final: 0.8404 (m100) REVERT: H 36 TRP cc_start: 0.8528 (m100) cc_final: 0.7239 (m100) REVERT: H 82 MET cc_start: 0.7160 (tpp) cc_final: 0.6400 (tpp) REVERT: L 4 MET cc_start: 0.6639 (mtm) cc_final: 0.6291 (mtm) REVERT: L 27 GLN cc_start: 0.7507 (tp-100) cc_final: 0.6933 (tm-30) REVERT: L 27 LEU cc_start: 0.8013 (mt) cc_final: 0.7480 (mt) REVERT: L 37 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7366 (pp30) REVERT: L 49 TYR cc_start: 0.7391 (p90) cc_final: 0.6927 (p90) REVERT: L 61 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: L 71 PHE cc_start: 0.8631 (m-80) cc_final: 0.8026 (m-80) REVERT: L 79 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7281 (tm-30) REVERT: L 94 PHE cc_start: 0.6390 (m-80) cc_final: 0.5922 (m-80) REVERT: L 96 TRP cc_start: 0.7556 (m-90) cc_final: 0.6246 (m-90) REVERT: M 72 ASP cc_start: 0.7910 (t0) cc_final: 0.7274 (t0) REVERT: M 86 ASP cc_start: 0.8036 (m-30) cc_final: 0.7753 (m-30) REVERT: M 87 THR cc_start: 0.9503 (t) cc_final: 0.9164 (m) REVERT: M 100 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8162 (mt-10) REVERT: M 100 MET cc_start: 0.6918 (ptp) cc_final: 0.6599 (mtt) REVERT: N 24 ASN cc_start: 0.8208 (t0) cc_final: 0.7703 (t0) REVERT: N 25 ASN cc_start: 0.8217 (m-40) cc_final: 0.7879 (m110) REVERT: N 34 TYR cc_start: 0.8204 (m-80) cc_final: 0.7760 (m-10) REVERT: N 36 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7301 (tm-30) REVERT: N 49 ASP cc_start: 0.8009 (m-30) cc_final: 0.7777 (m-30) REVERT: N 70 THR cc_start: 0.8763 (m) cc_final: 0.8513 (p) REVERT: N 71 LEU cc_start: 0.8560 (tp) cc_final: 0.8326 (tp) REVERT: N 81 GLU cc_start: 0.8588 (tt0) cc_final: 0.8062 (mt-10) REVERT: N 90 ASP cc_start: 0.8805 (t0) cc_final: 0.8161 (t0) REVERT: O 59 TYR cc_start: 0.6343 (m-80) cc_final: 0.5478 (m-80) REVERT: O 75 MET cc_start: 0.8215 (mmm) cc_final: 0.7681 (mtp) REVERT: O 82 VAL cc_start: 0.8249 (m) cc_final: 0.7888 (p) REVERT: O 100 MET cc_start: 0.8671 (mtp) cc_final: 0.8203 (mtt) REVERT: P 17 GLN cc_start: 0.8678 (tt0) cc_final: 0.8263 (mm-40) REVERT: P 27 GLN cc_start: 0.6945 (mt0) cc_final: 0.6671 (mp10) REVERT: P 50 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7603 (ptmt) REVERT: P 51 ILE cc_start: 0.8581 (mm) cc_final: 0.7637 (tp) REVERT: P 71 PHE cc_start: 0.7913 (m-80) cc_final: 0.7125 (m-10) REVERT: P 81 GLU cc_start: 0.8373 (pm20) cc_final: 0.7879 (tm-30) REVERT: P 100 GLN cc_start: 0.7785 (pm20) cc_final: 0.6831 (tm-30) REVERT: Q 36 TRP cc_start: 0.8584 (m100) cc_final: 0.8152 (m100) REVERT: Q 38 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7472 (ptm160) REVERT: Q 46 GLU cc_start: 0.8320 (tt0) cc_final: 0.7927 (tt0) REVERT: R 27 HIS cc_start: 0.8217 (t-90) cc_final: 0.7807 (t-170) REVERT: R 51 ILE cc_start: 0.8362 (mp) cc_final: 0.8042 (mm) REVERT: R 71 PHE cc_start: 0.7966 (m-80) cc_final: 0.7036 (m-80) REVERT: R 90 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6308 (pt0) REVERT: S 4 LEU cc_start: 0.7970 (mt) cc_final: 0.7742 (mp) REVERT: S 24 VAL cc_start: 0.8214 (t) cc_final: 0.7467 (t) REVERT: S 37 ILE cc_start: 0.7593 (mt) cc_final: 0.7374 (mm) REVERT: S 72 ASP cc_start: 0.7436 (t0) cc_final: 0.7025 (t0) REVERT: S 75 LYS cc_start: 0.8991 (mttt) cc_final: 0.8790 (mtmm) REVERT: S 100 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6996 (mt-10) REVERT: S 100 VAL cc_start: 0.9352 (t) cc_final: 0.9026 (m) REVERT: T 40 GLN cc_start: 0.7917 (mp10) cc_final: 0.7697 (mm-40) REVERT: T 104 VAL cc_start: 0.9101 (t) cc_final: 0.8807 (m) outliers start: 68 outliers final: 27 residues processed: 614 average time/residue: 0.1587 time to fit residues: 150.0014 Evaluate side-chains 446 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 414 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 chunk 190 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 425 ASN C 195 ASN C 425 ASN E 553 ASN E 616 ASN D 94 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 363 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS L 90 GLN L 93 GLN M 100CASN P 53 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN S 56 ASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086743 restraints weight = 62520.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086607 restraints weight = 47283.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087781 restraints weight = 39094.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088050 restraints weight = 31422.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088207 restraints weight = 29406.615| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24168 Z= 0.177 Angle : 0.777 20.320 33048 Z= 0.385 Chirality : 0.049 0.327 3946 Planarity : 0.005 0.076 4000 Dihedral : 5.560 26.665 3038 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.53 % Allowed : 14.14 % Favored : 82.33 % 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: 0.06 (0.16), residues: 2780 helix: 0.65 (0.27), residues: 406 sheet: 0.34 (0.17), residues: 885 loop : -0.23 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 108 TYR 0.029 0.002 TYR P 49 PHE 0.034 0.002 PHE C 277 TRP 0.026 0.002 TRP B 610 HIS 0.009 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (24027) covalent geometry : angle 0.73399 / 0.38 (32668) SS BOND : bond 0.00564 / 0.32 ( 43) SS BOND : angle 1.22861 / 0.83 ( 86) hydrogen bonds : bond 0.05063 / 3.36 ( 842) hydrogen bonds : angle 5.71439 / 3.94 ( 2214) link_ALPHA1-2 : bond 0.00505 / 0.27 ( 1) link_ALPHA1-2 : angle 5.34332 / 2.85 ( 3) link_ALPHA1-3 : bond 0.00891 / 0.48 ( 15) link_ALPHA1-3 : angle 2.46619 / 1.73 ( 45) link_ALPHA1-6 : bond 0.00757 / 0.40 ( 16) link_ALPHA1-6 : angle 1.65320 / 1.12 ( 48) link_BETA1-4 : bond 0.01259 / 0.69 ( 29) link_BETA1-4 : angle 3.51800 / 2.51 ( 87) link_NAG-ASN : bond 0.00438 / 0.25 ( 37) link_NAG-ASN : angle 2.40235 / 1.51 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 463 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8069 (t) cc_final: 0.7827 (p) REVERT: A 102 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 112 TRP cc_start: 0.8339 (m100) cc_final: 0.7863 (m100) REVERT: A 180 ASP cc_start: 0.8351 (m-30) cc_final: 0.8060 (m-30) REVERT: A 426 MET cc_start: 0.5981 (mtp) cc_final: 0.5363 (mtp) REVERT: B 601 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8393 (mmmm) REVERT: B 628 TRP cc_start: 0.2640 (m-10) cc_final: 0.2178 (m-10) REVERT: C 95 MET cc_start: 0.8538 (ptp) cc_final: 0.8287 (ptp) REVERT: C 180 ASP cc_start: 0.8680 (m-30) cc_final: 0.8365 (t0) REVERT: C 373 MET cc_start: 0.7351 (mmt) cc_final: 0.7071 (mmm) REVERT: E 644 ASN cc_start: 0.7935 (m-40) cc_final: 0.7696 (t0) REVERT: E 646 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8547 (mm) REVERT: E 647 GLU cc_start: 0.7580 (pp20) cc_final: 0.7085 (pp20) REVERT: E 648 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8020 (mt-10) REVERT: D 116 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8758 (mp) REVERT: D 468 PHE cc_start: 0.7795 (m-80) cc_final: 0.7382 (m-80) REVERT: F 623 TRP cc_start: 0.8739 (m100) cc_final: 0.8518 (m100) REVERT: H 33 TYR cc_start: 0.6938 (m-10) cc_final: 0.6733 (m-10) REVERT: H 36 TRP cc_start: 0.8597 (m100) cc_final: 0.7934 (m-10) REVERT: H 82 MET cc_start: 0.7804 (tpp) cc_final: 0.7127 (tpp) REVERT: L 27 LEU cc_start: 0.8231 (mt) cc_final: 0.7714 (mt) REVERT: L 42 GLN cc_start: 0.8705 (mp10) cc_final: 0.8166 (mp10) REVERT: L 79 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7474 (tm-30) REVERT: L 94 PHE cc_start: 0.6067 (m-80) cc_final: 0.5786 (m-80) REVERT: L 96 TRP cc_start: 0.7698 (m-90) cc_final: 0.6782 (m-90) REVERT: M 72 ASP cc_start: 0.8235 (t0) cc_final: 0.7707 (t0) REVERT: M 86 ASP cc_start: 0.8027 (m-30) cc_final: 0.7770 (m-30) REVERT: M 91 TYR cc_start: 0.7844 (m-80) cc_final: 0.7625 (m-10) REVERT: M 100 MET cc_start: 0.6894 (ptp) cc_final: 0.6473 (mtt) REVERT: N 24 ASN cc_start: 0.8054 (t0) cc_final: 0.7520 (t0) REVERT: N 25 ASN cc_start: 0.8224 (m-40) cc_final: 0.7936 (m-40) REVERT: N 34 TYR cc_start: 0.8492 (m-80) cc_final: 0.8078 (m-10) REVERT: N 49 ASP cc_start: 0.7975 (m-30) cc_final: 0.7765 (m-30) REVERT: N 50 SER cc_start: 0.8077 (p) cc_final: 0.7713 (t) REVERT: N 64 LYS cc_start: 0.8129 (ttpp) cc_final: 0.7601 (tttt) REVERT: N 70 THR cc_start: 0.8672 (m) cc_final: 0.8386 (p) REVERT: N 90 ASP cc_start: 0.8919 (t0) cc_final: 0.8416 (t0) REVERT: N 102 THR cc_start: 0.8657 (p) cc_final: 0.8406 (p) REVERT: O 59 TYR cc_start: 0.6446 (m-80) cc_final: 0.5997 (m-10) REVERT: P 33 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6957 (pt) REVERT: P 42 GLN cc_start: 0.8863 (mm110) cc_final: 0.8221 (tp40) REVERT: P 49 TYR cc_start: 0.7452 (p90) cc_final: 0.7078 (p90) REVERT: P 51 ILE cc_start: 0.8472 (mm) cc_final: 0.7691 (tp) REVERT: P 71 PHE cc_start: 0.7393 (m-80) cc_final: 0.6699 (m-10) REVERT: P 81 GLU cc_start: 0.8350 (pm20) cc_final: 0.7753 (tm-30) REVERT: Q 36 TRP cc_start: 0.8566 (m100) cc_final: 0.8310 (m100) REVERT: Q 46 GLU cc_start: 0.8207 (tt0) cc_final: 0.7998 (tt0) REVERT: Q 100 MET cc_start: 0.7644 (mmt) cc_final: 0.7038 (mmp) REVERT: R 27 HIS cc_start: 0.7756 (t-90) cc_final: 0.7431 (t-170) REVERT: R 51 ILE cc_start: 0.8325 (mp) cc_final: 0.8100 (mm) REVERT: R 71 PHE cc_start: 0.7282 (m-80) cc_final: 0.6359 (m-80) REVERT: R 90 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: S 72 ASP cc_start: 0.7575 (t0) cc_final: 0.7143 (t0) REVERT: S 75 LYS cc_start: 0.9043 (mttt) cc_final: 0.8737 (mtmm) REVERT: S 100 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7361 (mt-10) REVERT: T 73 ILE cc_start: 0.8992 (mt) cc_final: 0.8769 (mt) outliers start: 88 outliers final: 47 residues processed: 508 average time/residue: 0.1607 time to fit residues: 127.6088 Evaluate side-chains 440 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 389 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 258 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 374 HIS B 577 GLN C 195 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 653 GLN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN S 1 GLN T 35 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086830 restraints weight = 61633.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086441 restraints weight = 45565.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087668 restraints weight = 38639.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088132 restraints weight = 31073.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088227 restraints weight = 29086.124| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.004 0.075 24168 Z= 0.159 Angle : 0.746 19.624 33048 Z= 0.366 Chirality : 0.048 0.345 3946 Planarity : 0.005 0.058 4000 Dihedral : 5.396 23.596 3038 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.33 % Allowed : 15.58 % Favored : 81.08 % 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: -0.08 (0.16), residues: 2780 helix: 0.72 (0.27), residues: 395 sheet: 0.25 (0.17), residues: 895 loop : -0.38 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 108 TYR 0.027 0.002 TYR L 49 PHE 0.024 0.002 PHE C 277 TRP 0.045 0.002 TRP D 69 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24027) covalent geometry : angle 0.70840 / 0.36 (32668) SS BOND : bond 0.00379 / 0.27 ( 43) SS BOND : angle 1.20217 / 0.87 ( 86) hydrogen bonds : bond 0.04574 / 3.04 ( 842) hydrogen bonds : angle 5.52685 / 3.80 ( 2214) link_ALPHA1-2 : bond 0.00511 / 0.27 ( 1) link_ALPHA1-2 : angle 4.99157 / 2.66 ( 3) link_ALPHA1-3 : bond 0.00700 / 0.40 ( 15) link_ALPHA1-3 : angle 2.25401 / 1.60 ( 45) link_ALPHA1-6 : bond 0.00674 / 0.35 ( 16) link_ALPHA1-6 : angle 1.61278 / 1.10 ( 48) link_BETA1-4 : bond 0.01258 / 0.66 ( 29) link_BETA1-4 : angle 3.26421 / 2.34 ( 87) link_NAG-ASN : bond 0.00409 / 0.25 ( 37) link_NAG-ASN : angle 2.18545 / 1.36 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 429 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8107 (t) cc_final: 0.7783 (p) REVERT: A 102 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 180 ASP cc_start: 0.8412 (m-30) cc_final: 0.8076 (m-30) REVERT: B 601 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8273 (mmmm) REVERT: C 165 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7892 (mm) REVERT: C 180 ASP cc_start: 0.8671 (m-30) cc_final: 0.8357 (t0) REVERT: E 644 ASN cc_start: 0.8067 (m-40) cc_final: 0.7832 (t0) REVERT: E 646 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (mm) REVERT: E 647 GLU cc_start: 0.7587 (pp20) cc_final: 0.7076 (pp20) REVERT: E 648 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 180 ASP cc_start: 0.7556 (m-30) cc_final: 0.6956 (t0) REVERT: D 423 ILE cc_start: 0.9196 (mp) cc_final: 0.8191 (mp) REVERT: D 468 PHE cc_start: 0.7610 (m-80) cc_final: 0.7052 (m-80) REVERT: H 28 THR cc_start: 0.4463 (p) cc_final: 0.4228 (p) REVERT: H 82 MET cc_start: 0.7934 (tpp) cc_final: 0.7293 (tpp) REVERT: L 9 LEU cc_start: 0.8805 (mt) cc_final: 0.8486 (tp) REVERT: L 42 GLN cc_start: 0.8657 (mp10) cc_final: 0.8225 (mp10) REVERT: L 79 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7470 (tm-30) REVERT: L 93 GLN cc_start: 0.8235 (mm110) cc_final: 0.7966 (mm110) REVERT: L 94 PHE cc_start: 0.6165 (m-80) cc_final: 0.5949 (m-80) REVERT: L 96 TRP cc_start: 0.7628 (m-90) cc_final: 0.7043 (m-90) REVERT: M 72 ASP cc_start: 0.8157 (t0) cc_final: 0.7683 (t0) REVERT: M 86 ASP cc_start: 0.8080 (m-30) cc_final: 0.7745 (m-30) REVERT: M 91 TYR cc_start: 0.7802 (m-80) cc_final: 0.7477 (m-10) REVERT: M 100 MET cc_start: 0.7145 (ptp) cc_final: 0.6862 (mtt) REVERT: N 24 ASN cc_start: 0.8046 (t0) cc_final: 0.7594 (t0) REVERT: N 25 ASN cc_start: 0.8151 (m-40) cc_final: 0.7921 (m-40) REVERT: N 34 TYR cc_start: 0.8529 (m-80) cc_final: 0.8166 (m-10) REVERT: N 36 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7615 (tm-30) REVERT: N 50 SER cc_start: 0.8141 (p) cc_final: 0.7790 (t) REVERT: N 51 ASP cc_start: 0.6758 (t70) cc_final: 0.6260 (t70) REVERT: N 64 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7673 (tttt) REVERT: N 70 THR cc_start: 0.8636 (m) cc_final: 0.8334 (p) REVERT: N 102 THR cc_start: 0.8679 (p) cc_final: 0.8412 (p) REVERT: O 100 MET cc_start: 0.7875 (mtp) cc_final: 0.7609 (mmm) REVERT: P 42 GLN cc_start: 0.8860 (mm110) cc_final: 0.8291 (tp40) REVERT: P 51 ILE cc_start: 0.8129 (mm) cc_final: 0.7869 (mp) REVERT: P 71 PHE cc_start: 0.7390 (m-80) cc_final: 0.7071 (m-80) REVERT: P 81 GLU cc_start: 0.8398 (pm20) cc_final: 0.7742 (tm-30) REVERT: P 100 GLN cc_start: 0.7303 (pm20) cc_final: 0.6464 (tm-30) REVERT: Q 36 TRP cc_start: 0.8546 (m100) cc_final: 0.8217 (m100) REVERT: R 4 MET cc_start: 0.7087 (mmm) cc_final: 0.6659 (tpp) REVERT: R 27 HIS cc_start: 0.7860 (t-90) cc_final: 0.7491 (t-170) REVERT: R 71 PHE cc_start: 0.7442 (m-80) cc_final: 0.7239 (m-80) REVERT: S 72 ASP cc_start: 0.7756 (t0) cc_final: 0.7259 (t0) REVERT: S 75 LYS cc_start: 0.8921 (mttt) cc_final: 0.8717 (mtmm) REVERT: S 77 GLU cc_start: 0.7754 (tp30) cc_final: 0.7044 (tp30) outliers start: 83 outliers final: 53 residues processed: 475 average time/residue: 0.1645 time to fit residues: 121.8156 Evaluate side-chains 436 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 381 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 17 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 99 optimal weight: 3.9990 chunk 202 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 155 optimal weight: 0.0070 chunk 141 optimal weight: 9.9990 overall best weight: 2.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 105 HIS ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 616 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN R 37 GLN R 90 GLN S 100CASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078023 restraints weight = 64178.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078594 restraints weight = 39756.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079471 restraints weight = 29976.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079895 restraints weight = 25833.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080076 restraints weight = 24012.281| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24168 Z= 0.216 Angle : 0.784 20.375 33048 Z= 0.381 Chirality : 0.049 0.306 3946 Planarity : 0.005 0.071 4000 Dihedral : 5.421 26.434 3038 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 3.29 % Allowed : 16.63 % Favored : 80.08 % 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: -0.19 (0.16), residues: 2780 helix: 0.64 (0.28), residues: 395 sheet: 0.14 (0.17), residues: 916 loop : -0.45 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 617 TYR 0.029 0.002 TYR L 49 PHE 0.027 0.002 PHE T 98 TRP 0.050 0.002 TRP F 623 HIS 0.007 0.001 HIS T 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (24027) covalent geometry : angle 0.74649 / 0.37 (32668) SS BOND : bond 0.00438 / 0.32 ( 43) SS BOND : angle 1.21968 / 0.84 ( 86) hydrogen bonds : bond 0.04627 / 3.07 ( 842) hydrogen bonds : angle 5.55136 / 3.83 ( 2214) link_ALPHA1-2 : bond 0.00420 / 0.22 ( 1) link_ALPHA1-2 : angle 5.03792 / 2.69 ( 3) link_ALPHA1-3 : bond 0.00903 / 0.47 ( 15) link_ALPHA1-3 : angle 2.19054 / 1.56 ( 45) link_ALPHA1-6 : bond 0.00588 / 0.29 ( 16) link_ALPHA1-6 : angle 1.80403 / 1.26 ( 48) link_BETA1-4 : bond 0.01151 / 0.60 ( 29) link_BETA1-4 : angle 3.31648 / 2.38 ( 87) link_NAG-ASN : bond 0.00377 / 0.23 ( 37) link_NAG-ASN : angle 2.22623 / 1.39 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 404 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 180 ASP cc_start: 0.8590 (m-30) cc_final: 0.8146 (m-30) REVERT: A 434 MET cc_start: 0.8199 (ttp) cc_final: 0.7879 (ttm) REVERT: B 601 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8047 (mmmt) REVERT: B 621 MET cc_start: 0.8323 (ptm) cc_final: 0.8091 (ptm) REVERT: C 103 GLN cc_start: 0.8809 (tp40) cc_final: 0.8157 (tm-30) REVERT: C 165 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8204 (mm) REVERT: E 644 ASN cc_start: 0.8586 (m-40) cc_final: 0.8366 (t0) REVERT: D 180 ASP cc_start: 0.8053 (m-30) cc_final: 0.7186 (t0) REVERT: D 423 ILE cc_start: 0.9445 (mp) cc_final: 0.8415 (mp) REVERT: D 434 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: D 468 PHE cc_start: 0.7814 (m-80) cc_final: 0.6999 (m-80) REVERT: F 530 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (tpt) REVERT: F 655 LYS cc_start: 0.7930 (tppt) cc_final: 0.7708 (ttmt) REVERT: F 663 LEU cc_start: 0.8320 (mt) cc_final: 0.7696 (tp) REVERT: H 82 MET cc_start: 0.7762 (tpp) cc_final: 0.7029 (tpp) REVERT: H 102 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6770 (t80) REVERT: L 9 LEU cc_start: 0.8999 (mt) cc_final: 0.8640 (tp) REVERT: L 42 GLN cc_start: 0.8704 (mp10) cc_final: 0.8077 (mp10) REVERT: L 49 TYR cc_start: 0.8096 (p90) cc_final: 0.7893 (p90) REVERT: L 94 PHE cc_start: 0.6197 (m-80) cc_final: 0.5841 (m-80) REVERT: L 96 TRP cc_start: 0.7456 (m-90) cc_final: 0.6303 (m-90) REVERT: M 35 ASN cc_start: 0.8452 (m-40) cc_final: 0.8238 (m-40) REVERT: M 72 ASP cc_start: 0.8004 (t0) cc_final: 0.7314 (t0) REVERT: M 86 ASP cc_start: 0.8110 (m-30) cc_final: 0.7702 (m-30) REVERT: M 91 TYR cc_start: 0.8053 (m-80) cc_final: 0.7377 (m-10) REVERT: M 100 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8324 (mtm180) REVERT: N 24 ASN cc_start: 0.8158 (t0) cc_final: 0.7753 (t0) REVERT: N 34 TYR cc_start: 0.8619 (m-80) cc_final: 0.8200 (m-10) REVERT: N 36 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7586 (tm-30) REVERT: N 50 SER cc_start: 0.8442 (p) cc_final: 0.8007 (t) REVERT: N 51 ASP cc_start: 0.6936 (t0) cc_final: 0.6102 (t70) REVERT: N 70 THR cc_start: 0.8784 (m) cc_final: 0.8515 (p) REVERT: P 42 GLN cc_start: 0.8808 (mm110) cc_final: 0.8163 (tp40) REVERT: P 51 ILE cc_start: 0.8405 (mm) cc_final: 0.7528 (tp) REVERT: P 71 PHE cc_start: 0.7724 (m-80) cc_final: 0.7236 (m-10) REVERT: P 81 GLU cc_start: 0.8623 (pm20) cc_final: 0.8129 (tm-30) REVERT: Q 12 LEU cc_start: 0.7008 (tp) cc_final: 0.6763 (tp) REVERT: Q 46 GLU cc_start: 0.8539 (tt0) cc_final: 0.8281 (tt0) REVERT: R 27 HIS cc_start: 0.8385 (t-90) cc_final: 0.7793 (t-170) REVERT: S 72 ASP cc_start: 0.7637 (t0) cc_final: 0.7024 (t0) REVERT: S 75 LYS cc_start: 0.9033 (mttt) cc_final: 0.8784 (mtmm) REVERT: S 100 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 82 outliers final: 57 residues processed: 457 average time/residue: 0.1498 time to fit residues: 107.7385 Evaluate side-chains 429 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 368 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 275 optimal weight: 0.0030 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 553 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079990 restraints weight = 67140.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080308 restraints weight = 45306.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081102 restraints weight = 36316.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081474 restraints weight = 31195.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.081648 restraints weight = 29204.976| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24168 Z= 0.235 Angle : 0.802 20.476 33048 Z= 0.389 Chirality : 0.049 0.300 3946 Planarity : 0.005 0.052 4000 Dihedral : 5.502 33.744 3038 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 3.78 % Allowed : 16.95 % Favored : 79.28 % 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: -0.39 (0.16), residues: 2780 helix: 0.72 (0.28), residues: 389 sheet: -0.13 (0.16), residues: 953 loop : -0.54 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 108 TYR 0.029 0.002 TYR P 49 PHE 0.027 0.002 PHE D 317 TRP 0.043 0.002 TRP B 596 HIS 0.010 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (24027) covalent geometry : angle 0.76235 / 0.38 (32668) SS BOND : bond 0.00632 / 0.40 ( 43) SS BOND : angle 1.90222 / 1.16 ( 86) hydrogen bonds : bond 0.04602 / 3.06 ( 842) hydrogen bonds : angle 5.59748 / 3.86 ( 2214) link_ALPHA1-2 : bond 0.00452 / 0.24 ( 1) link_ALPHA1-2 : angle 5.00333 / 2.68 ( 3) link_ALPHA1-3 : bond 0.00732 / 0.40 ( 15) link_ALPHA1-3 : angle 2.18665 / 1.57 ( 45) link_ALPHA1-6 : bond 0.00544 / 0.27 ( 16) link_ALPHA1-6 : angle 1.82323 / 1.29 ( 48) link_BETA1-4 : bond 0.01090 / 0.58 ( 29) link_BETA1-4 : angle 3.28786 / 2.37 ( 87) link_NAG-ASN : bond 0.00368 / 0.25 ( 37) link_NAG-ASN : angle 2.25319 / 1.42 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 381 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 180 ASP cc_start: 0.8602 (m-30) cc_final: 0.8118 (m-30) REVERT: A 434 MET cc_start: 0.8296 (ttp) cc_final: 0.8090 (ttm) REVERT: B 601 LYS cc_start: 0.9072 (mmtm) cc_final: 0.8742 (mmmt) REVERT: C 103 GLN cc_start: 0.8766 (tp40) cc_final: 0.8229 (tm-30) REVERT: C 165 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8261 (mm) REVERT: C 371 ILE cc_start: 0.8958 (mm) cc_final: 0.8667 (tp) REVERT: E 644 ASN cc_start: 0.8593 (m-40) cc_final: 0.8360 (m-40) REVERT: D 180 ASP cc_start: 0.8117 (m-30) cc_final: 0.7233 (t0) REVERT: D 373 MET cc_start: 0.7660 (tpp) cc_final: 0.6110 (mmt) REVERT: D 423 ILE cc_start: 0.9452 (mp) cc_final: 0.8368 (mp) REVERT: D 468 PHE cc_start: 0.7883 (m-80) cc_final: 0.7146 (m-80) REVERT: F 530 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8710 (tpt) REVERT: F 542 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7265 (mmt180) REVERT: H 82 MET cc_start: 0.7815 (tpp) cc_final: 0.7070 (tpp) REVERT: H 102 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6710 (t80) REVERT: L 9 LEU cc_start: 0.8988 (mt) cc_final: 0.8628 (tp) REVERT: L 42 GLN cc_start: 0.8666 (mp10) cc_final: 0.8078 (mp10) REVERT: L 79 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7539 (tm-30) REVERT: L 94 PHE cc_start: 0.6187 (m-80) cc_final: 0.5720 (m-80) REVERT: L 96 TRP cc_start: 0.7514 (m-90) cc_final: 0.6329 (m-90) REVERT: M 35 ASN cc_start: 0.8327 (m-40) cc_final: 0.8086 (m-40) REVERT: M 56 ASN cc_start: 0.9048 (t0) cc_final: 0.8835 (t0) REVERT: M 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7497 (t0) REVERT: M 86 ASP cc_start: 0.8088 (m-30) cc_final: 0.7609 (m-30) REVERT: M 91 TYR cc_start: 0.8099 (m-80) cc_final: 0.7384 (m-10) REVERT: N 24 ASN cc_start: 0.8293 (t0) cc_final: 0.7859 (t0) REVERT: N 34 TYR cc_start: 0.8676 (m-80) cc_final: 0.8303 (m-10) REVERT: N 50 SER cc_start: 0.8564 (p) cc_final: 0.8179 (t) REVERT: N 51 ASP cc_start: 0.6820 (t0) cc_final: 0.6059 (t70) REVERT: N 70 THR cc_start: 0.8783 (m) cc_final: 0.8565 (p) REVERT: P 51 ILE cc_start: 0.8527 (mm) cc_final: 0.7583 (tp) REVERT: P 71 PHE cc_start: 0.7884 (m-80) cc_final: 0.7438 (m-10) REVERT: Q 12 LEU cc_start: 0.7510 (tp) cc_final: 0.7264 (tp) REVERT: R 27 HIS cc_start: 0.8388 (t-90) cc_final: 0.7747 (t-170) REVERT: S 72 ASP cc_start: 0.7670 (t0) cc_final: 0.6894 (t0) REVERT: S 75 LYS cc_start: 0.9072 (mttt) cc_final: 0.8842 (mtmm) REVERT: S 100 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7541 (mt-10) REVERT: T 18 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6774 (mmm160) REVERT: T 48 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6437 (m-80) outliers start: 94 outliers final: 71 residues processed: 441 average time/residue: 0.1532 time to fit residues: 106.6496 Evaluate side-chains 431 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.0050 chunk 188 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.108008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080421 restraints weight = 66758.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081915 restraints weight = 43489.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082745 restraints weight = 30732.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084037 restraints weight = 26993.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084014 restraints weight = 24633.184| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24168 Z= 0.154 Angle : 0.731 19.662 33048 Z= 0.354 Chirality : 0.047 0.356 3946 Planarity : 0.005 0.047 4000 Dihedral : 5.274 27.606 3038 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 3.53 % Allowed : 17.87 % Favored : 78.59 % 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: -0.30 (0.16), residues: 2780 helix: 0.71 (0.28), residues: 391 sheet: 0.04 (0.17), residues: 908 loop : -0.53 (0.17), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 75 TYR 0.028 0.002 TYR L 49 PHE 0.027 0.002 PHE D 317 TRP 0.048 0.002 TRP B 596 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24027) covalent geometry : angle 0.69787 / 0.35 (32668) SS BOND : bond 0.00311 / 0.22 ( 43) SS BOND : angle 1.12069 / 0.76 ( 86) hydrogen bonds : bond 0.04175 / 2.77 ( 842) hydrogen bonds : angle 5.46920 / 3.76 ( 2214) link_ALPHA1-2 : bond 0.00516 / 0.27 ( 1) link_ALPHA1-2 : angle 4.65308 / 2.50 ( 3) link_ALPHA1-3 : bond 0.00727 / 0.41 ( 15) link_ALPHA1-3 : angle 2.10577 / 1.51 ( 45) link_ALPHA1-6 : bond 0.00683 / 0.35 ( 16) link_ALPHA1-6 : angle 1.56943 / 1.10 ( 48) link_BETA1-4 : bond 0.01085 / 0.57 ( 29) link_BETA1-4 : angle 3.04456 / 2.21 ( 87) link_NAG-ASN : bond 0.00326 / 0.21 ( 37) link_NAG-ASN : angle 2.03280 / 1.26 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 392 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 104 MET cc_start: 0.8672 (tpp) cc_final: 0.8336 (tpp) REVERT: A 125 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9111 (mt) REVERT: A 180 ASP cc_start: 0.8649 (m-30) cc_final: 0.8151 (m-30) REVERT: C 92 ASN cc_start: 0.8346 (m-40) cc_final: 0.8000 (p0) REVERT: C 103 GLN cc_start: 0.8672 (tp40) cc_final: 0.8177 (tm-30) REVERT: C 165 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 371 ILE cc_start: 0.8926 (mm) cc_final: 0.8625 (tp) REVERT: C 434 MET cc_start: 0.8870 (ttm) cc_final: 0.8648 (ttp) REVERT: E 621 MET cc_start: 0.8290 (ppp) cc_final: 0.8067 (ppp) REVERT: E 644 ASN cc_start: 0.8557 (m-40) cc_final: 0.8248 (m-40) REVERT: E 647 GLU cc_start: 0.7910 (pp20) cc_final: 0.7494 (pp20) REVERT: D 125 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (mt) REVERT: D 180 ASP cc_start: 0.8020 (m-30) cc_final: 0.7665 (t0) REVERT: D 317 PHE cc_start: 0.7824 (t80) cc_final: 0.7621 (t80) REVERT: D 373 MET cc_start: 0.7592 (tpp) cc_final: 0.6059 (mmt) REVERT: D 468 PHE cc_start: 0.7599 (m-80) cc_final: 0.7107 (m-80) REVERT: F 530 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8635 (tpt) REVERT: H 82 MET cc_start: 0.7717 (tpp) cc_final: 0.7125 (tpp) REVERT: H 102 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6673 (t80) REVERT: L 9 LEU cc_start: 0.8986 (mt) cc_final: 0.8627 (tp) REVERT: L 42 GLN cc_start: 0.8748 (mp10) cc_final: 0.8138 (mp10) REVERT: L 79 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7588 (tm-30) REVERT: L 94 PHE cc_start: 0.6081 (m-80) cc_final: 0.5488 (m-80) REVERT: L 96 TRP cc_start: 0.7562 (m-90) cc_final: 0.6278 (m-90) REVERT: M 13 LYS cc_start: 0.9284 (tppt) cc_final: 0.9038 (mmmt) REVERT: M 46 GLU cc_start: 0.8307 (tp30) cc_final: 0.8086 (tp30) REVERT: M 56 ASN cc_start: 0.8982 (t0) cc_final: 0.8735 (t0) REVERT: M 86 ASP cc_start: 0.8107 (m-30) cc_final: 0.7629 (m-30) REVERT: M 91 TYR cc_start: 0.8152 (m-80) cc_final: 0.7429 (m-10) REVERT: N 34 TYR cc_start: 0.8623 (m-80) cc_final: 0.8206 (m-10) REVERT: N 50 SER cc_start: 0.8420 (p) cc_final: 0.8193 (t) REVERT: N 70 THR cc_start: 0.8770 (m) cc_final: 0.8476 (p) REVERT: P 51 ILE cc_start: 0.8511 (mm) cc_final: 0.7849 (tp) REVERT: P 71 PHE cc_start: 0.7907 (m-80) cc_final: 0.7639 (m-10) REVERT: Q 12 LEU cc_start: 0.7582 (tp) cc_final: 0.7349 (tp) REVERT: Q 57 THR cc_start: 0.9231 (p) cc_final: 0.8971 (t) REVERT: R 27 HIS cc_start: 0.8283 (t-90) cc_final: 0.7662 (t70) REVERT: R 71 PHE cc_start: 0.8157 (m-80) cc_final: 0.7827 (m-10) REVERT: S 72 ASP cc_start: 0.7762 (t0) cc_final: 0.6978 (t0) REVERT: S 100 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7440 (mt-10) REVERT: S 105 GLN cc_start: 0.8229 (mp10) cc_final: 0.7972 (tp40) REVERT: T 18 ARG cc_start: 0.7319 (mmm160) cc_final: 0.6928 (mmm160) REVERT: T 48 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: T 59 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7571 (mtm110) REVERT: T 73 ILE cc_start: 0.8945 (mp) cc_final: 0.8183 (mt) REVERT: T 75 ARG cc_start: 0.7534 (mpp80) cc_final: 0.7109 (mtm-85) outliers start: 88 outliers final: 56 residues processed: 441 average time/residue: 0.1488 time to fit residues: 103.5824 Evaluate side-chains 426 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 30 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN C 195 ASN C 425 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN D 203 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN N 87 GLN P 38 GLN R 37 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.106146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078348 restraints weight = 63671.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080737 restraints weight = 39526.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081503 restraints weight = 25875.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082543 restraints weight = 23685.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082561 restraints weight = 20924.441| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24168 Z= 0.129 Angle : 0.710 18.757 33048 Z= 0.340 Chirality : 0.047 0.391 3946 Planarity : 0.004 0.047 4000 Dihedral : 5.094 28.720 3038 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 3.05 % Allowed : 18.67 % Favored : 78.27 % 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: -0.29 (0.16), residues: 2780 helix: 0.60 (0.28), residues: 396 sheet: 0.18 (0.17), residues: 905 loop : -0.59 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 100F TYR 0.028 0.001 TYR L 49 PHE 0.023 0.002 PHE D 317 TRP 0.048 0.002 TRP B 596 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (24027) covalent geometry : angle 0.68020 / 0.33 (32668) SS BOND : bond 0.00254 / 0.17 ( 43) SS BOND : angle 0.95804 / 0.63 ( 86) hydrogen bonds : bond 0.03844 / 2.56 ( 842) hydrogen bonds : angle 5.41844 / 3.73 ( 2214) link_ALPHA1-2 : bond 0.00419 / 0.22 ( 1) link_ALPHA1-2 : angle 4.38351 / 2.36 ( 3) link_ALPHA1-3 : bond 0.00752 / 0.43 ( 15) link_ALPHA1-3 : angle 2.05495 / 1.46 ( 45) link_ALPHA1-6 : bond 0.00655 / 0.34 ( 16) link_ALPHA1-6 : angle 1.47954 / 1.02 ( 48) link_BETA1-4 : bond 0.01100 / 0.57 ( 29) link_BETA1-4 : angle 2.86388 / 2.08 ( 87) link_NAG-ASN : bond 0.00364 / 0.22 ( 37) link_NAG-ASN : angle 1.88476 / 1.16 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 410 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 180 ASP cc_start: 0.8634 (m-30) cc_final: 0.8192 (m-30) REVERT: B 610 TRP cc_start: 0.8042 (t-100) cc_final: 0.7785 (t-100) REVERT: C 92 ASN cc_start: 0.8424 (m-40) cc_final: 0.8135 (p0) REVERT: C 103 GLN cc_start: 0.8623 (tp40) cc_final: 0.8032 (tm-30) REVERT: C 165 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8084 (mm) REVERT: C 317 PHE cc_start: 0.8810 (t80) cc_final: 0.8363 (t80) REVERT: C 371 ILE cc_start: 0.8900 (mm) cc_final: 0.8551 (tp) REVERT: C 434 MET cc_start: 0.8845 (ttm) cc_final: 0.8644 (ttp) REVERT: E 621 MET cc_start: 0.8307 (ppp) cc_final: 0.8020 (ppp) REVERT: E 644 ASN cc_start: 0.8677 (m-40) cc_final: 0.8328 (m-40) REVERT: E 647 GLU cc_start: 0.7935 (pp20) cc_final: 0.7498 (pp20) REVERT: D 125 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8581 (mt) REVERT: D 180 ASP cc_start: 0.8088 (m-30) cc_final: 0.7777 (t0) REVERT: D 373 MET cc_start: 0.7590 (tpp) cc_final: 0.6056 (mmt) REVERT: D 468 PHE cc_start: 0.7425 (m-80) cc_final: 0.6944 (m-80) REVERT: F 530 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8364 (tpt) REVERT: F 534 SER cc_start: 0.9402 (m) cc_final: 0.8756 (p) REVERT: H 102 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6565 (t80) REVERT: L 9 LEU cc_start: 0.9074 (mt) cc_final: 0.8741 (tp) REVERT: L 42 GLN cc_start: 0.8651 (mp10) cc_final: 0.7980 (mp10) REVERT: L 79 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7657 (tm-30) REVERT: L 94 PHE cc_start: 0.5947 (m-80) cc_final: 0.5468 (m-80) REVERT: L 96 TRP cc_start: 0.7544 (m-90) cc_final: 0.6115 (m-90) REVERT: M 58 ASN cc_start: 0.7897 (t0) cc_final: 0.7646 (t0) REVERT: M 72 ASP cc_start: 0.7915 (t0) cc_final: 0.7256 (t0) REVERT: M 86 ASP cc_start: 0.8040 (m-30) cc_final: 0.7530 (m-30) REVERT: M 91 TYR cc_start: 0.8127 (m-80) cc_final: 0.7342 (m-10) REVERT: N 24 ASN cc_start: 0.7211 (p0) cc_final: 0.6953 (p0) REVERT: N 34 TYR cc_start: 0.8528 (m-80) cc_final: 0.8103 (m-10) REVERT: N 37 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7961 (mmmt) REVERT: N 50 SER cc_start: 0.8677 (p) cc_final: 0.8266 (t) REVERT: O 102 TYR cc_start: 0.5915 (m-80) cc_final: 0.5434 (m-80) REVERT: P 42 GLN cc_start: 0.8712 (mm110) cc_final: 0.8009 (tm-30) REVERT: P 51 ILE cc_start: 0.8573 (mm) cc_final: 0.8343 (mp) REVERT: P 90 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7899 (pp30) REVERT: Q 12 LEU cc_start: 0.7681 (tp) cc_final: 0.7466 (tp) REVERT: Q 46 GLU cc_start: 0.8501 (tt0) cc_final: 0.7902 (pt0) REVERT: Q 57 THR cc_start: 0.9192 (p) cc_final: 0.8961 (t) REVERT: R 27 HIS cc_start: 0.8362 (t-90) cc_final: 0.7772 (t70) REVERT: R 37 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: S 72 ASP cc_start: 0.7874 (t0) cc_final: 0.6987 (t0) REVERT: S 75 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8383 (mtmm) REVERT: S 100 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6571 (mm-30) REVERT: S 105 GLN cc_start: 0.8183 (mp10) cc_final: 0.7913 (tp40) REVERT: T 48 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: T 59 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7773 (mtm110) REVERT: T 73 ILE cc_start: 0.8874 (mp) cc_final: 0.8381 (mt) outliers start: 76 outliers final: 51 residues processed: 449 average time/residue: 0.1534 time to fit residues: 108.9458 Evaluate side-chains 433 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 375 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 90 GLN Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 139 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN C 195 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN N 87 GLN O 6 GLN R 37 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.109197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081378 restraints weight = 65561.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083188 restraints weight = 43999.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084132 restraints weight = 29684.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085314 restraints weight = 27467.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085488 restraints weight = 24394.183| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24168 Z= 0.136 Angle : 0.732 18.643 33048 Z= 0.350 Chirality : 0.047 0.389 3946 Planarity : 0.005 0.049 4000 Dihedral : 5.097 30.277 3038 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.77 % Allowed : 19.64 % Favored : 77.59 % 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: -0.25 (0.16), residues: 2780 helix: 0.72 (0.28), residues: 389 sheet: 0.22 (0.17), residues: 902 loop : -0.59 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 75 TYR 0.026 0.001 TYR L 49 PHE 0.028 0.002 PHE P 71 TRP 0.048 0.002 TRP B 596 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (24027) covalent geometry : angle 0.69877 / 0.34 (32668) SS BOND : bond 0.00270 / 0.19 ( 43) SS BOND : angle 1.88643 / 1.13 ( 86) hydrogen bonds : bond 0.03899 / 2.58 ( 842) hydrogen bonds : angle 5.38811 / 3.72 ( 2214) link_ALPHA1-2 : bond 0.00482 / 0.25 ( 1) link_ALPHA1-2 : angle 4.18940 / 2.26 ( 3) link_ALPHA1-3 : bond 0.00709 / 0.41 ( 15) link_ALPHA1-3 : angle 2.02067 / 1.43 ( 45) link_ALPHA1-6 : bond 0.00627 / 0.33 ( 16) link_ALPHA1-6 : angle 1.51854 / 1.05 ( 48) link_BETA1-4 : bond 0.01058 / 0.55 ( 29) link_BETA1-4 : angle 2.82696 / 2.06 ( 87) link_NAG-ASN : bond 0.00335 / 0.20 ( 37) link_NAG-ASN : angle 1.86339 / 1.15 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 387 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 180 ASP cc_start: 0.8551 (m-30) cc_final: 0.8150 (m-30) REVERT: B 610 TRP cc_start: 0.8088 (t-100) cc_final: 0.7800 (t-100) REVERT: B 626 MET cc_start: 0.6002 (tpt) cc_final: 0.5090 (tpt) REVERT: C 92 ASN cc_start: 0.8338 (m-40) cc_final: 0.8123 (p0) REVERT: C 103 GLN cc_start: 0.8481 (tp40) cc_final: 0.8057 (tm-30) REVERT: C 317 PHE cc_start: 0.8911 (t80) cc_final: 0.8475 (t80) REVERT: C 371 ILE cc_start: 0.8857 (mm) cc_final: 0.8567 (tp) REVERT: E 621 MET cc_start: 0.8302 (ppp) cc_final: 0.8026 (ppp) REVERT: E 644 ASN cc_start: 0.8574 (m-40) cc_final: 0.8255 (m-40) REVERT: E 647 GLU cc_start: 0.7912 (pp20) cc_final: 0.7467 (pp20) REVERT: D 125 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 180 ASP cc_start: 0.7992 (m-30) cc_final: 0.7687 (t0) REVERT: D 373 MET cc_start: 0.7621 (tpp) cc_final: 0.6172 (mmt) REVERT: D 427 TRP cc_start: 0.7723 (m100) cc_final: 0.7129 (m100) REVERT: D 468 PHE cc_start: 0.7442 (m-80) cc_final: 0.6958 (m-80) REVERT: F 530 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8409 (tpt) REVERT: F 534 SER cc_start: 0.9372 (m) cc_final: 0.8767 (p) REVERT: H 102 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6532 (t80) REVERT: L 9 LEU cc_start: 0.9084 (mt) cc_final: 0.8674 (tp) REVERT: L 42 GLN cc_start: 0.8697 (mp10) cc_final: 0.7999 (mp10) REVERT: L 79 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7687 (tm-30) REVERT: L 94 PHE cc_start: 0.5948 (m-80) cc_final: 0.5494 (m-80) REVERT: L 96 TRP cc_start: 0.7494 (m-90) cc_final: 0.6185 (m-90) REVERT: M 46 GLU cc_start: 0.7947 (tp30) cc_final: 0.7580 (tp30) REVERT: M 72 ASP cc_start: 0.8010 (t0) cc_final: 0.7413 (t0) REVERT: M 86 ASP cc_start: 0.8148 (m-30) cc_final: 0.7648 (m-30) REVERT: N 24 ASN cc_start: 0.7238 (p0) cc_final: 0.7028 (p0) REVERT: N 34 TYR cc_start: 0.8647 (m-80) cc_final: 0.8134 (m-10) REVERT: N 50 SER cc_start: 0.8565 (p) cc_final: 0.8207 (t) REVERT: N 51 ASP cc_start: 0.7623 (m-30) cc_final: 0.7414 (m-30) REVERT: P 42 GLN cc_start: 0.8701 (mm110) cc_final: 0.8074 (tm-30) REVERT: Q 46 GLU cc_start: 0.8522 (tt0) cc_final: 0.7829 (pt0) REVERT: Q 57 THR cc_start: 0.9263 (p) cc_final: 0.9039 (t) REVERT: R 27 HIS cc_start: 0.8339 (t-90) cc_final: 0.7677 (t70) REVERT: R 37 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: R 71 PHE cc_start: 0.8174 (m-80) cc_final: 0.7834 (m-10) REVERT: S 72 ASP cc_start: 0.7852 (t0) cc_final: 0.6978 (t0) REVERT: S 75 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8389 (mtmm) REVERT: S 100 GLU cc_start: 0.7858 (mt-10) cc_final: 0.6777 (mm-30) REVERT: T 40 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7111 (tp-100) REVERT: T 48 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: T 59 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7739 (mtm110) REVERT: T 73 ILE cc_start: 0.8849 (mp) cc_final: 0.8336 (mt) REVERT: T 75 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7429 (mtm-85) outliers start: 69 outliers final: 54 residues processed: 421 average time/residue: 0.1464 time to fit residues: 98.0009 Evaluate side-chains 430 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 178 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 229 optimal weight: 0.0770 chunk 225 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN R 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.109379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083216 restraints weight = 66600.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.084277 restraints weight = 43285.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084858 restraints weight = 32091.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085123 restraints weight = 30736.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085291 restraints weight = 27607.147| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24168 Z= 0.132 Angle : 0.725 18.382 33048 Z= 0.347 Chirality : 0.047 0.397 3946 Planarity : 0.004 0.047 4000 Dihedral : 5.025 27.864 3038 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.57 % Allowed : 19.88 % Favored : 77.55 % 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: -0.24 (0.16), residues: 2780 helix: 0.62 (0.28), residues: 395 sheet: 0.28 (0.17), residues: 900 loop : -0.60 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 75 TYR 0.027 0.001 TYR L 49 PHE 0.029 0.002 PHE T 98 TRP 0.052 0.002 TRP B 596 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (24027) covalent geometry : angle 0.69775 / 0.34 (32668) SS BOND : bond 0.00271 / 0.19 ( 43) SS BOND : angle 0.96165 / 0.62 ( 86) hydrogen bonds : bond 0.03823 / 2.54 ( 842) hydrogen bonds : angle 5.34938 / 3.69 ( 2214) link_ALPHA1-2 : bond 0.00466 / 0.25 ( 1) link_ALPHA1-2 : angle 3.98958 / 2.16 ( 3) link_ALPHA1-3 : bond 0.00701 / 0.40 ( 15) link_ALPHA1-3 : angle 1.99702 / 1.41 ( 45) link_ALPHA1-6 : bond 0.00631 / 0.33 ( 16) link_ALPHA1-6 : angle 1.49587 / 1.03 ( 48) link_BETA1-4 : bond 0.01063 / 0.55 ( 29) link_BETA1-4 : angle 2.77813 / 2.02 ( 87) link_NAG-ASN : bond 0.00351 / 0.21 ( 37) link_NAG-ASN : angle 1.82839 / 1.12 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 383 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 180 ASP cc_start: 0.8509 (m-30) cc_final: 0.8147 (m-30) REVERT: B 610 TRP cc_start: 0.8076 (t-100) cc_final: 0.7845 (t-100) REVERT: B 626 MET cc_start: 0.5416 (tpt) cc_final: 0.5105 (tpt) REVERT: C 103 GLN cc_start: 0.8463 (tp40) cc_final: 0.8012 (tm-30) REVERT: C 317 PHE cc_start: 0.8912 (t80) cc_final: 0.8507 (t80) REVERT: C 371 ILE cc_start: 0.8879 (mm) cc_final: 0.8594 (tp) REVERT: E 621 MET cc_start: 0.8272 (ppp) cc_final: 0.7991 (ppp) REVERT: E 644 ASN cc_start: 0.8735 (m-40) cc_final: 0.8413 (m-40) REVERT: E 647 GLU cc_start: 0.7799 (pp20) cc_final: 0.7355 (pp20) REVERT: D 125 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8541 (mt) REVERT: D 180 ASP cc_start: 0.8076 (m-30) cc_final: 0.7771 (t0) REVERT: D 373 MET cc_start: 0.7512 (tpp) cc_final: 0.6021 (mmt) REVERT: D 427 TRP cc_start: 0.7768 (m100) cc_final: 0.7139 (m100) REVERT: D 468 PHE cc_start: 0.7405 (m-80) cc_final: 0.6929 (m-80) REVERT: F 530 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8392 (tpt) REVERT: F 534 SER cc_start: 0.9300 (m) cc_final: 0.8726 (p) REVERT: F 535 MET cc_start: 0.9094 (tpp) cc_final: 0.8793 (tpt) REVERT: F 621 MET cc_start: 0.8361 (tpp) cc_final: 0.8078 (tpp) REVERT: H 102 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6469 (t80) REVERT: L 9 LEU cc_start: 0.9077 (mt) cc_final: 0.8676 (tp) REVERT: L 42 GLN cc_start: 0.8661 (mp10) cc_final: 0.7960 (mp10) REVERT: L 77 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8152 (ptp-170) REVERT: L 94 PHE cc_start: 0.5884 (m-80) cc_final: 0.5472 (m-80) REVERT: L 96 TRP cc_start: 0.7393 (m-90) cc_final: 0.6021 (m-90) REVERT: M 46 GLU cc_start: 0.7940 (tp30) cc_final: 0.7547 (tp30) REVERT: M 58 ASN cc_start: 0.8356 (t0) cc_final: 0.8154 (t0) REVERT: M 72 ASP cc_start: 0.7851 (t0) cc_final: 0.7201 (t0) REVERT: M 86 ASP cc_start: 0.8052 (m-30) cc_final: 0.7544 (m-30) REVERT: N 24 ASN cc_start: 0.7226 (p0) cc_final: 0.6999 (p0) REVERT: N 34 TYR cc_start: 0.8686 (m-80) cc_final: 0.8170 (m-10) REVERT: N 50 SER cc_start: 0.8523 (p) cc_final: 0.8182 (t) REVERT: N 51 ASP cc_start: 0.7646 (m-30) cc_final: 0.7420 (m-30) REVERT: N 94 ASP cc_start: 0.8287 (m-30) cc_final: 0.7959 (t0) REVERT: O 102 TYR cc_start: 0.5957 (m-80) cc_final: 0.5380 (m-80) REVERT: P 42 GLN cc_start: 0.8674 (mm110) cc_final: 0.8077 (tm-30) REVERT: P 87 TYR cc_start: 0.5933 (m-80) cc_final: 0.5671 (m-10) REVERT: Q 46 GLU cc_start: 0.8401 (tt0) cc_final: 0.7700 (pt0) REVERT: Q 57 THR cc_start: 0.9242 (p) cc_final: 0.9015 (t) REVERT: R 27 HIS cc_start: 0.8374 (t-90) cc_final: 0.7705 (t70) REVERT: R 37 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: S 72 ASP cc_start: 0.7788 (t0) cc_final: 0.6894 (t0) REVERT: S 75 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8385 (mtmm) REVERT: S 100 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7409 (mt-10) REVERT: T 40 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7125 (tp-100) REVERT: T 48 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: T 59 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7332 (mtm110) outliers start: 64 outliers final: 49 residues processed: 416 average time/residue: 0.1486 time to fit residues: 98.2311 Evaluate side-chains 430 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 222 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 265 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 chunk 254 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN C 425 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS O 6 GLN R 37 GLN T 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.109516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083167 restraints weight = 67002.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084620 restraints weight = 45990.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085255 restraints weight = 33638.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085510 restraints weight = 30141.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085621 restraints weight = 28025.108| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24168 Z= 0.134 Angle : 0.735 18.326 33048 Z= 0.351 Chirality : 0.047 0.391 3946 Planarity : 0.005 0.050 4000 Dihedral : 5.023 32.581 3038 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.45 % Allowed : 20.72 % Favored : 76.83 % 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: -0.22 (0.16), residues: 2780 helix: 0.70 (0.28), residues: 394 sheet: 0.28 (0.17), residues: 910 loop : -0.61 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 39 TYR 0.026 0.001 TYR L 49 PHE 0.032 0.002 PHE A 93 TRP 0.046 0.002 TRP B 596 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24027) covalent geometry : angle 0.70500 / 0.34 (32668) SS BOND : bond 0.00284 / 0.20 ( 43) SS BOND : angle 1.70499 / 1.03 ( 86) hydrogen bonds : bond 0.03783 / 2.51 ( 842) hydrogen bonds : angle 5.30657 / 3.66 ( 2214) link_ALPHA1-2 : bond 0.00465 / 0.24 ( 1) link_ALPHA1-2 : angle 3.76469 / 2.04 ( 3) link_ALPHA1-3 : bond 0.00703 / 0.40 ( 15) link_ALPHA1-3 : angle 1.96395 / 1.38 ( 45) link_ALPHA1-6 : bond 0.00622 / 0.32 ( 16) link_ALPHA1-6 : angle 1.50422 / 1.04 ( 48) link_BETA1-4 : bond 0.01050 / 0.54 ( 29) link_BETA1-4 : angle 2.75719 / 2.01 ( 87) link_NAG-ASN : bond 0.00340 / 0.21 ( 37) link_NAG-ASN : angle 1.81169 / 1.11 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3943.80 seconds wall clock time: 69 minutes 5.46 seconds (4145.46 seconds total)