Starting phenix.real_space_refine on Sat Feb 7 13:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6d_61168/02_2026/9j6d_61168_neut.cif" } resolution = 3.11 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= 0.007 sd= 0.043 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 276 5.16 5 C 20777 2.51 5 N 5652 2.21 5 O 6288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32993 Number of models: 1 Model: "" Number of chains: 24 Chain: "U" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 7, 'TRANS': 47} Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3327 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3327 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3327 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3327 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "E" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3249 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 31, 'TRANS': 381} Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3257 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "G" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3257 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "H" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3238 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 31, 'TRANS': 380} Chain: "I" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "J" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "K" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "L" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "V" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 7, 'TRANS': 47} Chain: "W" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 7, 'TRANS': 47} Chain: "X" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 7, 'TRANS': 47} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.03, per 1000 atoms: 0.24 Number of scatterers: 32993 At special positions: 0 Unit cell: (186.12, 183.48, 195.36, 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 276 16.00 O 6288 8.00 N 5652 7.00 C 20777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS U 8 " - pdb=" SG CYS U 17 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 26 " distance=2.05 Simple disulfide: pdb=" SG CYS U 25 " - pdb=" SG CYS U 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.19 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.01 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.02 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.02 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.02 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.05 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.16 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.05 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.02 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.02 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.01 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.05 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.02 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.02 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.02 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.11 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 125 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 28 " distance=2.02 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.02 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 266 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 125 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 28 " distance=2.02 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.02 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 266 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 225 " distance=2.04 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 125 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.02 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.02 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 266 " distance=2.04 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 225 " distance=2.02 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 125 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.02 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.02 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 266 " distance=2.02 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 225 " distance=2.02 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.02 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 128 " distance=2.45 Simple disulfide: pdb=" SG CYS V 8 " - pdb=" SG CYS V 17 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 26 " distance=2.03 Simple disulfide: pdb=" SG CYS V 25 " - pdb=" SG CYS V 57 " distance=2.11 Simple disulfide: pdb=" SG CYS W 8 " - pdb=" SG CYS W 17 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 26 " distance=2.03 Simple disulfide: pdb=" SG CYS W 25 " - pdb=" SG CYS W 57 " distance=2.03 Simple disulfide: pdb=" SG CYS X 8 " - pdb=" SG CYS X 17 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 26 " distance=2.03 Simple disulfide: pdb=" SG CYS X 25 " - pdb=" SG CYS X 57 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " BETA1-6 " NAG M 1 " - " FUC M 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 4 " " NAG O 1 " - " FUC O 4 " " NAG P 1 " - " FUC P 4 " NAG-ASN " NAG M 1 " - " ASN A 141 " " NAG N 1 " - " ASN B 141 " " NAG O 1 " - " ASN C 141 " " NAG P 1 " - " ASN D 141 " " NAG Q 1 " - " ASN E 345 " " NAG R 1 " - " ASN F 345 " " NAG S 1 " - " ASN G 345 " " NAG T 1 " - " ASN H 345 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7906 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 16.5% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'U' and resid 25 through 30 Processing helix chain 'U' and resid 30 through 40 Processing helix chain 'U' and resid 46 through 56 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.549A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 438 Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.042A pdb=" N LYS B 115 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 403 through 438 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.906A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 403 through 436 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 403 through 436 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 365 through 402 Proline residue: E 399 - end of helix Processing helix chain 'E' and resid 409 through 416 Processing helix chain 'F' and resid 7 through 12 Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 403 Proline residue: F 399 - end of helix Processing helix chain 'F' and resid 409 through 416 Processing helix chain 'G' and resid 7 through 12 Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 365 through 402 Proline residue: G 399 - end of helix Processing helix chain 'G' and resid 409 through 416 Processing helix chain 'H' and resid 7 through 12 Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 363 through 402 removed outlier: 3.881A pdb=" N VAL H 368 " --> pdb=" O PRO H 364 " (cutoff:3.500A) Proline residue: H 399 - end of helix Processing helix chain 'H' and resid 409 through 416 Processing helix chain 'I' and resid 146 through 151 Processing helix chain 'I' and resid 168 through 175 removed outlier: 4.827A pdb=" N SER I 173 " --> pdb=" O HIS I 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 151 Processing helix chain 'J' and resid 168 through 175 removed outlier: 5.324A pdb=" N SER J 173 " --> pdb=" O HIS J 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 151 Processing helix chain 'L' and resid 146 through 151 Processing helix chain 'L' and resid 168 through 172 Processing helix chain 'V' and resid 30 through 41 Processing helix chain 'V' and resid 46 through 56 Processing helix chain 'W' and resid 25 through 30 Processing helix chain 'W' and resid 30 through 41 Processing helix chain 'W' and resid 46 through 56 Processing helix chain 'X' and resid 25 through 30 Processing helix chain 'X' and resid 30 through 40 Processing helix chain 'X' and resid 46 through 56 Processing sheet with id=AA1, first strand: chain 'U' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 19 removed outlier: 8.698A pdb=" N LEU A 29 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR A 137 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET A 31 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 135 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 33 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 133 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 131 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR A 37 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA A 129 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA A 127 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N THR A 41 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA A 121 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 147 current: chain 'A' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 185 current: chain 'A' and resid 267 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 100 through 110 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 305 removed outlier: 5.596A pdb=" N ASP A 298 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AB3, first strand: chain 'B' and resid 14 through 19 removed outlier: 3.682A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 132 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 147 current: chain 'B' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 186 current: chain 'B' and resid 213 through 215 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 213 through 215 current: chain 'B' and resid 267 through 269 Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 100 through 110 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB6, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB7, first strand: chain 'B' and resid 296 through 306 removed outlier: 5.409A pdb=" N ASP B 298 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB9, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AC1, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 19 removed outlier: 9.137A pdb=" N LEU C 29 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR C 137 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET C 31 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 135 " --> pdb=" O MET C 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU C 33 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU C 133 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER C 35 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 131 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C 37 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA C 129 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU C 39 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA C 127 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR C 41 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA C 121 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 119 " --> pdb=" O ILE C 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 147 current: chain 'C' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 185 current: chain 'C' and resid 267 through 269 Processing sheet with id=AC3, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC5, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AC6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC7, first strand: chain 'C' and resid 296 through 305 removed outlier: 5.522A pdb=" N ASP C 298 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA C 321 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AC9, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AD1, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AD2, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.153A pdb=" N MET D 31 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU D 136 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG D 134 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR D 126 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N SER D 43 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA D 124 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP D 45 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TYR D 122 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 47 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER D 120 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS D 49 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE D 118 " --> pdb=" O CYS D 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 147 current: chain 'D' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 186 current: chain 'D' and resid 213 through 215 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 213 through 215 current: chain 'D' and resid 267 through 269 Processing sheet with id=AD3, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 101 through 110 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD6, first strand: chain 'D' and resid 296 through 305 removed outlier: 5.496A pdb=" N ASP D 298 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA D 321 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL D 315 " --> pdb=" O PRO D 304 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 326 through 329 Processing sheet with id=AD8, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AD9, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AE2, first strand: chain 'E' and resid 34 through 38 removed outlier: 8.728A pdb=" N LEU E 34 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER E 51 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG E 36 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N SER E 51 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET E 70 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 84 through 86 removed outlier: 4.037A pdb=" N GLU E 109 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 149 through 156 Processing sheet with id=AE5, first strand: chain 'E' and resid 236 through 237 Processing sheet with id=AE6, first strand: chain 'E' and resid 175 through 176 removed outlier: 6.015A pdb=" N TYR E 199 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY E 209 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE8, first strand: chain 'E' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AF1, first strand: chain 'F' and resid 34 through 38 removed outlier: 8.768A pdb=" N LEU F 34 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER F 51 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG F 36 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N SER F 51 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET F 70 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS F 66 " --> pdb=" O GLY F 55 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 84 through 86 removed outlier: 4.060A pdb=" N GLU F 109 " --> pdb=" O PHE F 129 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 149 through 156 Processing sheet with id=AF4, first strand: chain 'F' and resid 236 through 237 Processing sheet with id=AF5, first strand: chain 'F' and resid 175 through 176 removed outlier: 4.711A pdb=" N TYR F 199 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY F 209 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 181 through 184 Processing sheet with id=AF7, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AF8, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AF9, first strand: chain 'G' and resid 34 through 38 removed outlier: 6.768A pdb=" N GLN G 49 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE G 37 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS G 47 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 27.763A pdb=" N LYS G 47 " --> pdb=" O ASP G 71 " (cutoff:3.500A) removed outlier: 22.907A pdb=" N ASP G 71 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 17.041A pdb=" N GLN G 49 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 13.853A pdb=" N TYR G 69 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 12.078A pdb=" N SER G 51 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N LEU G 67 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N GLN G 53 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N THR G 65 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY G 55 " --> pdb=" O ASP G 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 74 through 79 current: chain 'G' and resid 90 through 104 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 104 current: chain 'G' and resid 122 through 131 Processing sheet with id=AG1, first strand: chain 'G' and resid 148 through 156 Processing sheet with id=AG2, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AG3, first strand: chain 'G' and resid 175 through 176 removed outlier: 4.241A pdb=" N THR G 196 " --> pdb=" O THR G 230 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AG5, first strand: chain 'G' and resid 275 through 279 Processing sheet with id=AG6, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG7, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.757A pdb=" N GLN H 49 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE H 37 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS H 47 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N SER H 51 " --> pdb=" O MET H 70 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N MET H 70 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS H 66 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 84 through 86 removed outlier: 4.294A pdb=" N GLU H 109 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 149 through 156 Processing sheet with id=AH1, first strand: chain 'H' and resid 236 through 237 Processing sheet with id=AH2, first strand: chain 'H' and resid 175 through 176 Processing sheet with id=AH3, first strand: chain 'H' and resid 181 through 184 Processing sheet with id=AH4, first strand: chain 'H' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'I' and resid 143 through 144 removed outlier: 3.790A pdb=" N GLY I 125 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS I 119 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL I 123 " --> pdb=" O HIS I 119 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR I 126 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 185 through 189 removed outlier: 3.647A pdb=" N GLY I 192 " --> pdb=" O TRP I 189 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA I 193 " --> pdb=" O PRO I 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 200 through 204 current: chain 'I' and resid 224 through 234 removed outlier: 8.234A pdb=" N VAL I 225 " --> pdb=" O TRP I 245 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP I 245 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER I 241 " --> pdb=" O LEU I 229 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY I 231 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA I 239 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN I 233 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG I 237 " --> pdb=" O ASN I 233 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 117 through 118 removed outlier: 7.780A pdb=" N TYR J 126 " --> pdb=" O PRO J 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 185 through 189 removed outlier: 8.517A pdb=" N ALA J 193 " --> pdb=" O PRO J 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 200 through 204 current: chain 'J' and resid 224 through 234 removed outlier: 8.267A pdb=" N VAL J 225 " --> pdb=" O TRP J 245 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TRP J 245 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER J 241 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY J 231 " --> pdb=" O ALA J 239 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA J 239 " --> pdb=" O GLY J 231 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN J 233 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG J 237 " --> pdb=" O ASN J 233 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 143 through 144 removed outlier: 6.158A pdb=" N HIS K 119 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL K 123 " --> pdb=" O HIS K 119 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR K 126 " --> pdb=" O PRO K 137 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 185 through 189 removed outlier: 8.651A pdb=" N ALA K 193 " --> pdb=" O PRO K 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 200 through 204 current: chain 'K' and resid 224 through 234 removed outlier: 7.924A pdb=" N VAL K 225 " --> pdb=" O TRP K 245 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TRP K 245 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER K 241 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY K 231 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA K 239 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN K 233 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG K 237 " --> pdb=" O ASN K 233 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 143 through 144 removed outlier: 4.096A pdb=" N GLY L 125 " --> pdb=" O VAL L 117 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR L 126 " --> pdb=" O PRO L 137 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 185 through 188 removed outlier: 8.763A pdb=" N ALA L 193 " --> pdb=" O PRO L 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 200 through 204 current: chain 'L' and resid 224 through 233 removed outlier: 8.302A pdb=" N VAL L 225 " --> pdb=" O TRP L 245 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP L 245 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER L 241 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY L 231 " --> pdb=" O ALA L 239 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA L 239 " --> pdb=" O GLY L 231 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASN L 233 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG L 237 " --> pdb=" O ASN L 233 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 7 through 9 Processing sheet with id=AI5, first strand: chain 'W' and resid 7 through 9 Processing sheet with id=AI6, first strand: chain 'X' and resid 7 through 10 1164 hydrogen bonds defined for protein. 2976 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: 8.07 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8513 1.33 - 1.45: 7516 1.45 - 1.58: 17415 1.58 - 1.71: 0 1.71 - 1.83: 380 Bond restraints: 33824 Sorted by residual: bond pdb=" NE ARG V 36 " pdb=" CZ ARG V 36 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 9.17e+00 bond pdb=" CZ2 TRP J 261 " pdb=" CH2 TRP J 261 " ideal model delta sigma weight residual 1.368 1.424 -0.056 1.90e-02 2.77e+03 8.65e+00 bond pdb=" CZ2 TRP L 261 " pdb=" CH2 TRP L 261 " ideal model delta sigma weight residual 1.368 1.423 -0.055 1.90e-02 2.77e+03 8.25e+00 bond pdb=" CZ2 TRP I 261 " pdb=" CH2 TRP I 261 " ideal model delta sigma weight residual 1.368 1.422 -0.054 1.90e-02 2.77e+03 8.15e+00 bond pdb=" CZ2 TRP K 261 " pdb=" CH2 TRP K 261 " ideal model delta sigma weight residual 1.368 1.421 -0.053 1.90e-02 2.77e+03 7.80e+00 ... (remaining 33819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 40330 1.65 - 3.29: 4563 3.29 - 4.94: 572 4.94 - 6.59: 472 6.59 - 8.24: 141 Bond angle restraints: 46078 Sorted by residual: angle pdb=" C GLN U 19 " pdb=" N PRO U 20 " pdb=" CA PRO U 20 " ideal model delta sigma weight residual 119.66 126.83 -7.17 7.30e-01 1.88e+00 9.66e+01 angle pdb=" C TYR A 189 " pdb=" N PRO A 190 " pdb=" CA PRO A 190 " ideal model delta sigma weight residual 119.66 126.09 -6.43 7.20e-01 1.93e+00 7.99e+01 angle pdb=" C TYR D 189 " pdb=" N PRO D 190 " pdb=" CA PRO D 190 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.30e-01 1.88e+00 7.83e+01 angle pdb=" C HIS B 381 " pdb=" N PRO B 382 " pdb=" CA PRO B 382 " ideal model delta sigma weight residual 119.66 125.65 -5.99 7.20e-01 1.93e+00 6.92e+01 angle pdb=" C HIS A 381 " pdb=" N PRO A 382 " pdb=" CA PRO A 382 " ideal model delta sigma weight residual 119.66 125.58 -5.92 7.20e-01 1.93e+00 6.75e+01 ... (remaining 46073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 20181 21.33 - 42.67: 466 42.67 - 64.00: 89 64.00 - 85.33: 92 85.33 - 106.66: 42 Dihedral angle restraints: 20870 sinusoidal: 8567 harmonic: 12303 Sorted by residual: dihedral pdb=" CB CYS G 203 " pdb=" SG CYS G 203 " pdb=" SG CYS G 220 " pdb=" CB CYS G 220 " ideal model delta sinusoidal sigma weight residual -86.00 -169.61 83.61 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS V 22 " pdb=" SG CYS V 22 " pdb=" SG CYS V 26 " pdb=" CB CYS V 26 " ideal model delta sinusoidal sigma weight residual 93.00 172.61 -79.61 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 168.95 -75.95 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 20867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 5255 0.973 - 1.946: 0 1.946 - 2.918: 0 2.918 - 3.891: 0 3.891 - 4.864: 5 Chirality restraints: 5260 Sorted by residual: chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.47e+04 ... (remaining 5257 not shown) Planarity restraints: 5923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP K 261 " 0.029 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C TRP K 261 " -0.102 2.00e-02 2.50e+03 pdb=" O TRP K 261 " 0.037 2.00e-02 2.50e+03 pdb=" OXT TRP K 261 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 261 " -0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C TRP L 261 " 0.096 2.00e-02 2.50e+03 pdb=" O TRP L 261 " -0.035 2.00e-02 2.50e+03 pdb=" OXT TRP L 261 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 439 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C HIS C 439 " 0.074 2.00e-02 2.50e+03 pdb=" O HIS C 439 " -0.026 2.00e-02 2.50e+03 pdb=" OXT HIS C 439 " -0.026 2.00e-02 2.50e+03 ... (remaining 5920 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1142 2.69 - 3.24: 31265 3.24 - 3.80: 53230 3.80 - 4.35: 68060 4.35 - 4.90: 114844 Nonbonded interactions: 268541 Sorted by model distance: nonbonded pdb=" OH TYR G 69 " pdb=" OD1 ASP G 117 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR H 69 " pdb=" OD1 ASP H 117 " model vdw 2.139 3.040 nonbonded pdb=" OE1 GLU G 40 " pdb=" OH TYR G 156 " model vdw 2.164 3.040 nonbonded pdb=" OE1 GLU F 40 " pdb=" OH TYR F 156 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLU H 166 " pdb=" OH TYR X 48 " model vdw 2.249 3.040 ... (remaining 268536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 7 through 417) selection = (chain 'F' and resid 7 through 417) selection = (chain 'G' and resid 7 through 417) selection = (chain 'H' and resid 7 through 417) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.100 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.130 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.012 0.424 33919 Z= 0.651 Angle : 1.292 15.221 46296 Z= 0.885 Chirality : 0.157 4.864 5260 Planarity : 0.005 0.059 5915 Dihedral : 12.462 106.664 12763 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.69 % Favored : 98.21 % Rotamer: Outliers : 0.08 % Allowed : 0.72 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.47 (0.12), residues: 4201 helix: 0.26 (0.19), residues: 568 sheet: 1.28 (0.14), residues: 1333 loop : 1.18 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 244 TYR 0.023 0.003 TYR V 27 PHE 0.012 0.002 PHE H 100 TRP 0.026 0.003 TRP G 235 HIS 0.005 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.01140 (33824) covalent geometry : angle 1.26580 (46078) SS BOND : bond 0.06018 ( 67) SS BOND : angle 4.58115 ( 134) hydrogen bonds : bond 0.15699 ( 1164) hydrogen bonds : angle 7.58219 ( 2976) link_BETA1-4 : bond 0.05400 ( 16) link_BETA1-4 : angle 2.86513 ( 48) link_BETA1-6 : bond 0.04498 ( 4) link_BETA1-6 : angle 2.19099 ( 12) link_NAG-ASN : bond 0.04548 ( 8) link_NAG-ASN : angle 2.33532 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 837 time to evaluate : 1.341 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: U 15 PHE cc_start: 0.7404 (p90) cc_final: 0.6870 (p90) REVERT: U 48 TYR cc_start: 0.7442 (m-80) cc_final: 0.6978 (m-80) REVERT: A 311 ASP cc_start: 0.8152 (t0) cc_final: 0.7903 (t0) REVERT: A 401 ASP cc_start: 0.8509 (m-30) cc_final: 0.8121 (m-30) REVERT: B 212 ASP cc_start: 0.8054 (t0) cc_final: 0.7556 (p0) REVERT: B 269 MET cc_start: 0.8592 (mtm) cc_final: 0.8380 (mtp) REVERT: B 428 LEU cc_start: 0.8822 (tp) cc_final: 0.8412 (tp) REVERT: C 166 MET cc_start: 0.8469 (mmm) cc_final: 0.8086 (mmt) REVERT: C 324 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8062 (mttp) REVERT: E 97 MET cc_start: 0.8860 (tpp) cc_final: 0.8448 (tpt) REVERT: F 97 MET cc_start: 0.8710 (tpp) cc_final: 0.8479 (tpp) REVERT: F 366 MET cc_start: 0.8335 (tpt) cc_final: 0.7964 (ttp) REVERT: G 6 PHE cc_start: 0.6320 (m-80) cc_final: 0.5485 (m-10) REVERT: G 70 MET cc_start: 0.8547 (mmm) cc_final: 0.8062 (mmp) REVERT: G 171 MET cc_start: 0.8317 (ttm) cc_final: 0.7272 (ttp) REVERT: G 248 LEU cc_start: 0.8603 (mt) cc_final: 0.8269 (tt) REVERT: H 232 HIS cc_start: 0.7442 (m170) cc_final: 0.7237 (m90) REVERT: H 314 LYS cc_start: 0.7548 (mttt) cc_final: 0.6028 (ttpp) REVERT: H 401 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7228 (mm-30) REVERT: J 172 LYS cc_start: 0.9327 (ttmt) cc_final: 0.8515 (ttmm) REVERT: J 179 THR cc_start: 0.9122 (t) cc_final: 0.8882 (m) REVERT: K 119 HIS cc_start: 0.8043 (t70) cc_final: 0.7521 (t70) REVERT: K 133 LYS cc_start: 0.8140 (mttp) cc_final: 0.7879 (mttp) REVERT: K 221 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8205 (tptp) REVERT: L 111 ASN cc_start: 0.7677 (t0) cc_final: 0.6631 (p0) REVERT: L 155 LYS cc_start: 0.7595 (mttt) cc_final: 0.7237 (mtmm) REVERT: L 205 THR cc_start: 0.8078 (p) cc_final: 0.7818 (p) REVERT: L 219 ASP cc_start: 0.8063 (p0) cc_final: 0.7561 (p0) REVERT: L 223 ARG cc_start: 0.8416 (mpp80) cc_final: 0.7511 (mtm180) REVERT: L 225 VAL cc_start: 0.8912 (t) cc_final: 0.8683 (p) REVERT: W 7 MET cc_start: 0.7461 (mmm) cc_final: 0.7150 (mmp) REVERT: X 43 MET cc_start: 0.8018 (mmm) cc_final: 0.7769 (tpp) outliers start: 3 outliers final: 1 residues processed: 839 average time/residue: 0.2373 time to fit residues: 308.7377 Evaluate side-chains 520 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.0010 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 ASN C 138 GLN C 331 HIS D 252 GLN E 218 ASN F 72 ASN F 195 GLN G 146 GLN ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 341 GLN H 158 GLN I 180 HIS ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 233 ASN K 233 ASN L 139 HIS ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN ** X 41 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.134491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.089956 restraints weight = 53567.637| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.67 r_work: 0.2939 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33919 Z= 0.161 Angle : 0.654 18.004 46296 Z= 0.336 Chirality : 0.048 0.897 5260 Planarity : 0.004 0.068 5915 Dihedral : 8.550 77.427 5130 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.52 % Favored : 98.45 % Rotamer: Outliers : 1.93 % Allowed : 7.14 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.33 (0.12), residues: 4201 helix: 1.33 (0.21), residues: 565 sheet: 1.21 (0.14), residues: 1276 loop : 0.72 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 200 TYR 0.033 0.002 TYR U 27 PHE 0.021 0.002 PHE V 15 TRP 0.012 0.001 TRP G 235 HIS 0.008 0.001 HIS I 191 Details of bonding type rmsd covalent geometry : bond 0.00367 (33824) covalent geometry : angle 0.63215 (46078) SS BOND : bond 0.00416 ( 67) SS BOND : angle 1.53873 ( 134) hydrogen bonds : bond 0.04248 ( 1164) hydrogen bonds : angle 5.80287 ( 2976) link_BETA1-4 : bond 0.01015 ( 16) link_BETA1-4 : angle 3.15119 ( 48) link_BETA1-6 : bond 0.00287 ( 4) link_BETA1-6 : angle 1.54150 ( 12) link_NAG-ASN : bond 0.00464 ( 8) link_NAG-ASN : angle 4.96476 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 575 time to evaluate : 1.259 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: U 15 PHE cc_start: 0.6576 (p90) cc_final: 0.6315 (p90) REVERT: U 32 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8132 (tm-30) REVERT: U 36 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7576 (mtp-110) REVERT: U 48 TYR cc_start: 0.7404 (m-80) cc_final: 0.7126 (m-80) REVERT: A 30 GLU cc_start: 0.8648 (tt0) cc_final: 0.8286 (tt0) REVERT: A 95 PHE cc_start: 0.7993 (t80) cc_final: 0.7774 (t80) REVERT: A 374 VAL cc_start: 0.8813 (m) cc_final: 0.8559 (p) REVERT: B 88 MET cc_start: 0.8055 (mmm) cc_final: 0.7561 (mtp) REVERT: B 166 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8715 (mpp) REVERT: B 212 ASP cc_start: 0.8277 (t0) cc_final: 0.7276 (p0) REVERT: B 364 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8753 (mm-30) REVERT: C 166 MET cc_start: 0.8551 (mmm) cc_final: 0.8106 (mmt) REVERT: C 189 TYR cc_start: 0.9109 (p90) cc_final: 0.8727 (p90) REVERT: C 298 ASP cc_start: 0.8696 (t0) cc_final: 0.8395 (t0) REVERT: C 324 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7525 (mttp) REVERT: D 284 ASP cc_start: 0.8788 (m-30) cc_final: 0.8547 (m-30) REVERT: D 295 SER cc_start: 0.9100 (t) cc_final: 0.8778 (p) REVERT: D 300 SER cc_start: 0.9287 (t) cc_final: 0.8925 (p) REVERT: E 70 MET cc_start: 0.8563 (mmm) cc_final: 0.8038 (mmp) REVERT: E 97 MET cc_start: 0.9009 (tpp) cc_final: 0.8626 (tpt) REVERT: E 171 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8259 (ttp) REVERT: E 251 ARG cc_start: 0.6013 (ttm170) cc_final: 0.5657 (ttm170) REVERT: F 97 MET cc_start: 0.8869 (tpp) cc_final: 0.8614 (tpp) REVERT: F 121 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8757 (pt) REVERT: F 307 GLN cc_start: 0.8700 (mt0) cc_final: 0.8419 (mm-40) REVERT: F 366 MET cc_start: 0.8397 (tpt) cc_final: 0.7465 (ttp) REVERT: G 70 MET cc_start: 0.8761 (mmm) cc_final: 0.8472 (tpp) REVERT: G 171 MET cc_start: 0.8513 (ttm) cc_final: 0.8025 (ttm) REVERT: G 199 TYR cc_start: 0.7412 (p90) cc_final: 0.6514 (p90) REVERT: G 307 GLN cc_start: 0.8848 (mt0) cc_final: 0.8638 (mt0) REVERT: H 74 MET cc_start: 0.8105 (mmm) cc_final: 0.7841 (mmm) REVERT: H 79 GLU cc_start: 0.8481 (mp0) cc_final: 0.8184 (pm20) REVERT: H 166 GLU cc_start: 0.8929 (pm20) cc_final: 0.8203 (pm20) REVERT: H 168 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: H 181 MET cc_start: 0.8333 (mmt) cc_final: 0.7646 (mmp) REVERT: H 188 VAL cc_start: 0.8460 (t) cc_final: 0.8089 (t) REVERT: H 200 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8228 (ttmm) REVERT: H 314 LYS cc_start: 0.7512 (mttt) cc_final: 0.6042 (ttmt) REVERT: H 372 SER cc_start: 0.8671 (t) cc_final: 0.8426 (p) REVERT: H 382 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (p) REVERT: I 161 ASP cc_start: 0.8090 (t0) cc_final: 0.7766 (t0) REVERT: I 188 ASN cc_start: 0.8135 (m-40) cc_final: 0.7621 (t0) REVERT: I 190 HIS cc_start: 0.8716 (t70) cc_final: 0.8472 (t70) REVERT: I 195 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7447 (pp30) REVERT: I 223 ARG cc_start: 0.6931 (mtm180) cc_final: 0.6712 (mtm110) REVERT: J 161 ASP cc_start: 0.7739 (t0) cc_final: 0.7534 (t0) REVERT: J 163 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7869 (mt-10) REVERT: J 168 PRO cc_start: 0.8315 (Cg_exo) cc_final: 0.7783 (Cg_endo) REVERT: J 172 LYS cc_start: 0.9568 (ttmt) cc_final: 0.8899 (ttmm) REVERT: J 215 ARG cc_start: 0.8393 (mmt90) cc_final: 0.8029 (mmt90) REVERT: J 219 ASP cc_start: 0.7758 (p0) cc_final: 0.7539 (p0) REVERT: J 223 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7704 (mtm110) REVERT: K 117 VAL cc_start: 0.8173 (t) cc_final: 0.7765 (p) REVERT: K 135 MET cc_start: 0.7535 (mtt) cc_final: 0.7314 (mmm) REVERT: K 151 LYS cc_start: 0.9139 (pttm) cc_final: 0.8873 (pttm) REVERT: K 178 PHE cc_start: 0.8290 (p90) cc_final: 0.7959 (p90) REVERT: K 218 PHE cc_start: 0.8171 (m-80) cc_final: 0.7927 (m-80) REVERT: K 221 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8034 (tptp) REVERT: K 245 TRP cc_start: 0.8318 (p90) cc_final: 0.7834 (p90) REVERT: L 111 ASN cc_start: 0.7302 (t0) cc_final: 0.6486 (p0) REVERT: L 112 ASP cc_start: 0.6910 (t70) cc_final: 0.6684 (t70) REVERT: L 155 LYS cc_start: 0.7368 (mttt) cc_final: 0.7165 (mtmt) REVERT: L 173 SER cc_start: 0.8606 (p) cc_final: 0.8165 (m) REVERT: L 187 TYR cc_start: 0.9071 (m-80) cc_final: 0.8699 (m-80) REVERT: L 219 ASP cc_start: 0.7736 (p0) cc_final: 0.7031 (p0) REVERT: L 223 ARG cc_start: 0.7266 (mpp80) cc_final: 0.6542 (mtm180) REVERT: L 225 VAL cc_start: 0.8917 (t) cc_final: 0.8548 (p) REVERT: L 234 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8724 (mt-10) REVERT: V 37 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7386 (tmm) REVERT: W 15 PHE cc_start: 0.5523 (p90) cc_final: 0.4693 (p90) REVERT: W 49 GLN cc_start: 0.7867 (mp10) cc_final: 0.7514 (mp10) REVERT: X 7 MET cc_start: 0.5947 (mmm) cc_final: 0.5732 (mmm) REVERT: X 49 GLN cc_start: 0.8315 (mp10) cc_final: 0.7880 (mp10) outliers start: 70 outliers final: 44 residues processed: 614 average time/residue: 0.2114 time to fit residues: 208.3987 Evaluate side-chains 555 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 505 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 252 LYS Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain V residue 37 MET Chi-restraints excluded: chain V residue 51 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 54 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 359 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 377 optimal weight: 20.0000 chunk 409 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 41 ASN C 252 GLN C 260 GLN D 331 HIS F 127 HIS F 195 GLN G 236 GLN H 158 GLN I 180 HIS I 190 HIS J 233 ASN ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.085032 restraints weight = 53973.664| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.64 r_work: 0.2855 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 33919 Z= 0.274 Angle : 0.655 15.699 46296 Z= 0.335 Chirality : 0.048 0.599 5260 Planarity : 0.005 0.057 5915 Dihedral : 6.585 86.068 5130 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 8.77 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.91 (0.12), residues: 4201 helix: 1.52 (0.21), residues: 565 sheet: 0.87 (0.14), residues: 1258 loop : 0.33 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 289 TYR 0.025 0.002 TYR U 27 PHE 0.020 0.002 PHE L 218 TRP 0.014 0.002 TRP E 339 HIS 0.011 0.001 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00642 (33824) covalent geometry : angle 0.63911 (46078) SS BOND : bond 0.00506 ( 67) SS BOND : angle 1.27255 ( 134) hydrogen bonds : bond 0.04014 ( 1164) hydrogen bonds : angle 5.51626 ( 2976) link_BETA1-4 : bond 0.00558 ( 16) link_BETA1-4 : angle 2.58884 ( 48) link_BETA1-6 : bond 0.00270 ( 4) link_BETA1-6 : angle 1.29044 ( 12) link_NAG-ASN : bond 0.00413 ( 8) link_NAG-ASN : angle 4.41047 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 528 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6465 (p90) cc_final: 0.6068 (p90) REVERT: U 32 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7826 (tm-30) REVERT: U 36 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7193 (ttm110) REVERT: U 37 MET cc_start: 0.8582 (ptm) cc_final: 0.8271 (ptm) REVERT: A 95 PHE cc_start: 0.8137 (t80) cc_final: 0.7914 (t80) REVERT: B 88 MET cc_start: 0.8139 (mmm) cc_final: 0.7817 (mtp) REVERT: B 166 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: B 212 ASP cc_start: 0.8294 (t0) cc_final: 0.7172 (p0) REVERT: B 364 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 298 ASP cc_start: 0.8879 (t0) cc_final: 0.8435 (t0) REVERT: C 324 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7606 (mttp) REVERT: D 284 ASP cc_start: 0.8675 (m-30) cc_final: 0.8395 (m-30) REVERT: D 295 SER cc_start: 0.9141 (t) cc_final: 0.8812 (p) REVERT: D 407 MET cc_start: 0.8331 (tpt) cc_final: 0.7916 (tpt) REVERT: E 70 MET cc_start: 0.8551 (mmm) cc_final: 0.8083 (mmp) REVERT: E 97 MET cc_start: 0.9008 (tpp) cc_final: 0.8635 (tpt) REVERT: F 97 MET cc_start: 0.8845 (tpp) cc_final: 0.8642 (tpp) REVERT: F 121 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8535 (pt) REVERT: F 190 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7202 (pt) REVERT: F 215 LYS cc_start: 0.7240 (mttt) cc_final: 0.6936 (mttt) REVERT: F 307 GLN cc_start: 0.8715 (mt0) cc_final: 0.8447 (mm-40) REVERT: F 366 MET cc_start: 0.8365 (tpt) cc_final: 0.7375 (ttt) REVERT: G 70 MET cc_start: 0.8878 (mmm) cc_final: 0.8504 (tpp) REVERT: G 171 MET cc_start: 0.8441 (ttm) cc_final: 0.8093 (ttm) REVERT: G 199 TYR cc_start: 0.7292 (p90) cc_final: 0.6889 (p90) REVERT: G 224 GLN cc_start: 0.8835 (mt0) cc_final: 0.8561 (mt0) REVERT: G 307 GLN cc_start: 0.8873 (mt0) cc_final: 0.8565 (mt0) REVERT: G 362 LEU cc_start: 0.8791 (mt) cc_final: 0.8525 (mt) REVERT: H 79 GLU cc_start: 0.8530 (mp0) cc_final: 0.8269 (pm20) REVERT: H 168 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: H 181 MET cc_start: 0.8243 (mmt) cc_final: 0.7433 (mmp) REVERT: H 200 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8166 (ttmm) REVERT: H 314 LYS cc_start: 0.7673 (mttt) cc_final: 0.5254 (tttt) REVERT: H 372 SER cc_start: 0.8671 (t) cc_final: 0.8442 (p) REVERT: I 161 ASP cc_start: 0.8331 (t0) cc_final: 0.7965 (t0) REVERT: I 188 ASN cc_start: 0.8266 (m-40) cc_final: 0.7698 (t0) REVERT: I 190 HIS cc_start: 0.8564 (t-90) cc_final: 0.8359 (t70) REVERT: J 161 ASP cc_start: 0.7746 (t0) cc_final: 0.7206 (t0) REVERT: J 163 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7708 (mt-10) REVERT: J 168 PRO cc_start: 0.8216 (Cg_exo) cc_final: 0.7680 (Cg_endo) REVERT: J 172 LYS cc_start: 0.9541 (ttmt) cc_final: 0.8985 (ptmt) REVERT: J 190 HIS cc_start: 0.8895 (t-90) cc_final: 0.8509 (t-90) REVERT: K 135 MET cc_start: 0.8166 (mtt) cc_final: 0.7429 (mmm) REVERT: K 151 LYS cc_start: 0.9086 (pttm) cc_final: 0.8842 (pttm) REVERT: K 161 ASP cc_start: 0.8061 (t70) cc_final: 0.7806 (t0) REVERT: K 178 PHE cc_start: 0.8581 (p90) cc_final: 0.8368 (p90) REVERT: K 218 PHE cc_start: 0.8218 (m-80) cc_final: 0.7983 (m-80) REVERT: K 221 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7852 (tptp) REVERT: K 245 TRP cc_start: 0.8380 (p90) cc_final: 0.7951 (p90) REVERT: L 111 ASN cc_start: 0.6879 (t0) cc_final: 0.6025 (p0) REVERT: L 112 ASP cc_start: 0.6780 (t70) cc_final: 0.6504 (t70) REVERT: L 161 ASP cc_start: 0.8863 (t0) cc_final: 0.8626 (t0) REVERT: L 173 SER cc_start: 0.8746 (p) cc_final: 0.8382 (m) REVERT: L 190 HIS cc_start: 0.9146 (t-90) cc_final: 0.8940 (t70) REVERT: L 219 ASP cc_start: 0.7932 (p0) cc_final: 0.7278 (p0) REVERT: L 223 ARG cc_start: 0.7274 (mpp80) cc_final: 0.6340 (mtm180) REVERT: L 260 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8982 (mt-10) REVERT: V 37 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: W 15 PHE cc_start: 0.5871 (p90) cc_final: 0.5152 (p90) REVERT: W 49 GLN cc_start: 0.8086 (mp10) cc_final: 0.7682 (mp10) REVERT: X 32 GLU cc_start: 0.6582 (tp30) cc_final: 0.6369 (tp30) REVERT: X 41 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8041 (t0) REVERT: X 49 GLN cc_start: 0.8442 (mp10) cc_final: 0.7931 (mp10) outliers start: 98 outliers final: 65 residues processed: 583 average time/residue: 0.2145 time to fit residues: 201.4583 Evaluate side-chains 571 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 500 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 373 VAL Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain V residue 37 MET Chi-restraints excluded: chain W residue 26 CYS Chi-restraints excluded: chain X residue 41 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 301 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 139 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 368 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS F 195 GLN I 180 HIS J 233 ASN ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.084998 restraints weight = 53693.929| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.63 r_work: 0.2848 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 33919 Z= 0.238 Angle : 0.618 15.281 46296 Z= 0.314 Chirality : 0.047 0.522 5260 Planarity : 0.004 0.049 5915 Dihedral : 5.842 87.349 5130 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.81 % Allowed : 10.12 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.69 (0.12), residues: 4201 helix: 1.58 (0.21), residues: 566 sheet: 0.65 (0.14), residues: 1248 loop : 0.17 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 119 TYR 0.027 0.002 TYR U 27 PHE 0.038 0.002 PHE F 410 TRP 0.013 0.001 TRP G 235 HIS 0.011 0.001 HIS K 119 Details of bonding type rmsd covalent geometry : bond 0.00559 (33824) covalent geometry : angle 0.60305 (46078) SS BOND : bond 0.00411 ( 67) SS BOND : angle 1.19763 ( 134) hydrogen bonds : bond 0.03693 ( 1164) hydrogen bonds : angle 5.39561 ( 2976) link_BETA1-4 : bond 0.00500 ( 16) link_BETA1-4 : angle 2.35114 ( 48) link_BETA1-6 : bond 0.00245 ( 4) link_BETA1-6 : angle 1.34973 ( 12) link_NAG-ASN : bond 0.00369 ( 8) link_NAG-ASN : angle 4.29805 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 531 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6501 (p90) cc_final: 0.6083 (p90) REVERT: U 30 GLU cc_start: 0.7226 (tt0) cc_final: 0.6955 (tt0) REVERT: U 32 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7742 (tm-30) REVERT: U 36 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7323 (ttm110) REVERT: A 95 PHE cc_start: 0.8125 (t80) cc_final: 0.7920 (t80) REVERT: B 88 MET cc_start: 0.8177 (mmm) cc_final: 0.7887 (mtp) REVERT: B 166 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8813 (mtm) REVERT: B 212 ASP cc_start: 0.8288 (t0) cc_final: 0.7138 (p0) REVERT: B 364 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8656 (mm-30) REVERT: C 298 ASP cc_start: 0.8955 (t0) cc_final: 0.8571 (t0) REVERT: C 311 ASP cc_start: 0.8484 (t0) cc_final: 0.8271 (p0) REVERT: C 324 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7667 (mttp) REVERT: C 338 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8409 (p) REVERT: D 284 ASP cc_start: 0.8701 (m-30) cc_final: 0.8386 (m-30) REVERT: D 295 SER cc_start: 0.9249 (t) cc_final: 0.8961 (p) REVERT: D 298 ASP cc_start: 0.8064 (t0) cc_final: 0.7858 (t0) REVERT: D 338 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8754 (p) REVERT: D 407 MET cc_start: 0.8319 (tpt) cc_final: 0.8002 (tpt) REVERT: E 70 MET cc_start: 0.8523 (mmm) cc_final: 0.8149 (tpt) REVERT: E 97 MET cc_start: 0.8992 (tpp) cc_final: 0.8680 (tpt) REVERT: E 199 TYR cc_start: 0.8368 (p90) cc_final: 0.8047 (p90) REVERT: E 251 ARG cc_start: 0.6332 (ttm170) cc_final: 0.5893 (ttm170) REVERT: F 107 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8829 (tmtm) REVERT: F 121 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (pt) REVERT: F 215 LYS cc_start: 0.7368 (mttt) cc_final: 0.6854 (mtpt) REVERT: F 307 GLN cc_start: 0.8679 (mt0) cc_final: 0.8434 (mm-40) REVERT: F 366 MET cc_start: 0.8335 (tpt) cc_final: 0.7341 (ttt) REVERT: G 70 MET cc_start: 0.8931 (mmm) cc_final: 0.8508 (tpp) REVERT: G 171 MET cc_start: 0.8491 (ttm) cc_final: 0.8067 (ttm) REVERT: G 181 MET cc_start: 0.8446 (mtm) cc_final: 0.8115 (mtp) REVERT: G 224 GLN cc_start: 0.8838 (mt0) cc_final: 0.8591 (mt0) REVERT: G 307 GLN cc_start: 0.8881 (mt0) cc_final: 0.8563 (mt0) REVERT: H 79 GLU cc_start: 0.8547 (mp0) cc_final: 0.8295 (pm20) REVERT: H 127 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8628 (m-70) REVERT: H 168 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: H 181 MET cc_start: 0.8122 (mmt) cc_final: 0.7571 (mmp) REVERT: H 314 LYS cc_start: 0.7728 (mttt) cc_final: 0.5351 (tttt) REVERT: H 372 SER cc_start: 0.8537 (t) cc_final: 0.8326 (p) REVERT: I 161 ASP cc_start: 0.8412 (t0) cc_final: 0.8022 (t0) REVERT: I 188 ASN cc_start: 0.8215 (m-40) cc_final: 0.7868 (p0) REVERT: I 190 HIS cc_start: 0.8621 (t-90) cc_final: 0.8364 (t70) REVERT: J 141 LYS cc_start: 0.6544 (tmtt) cc_final: 0.6336 (tmtt) REVERT: J 161 ASP cc_start: 0.7668 (t0) cc_final: 0.7278 (t0) REVERT: J 162 LEU cc_start: 0.8184 (tt) cc_final: 0.7980 (tt) REVERT: J 163 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7506 (mt-10) REVERT: J 168 PRO cc_start: 0.8143 (Cg_exo) cc_final: 0.7532 (Cg_endo) REVERT: J 172 LYS cc_start: 0.9533 (ttmt) cc_final: 0.8881 (mtmm) REVERT: J 190 HIS cc_start: 0.8975 (t-90) cc_final: 0.8549 (t-90) REVERT: J 252 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8693 (tttm) REVERT: J 260 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7201 (tp30) REVERT: K 119 HIS cc_start: 0.8567 (t-90) cc_final: 0.8312 (t-90) REVERT: K 151 LYS cc_start: 0.9078 (pttm) cc_final: 0.8788 (pttt) REVERT: K 161 ASP cc_start: 0.8109 (t70) cc_final: 0.7769 (t0) REVERT: K 187 TYR cc_start: 0.8009 (m-80) cc_final: 0.7618 (m-80) REVERT: K 212 ASP cc_start: 0.8635 (t0) cc_final: 0.8234 (m-30) REVERT: K 218 PHE cc_start: 0.8256 (m-80) cc_final: 0.7982 (m-80) REVERT: K 245 TRP cc_start: 0.8341 (p90) cc_final: 0.7852 (p90) REVERT: L 161 ASP cc_start: 0.8879 (t0) cc_final: 0.8611 (t0) REVERT: L 173 SER cc_start: 0.8524 (p) cc_final: 0.8151 (m) REVERT: L 186 TYR cc_start: 0.8740 (m-80) cc_final: 0.8302 (m-80) REVERT: L 219 ASP cc_start: 0.7991 (p0) cc_final: 0.7361 (p0) REVERT: L 223 ARG cc_start: 0.7326 (mpp80) cc_final: 0.6510 (mtm180) REVERT: L 260 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8982 (mt-10) REVERT: V 49 GLN cc_start: 0.8043 (mp10) cc_final: 0.7673 (pm20) REVERT: W 15 PHE cc_start: 0.5994 (p90) cc_final: 0.5385 (p90) REVERT: W 43 MET cc_start: 0.8653 (mmp) cc_final: 0.8439 (mmp) REVERT: W 49 GLN cc_start: 0.8212 (mp10) cc_final: 0.7817 (mp10) REVERT: X 37 MET cc_start: 0.8766 (ptm) cc_final: 0.8548 (ptm) REVERT: X 41 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7989 (t0) REVERT: X 49 GLN cc_start: 0.8474 (mp10) cc_final: 0.8059 (mp10) outliers start: 102 outliers final: 73 residues processed: 586 average time/residue: 0.2160 time to fit residues: 203.7403 Evaluate side-chains 592 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 511 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 371 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 252 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain X residue 41 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 257 optimal weight: 5.9990 chunk 6 optimal weight: 0.0030 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 401 optimal weight: 40.0000 chunk 191 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 312 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 HIS D 264 ASN E 72 ASN F 195 GLN I 180 HIS J 233 ASN L 139 HIS ** X 41 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.128662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.085563 restraints weight = 53980.855| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.48 r_work: 0.2889 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33919 Z= 0.138 Angle : 0.568 17.593 46296 Z= 0.286 Chirality : 0.045 0.472 5260 Planarity : 0.004 0.051 5915 Dihedral : 5.408 88.625 5130 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.26 % Allowed : 11.39 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.70 (0.12), residues: 4201 helix: 1.67 (0.22), residues: 565 sheet: 0.67 (0.15), residues: 1179 loop : 0.15 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 223 TYR 0.022 0.001 TYR U 27 PHE 0.017 0.001 PHE F 410 TRP 0.015 0.001 TRP G 235 HIS 0.006 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00314 (33824) covalent geometry : angle 0.55232 (46078) SS BOND : bond 0.00381 ( 67) SS BOND : angle 1.36566 ( 134) hydrogen bonds : bond 0.03342 ( 1164) hydrogen bonds : angle 5.18328 ( 2976) link_BETA1-4 : bond 0.00447 ( 16) link_BETA1-4 : angle 2.07308 ( 48) link_BETA1-6 : bond 0.00325 ( 4) link_BETA1-6 : angle 1.29917 ( 12) link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 4.10904 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 542 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6920 (p90) cc_final: 0.6480 (p90) REVERT: U 30 GLU cc_start: 0.7419 (tt0) cc_final: 0.6965 (tt0) REVERT: U 32 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7855 (tm-30) REVERT: U 36 ARG cc_start: 0.7393 (ttm110) cc_final: 0.6763 (mtp-110) REVERT: U 52 GLN cc_start: 0.8226 (mm110) cc_final: 0.8011 (mm110) REVERT: B 88 MET cc_start: 0.8335 (mmm) cc_final: 0.7954 (mtp) REVERT: B 166 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8616 (mtm) REVERT: B 212 ASP cc_start: 0.8419 (t0) cc_final: 0.7306 (p0) REVERT: B 364 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8622 (mm-30) REVERT: C 2 GLU cc_start: 0.8607 (tt0) cc_final: 0.8232 (tp30) REVERT: C 298 ASP cc_start: 0.8870 (t0) cc_final: 0.8586 (t0) REVERT: C 324 LYS cc_start: 0.8418 (mtmm) cc_final: 0.7967 (mttp) REVERT: C 400 GLN cc_start: 0.8742 (pm20) cc_final: 0.8446 (pm20) REVERT: D 166 MET cc_start: 0.8935 (mmt) cc_final: 0.8653 (mmp) REVERT: D 284 ASP cc_start: 0.8729 (m-30) cc_final: 0.8455 (m-30) REVERT: D 295 SER cc_start: 0.9303 (t) cc_final: 0.9070 (p) REVERT: D 407 MET cc_start: 0.8619 (tpt) cc_final: 0.8264 (tpt) REVERT: E 70 MET cc_start: 0.8665 (mmm) cc_final: 0.8279 (tpt) REVERT: E 97 MET cc_start: 0.9181 (tpp) cc_final: 0.8973 (tpt) REVERT: E 199 TYR cc_start: 0.8291 (p90) cc_final: 0.7967 (p90) REVERT: E 251 ARG cc_start: 0.6329 (ttm170) cc_final: 0.5792 (ttm170) REVERT: E 381 MET cc_start: 0.7793 (mmm) cc_final: 0.7396 (mmm) REVERT: F 158 GLN cc_start: 0.8609 (mt0) cc_final: 0.8340 (mm-40) REVERT: F 166 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7979 (mm-30) REVERT: F 215 LYS cc_start: 0.7344 (mttt) cc_final: 0.6992 (mttt) REVERT: F 366 MET cc_start: 0.8618 (tpt) cc_final: 0.7635 (ttp) REVERT: G 70 MET cc_start: 0.9107 (mmm) cc_final: 0.8532 (tpt) REVERT: G 171 MET cc_start: 0.8332 (ttm) cc_final: 0.8081 (ttm) REVERT: G 199 TYR cc_start: 0.7465 (p90) cc_final: 0.7019 (p90) REVERT: G 224 GLN cc_start: 0.8908 (mt0) cc_final: 0.8652 (mt0) REVERT: G 307 GLN cc_start: 0.8919 (mt0) cc_final: 0.8698 (mt0) REVERT: H 74 MET cc_start: 0.8110 (mmm) cc_final: 0.7898 (mmm) REVERT: H 181 MET cc_start: 0.7990 (mmt) cc_final: 0.7419 (mmp) REVERT: H 314 LYS cc_start: 0.7932 (mttt) cc_final: 0.5674 (tttt) REVERT: I 161 ASP cc_start: 0.8530 (t0) cc_final: 0.8061 (t0) REVERT: I 188 ASN cc_start: 0.8355 (m-40) cc_final: 0.8064 (p0) REVERT: I 190 HIS cc_start: 0.8443 (t-90) cc_final: 0.8206 (t70) REVERT: I 219 ASP cc_start: 0.7688 (p0) cc_final: 0.6788 (p0) REVERT: I 223 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7138 (mtm-85) REVERT: J 141 LYS cc_start: 0.6838 (tmtt) cc_final: 0.6568 (tmtt) REVERT: J 161 ASP cc_start: 0.7931 (t0) cc_final: 0.7539 (t0) REVERT: J 162 LEU cc_start: 0.8566 (tt) cc_final: 0.8357 (tt) REVERT: J 163 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7833 (mt-10) REVERT: J 168 PRO cc_start: 0.8554 (Cg_exo) cc_final: 0.8065 (Cg_endo) REVERT: J 172 LYS cc_start: 0.9621 (ttmt) cc_final: 0.8891 (ttmm) REVERT: J 190 HIS cc_start: 0.8942 (t-90) cc_final: 0.8505 (t-90) REVERT: J 219 ASP cc_start: 0.7782 (p0) cc_final: 0.7486 (p0) REVERT: J 223 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7966 (mtm110) REVERT: J 252 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8912 (tttm) REVERT: J 260 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7356 (tp30) REVERT: K 151 LYS cc_start: 0.9180 (pttm) cc_final: 0.8867 (pttt) REVERT: K 161 ASP cc_start: 0.8365 (t70) cc_final: 0.7938 (t0) REVERT: K 209 LYS cc_start: 0.9115 (pttm) cc_final: 0.8678 (pttm) REVERT: K 218 PHE cc_start: 0.8367 (m-80) cc_final: 0.8110 (m-80) REVERT: K 221 LYS cc_start: 0.8485 (mmtt) cc_final: 0.7939 (tptp) REVERT: K 245 TRP cc_start: 0.8394 (p90) cc_final: 0.8052 (p90) REVERT: L 161 ASP cc_start: 0.9108 (t0) cc_final: 0.8854 (t0) REVERT: L 173 SER cc_start: 0.8667 (p) cc_final: 0.8258 (m) REVERT: L 219 ASP cc_start: 0.8260 (p0) cc_final: 0.7829 (p0) REVERT: L 223 ARG cc_start: 0.7777 (mpp80) cc_final: 0.7170 (mtm180) REVERT: L 234 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8617 (mt-10) REVERT: V 49 GLN cc_start: 0.8182 (mp10) cc_final: 0.7783 (pm20) REVERT: W 15 PHE cc_start: 0.6036 (p90) cc_final: 0.5206 (p90) REVERT: W 49 GLN cc_start: 0.8339 (mp10) cc_final: 0.7885 (mp10) REVERT: X 37 MET cc_start: 0.8789 (ptm) cc_final: 0.8564 (ptm) REVERT: X 49 GLN cc_start: 0.8624 (mp10) cc_final: 0.8060 (mp10) outliers start: 82 outliers final: 55 residues processed: 586 average time/residue: 0.2182 time to fit residues: 205.2146 Evaluate side-chains 561 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 505 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 194 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 411 optimal weight: 50.0000 chunk 253 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 175 ASN E 72 ASN E 131 HIS F 146 GLN F 195 GLN H 127 HIS I 180 HIS J 233 ASN L 139 HIS ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.086935 restraints weight = 53935.265| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.47 r_work: 0.2889 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33919 Z= 0.152 Angle : 0.563 14.711 46296 Z= 0.284 Chirality : 0.045 0.448 5260 Planarity : 0.004 0.049 5915 Dihedral : 5.205 85.914 5130 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.57 % Allowed : 11.81 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.66 (0.13), residues: 4201 helix: 1.76 (0.22), residues: 562 sheet: 0.60 (0.14), residues: 1208 loop : 0.12 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 119 TYR 0.023 0.001 TYR U 27 PHE 0.019 0.001 PHE L 218 TRP 0.014 0.001 TRP G 235 HIS 0.006 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00355 (33824) covalent geometry : angle 0.55012 (46078) SS BOND : bond 0.00342 ( 67) SS BOND : angle 1.08235 ( 134) hydrogen bonds : bond 0.03303 ( 1164) hydrogen bonds : angle 5.11034 ( 2976) link_BETA1-4 : bond 0.00458 ( 16) link_BETA1-4 : angle 1.91441 ( 48) link_BETA1-6 : bond 0.00310 ( 4) link_BETA1-6 : angle 1.30886 ( 12) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 3.99165 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 518 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6833 (p90) cc_final: 0.6366 (p90) REVERT: U 30 GLU cc_start: 0.7215 (tt0) cc_final: 0.6841 (tt0) REVERT: U 32 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7906 (tm-30) REVERT: U 36 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6982 (ptm-80) REVERT: U 52 GLN cc_start: 0.8190 (mm110) cc_final: 0.7979 (mm110) REVERT: A 187 MET cc_start: 0.8774 (ttm) cc_final: 0.8400 (ttm) REVERT: B 88 MET cc_start: 0.8387 (mmm) cc_final: 0.7970 (mtp) REVERT: B 212 ASP cc_start: 0.8408 (t0) cc_final: 0.7333 (p0) REVERT: B 279 SER cc_start: 0.9042 (m) cc_final: 0.8502 (p) REVERT: B 319 LYS cc_start: 0.8827 (mttp) cc_final: 0.8463 (mtpp) REVERT: B 428 LEU cc_start: 0.8540 (tp) cc_final: 0.8328 (tt) REVERT: C 2 GLU cc_start: 0.8600 (tt0) cc_final: 0.8226 (tp30) REVERT: C 298 ASP cc_start: 0.8861 (t0) cc_final: 0.8593 (t0) REVERT: C 324 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7965 (mttp) REVERT: C 338 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8861 (p) REVERT: C 400 GLN cc_start: 0.8692 (pm20) cc_final: 0.8363 (pm20) REVERT: D 166 MET cc_start: 0.8925 (mmt) cc_final: 0.8666 (mmp) REVERT: D 229 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8399 (t) REVERT: D 295 SER cc_start: 0.9309 (t) cc_final: 0.9079 (p) REVERT: D 407 MET cc_start: 0.8631 (tpt) cc_final: 0.8295 (tpt) REVERT: E 70 MET cc_start: 0.8604 (mmm) cc_final: 0.8202 (tpt) REVERT: E 199 TYR cc_start: 0.8398 (p90) cc_final: 0.8179 (p90) REVERT: E 251 ARG cc_start: 0.6303 (ttm170) cc_final: 0.5822 (ttm170) REVERT: E 381 MET cc_start: 0.7671 (mmm) cc_final: 0.7360 (mmm) REVERT: F 166 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8050 (mm-30) REVERT: F 168 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: F 215 LYS cc_start: 0.7382 (mttt) cc_final: 0.6959 (mtpt) REVERT: F 252 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7825 (mtmm) REVERT: F 366 MET cc_start: 0.8680 (tpt) cc_final: 0.7662 (ttp) REVERT: G 70 MET cc_start: 0.8885 (mmm) cc_final: 0.8525 (tpt) REVERT: G 171 MET cc_start: 0.8401 (ttm) cc_final: 0.8178 (ttm) REVERT: G 199 TYR cc_start: 0.7531 (p90) cc_final: 0.7096 (p90) REVERT: G 224 GLN cc_start: 0.8915 (mt0) cc_final: 0.8658 (mt0) REVERT: G 307 GLN cc_start: 0.8927 (mt0) cc_final: 0.8692 (mt0) REVERT: H 74 MET cc_start: 0.8309 (mmm) cc_final: 0.8010 (mmm) REVERT: H 181 MET cc_start: 0.8102 (mmt) cc_final: 0.7649 (mmp) REVERT: H 235 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: H 314 LYS cc_start: 0.7956 (mttt) cc_final: 0.5660 (tttt) REVERT: I 161 ASP cc_start: 0.8546 (t0) cc_final: 0.8067 (t0) REVERT: I 190 HIS cc_start: 0.8560 (t-90) cc_final: 0.8354 (t-90) REVERT: I 219 ASP cc_start: 0.7777 (p0) cc_final: 0.7161 (p0) REVERT: I 223 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7340 (mtm-85) REVERT: J 141 LYS cc_start: 0.6789 (tmtt) cc_final: 0.6529 (tmtt) REVERT: J 151 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8976 (mttt) REVERT: J 161 ASP cc_start: 0.8027 (t0) cc_final: 0.7632 (t0) REVERT: J 163 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7765 (mt-10) REVERT: J 172 LYS cc_start: 0.9604 (ttmt) cc_final: 0.8785 (ttmm) REVERT: J 190 HIS cc_start: 0.9010 (t-90) cc_final: 0.8563 (t-90) REVERT: J 223 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8092 (mtm110) REVERT: J 241 SER cc_start: 0.8677 (m) cc_final: 0.8198 (p) REVERT: J 252 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8890 (tttm) REVERT: J 260 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7407 (tp30) REVERT: K 161 ASP cc_start: 0.8389 (t70) cc_final: 0.7947 (t0) REVERT: K 187 TYR cc_start: 0.7936 (m-80) cc_final: 0.7587 (m-80) REVERT: K 218 PHE cc_start: 0.8372 (m-80) cc_final: 0.8128 (m-80) REVERT: K 221 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7932 (tptp) REVERT: L 161 ASP cc_start: 0.9121 (t0) cc_final: 0.8888 (t0) REVERT: L 173 SER cc_start: 0.8652 (p) cc_final: 0.8239 (m) REVERT: L 219 ASP cc_start: 0.7992 (p0) cc_final: 0.7562 (p0) REVERT: L 223 ARG cc_start: 0.7776 (mpp80) cc_final: 0.7215 (mtm180) REVERT: L 234 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8647 (mt-10) REVERT: V 7 MET cc_start: 0.6832 (tpp) cc_final: 0.6566 (tpp) REVERT: V 49 GLN cc_start: 0.8187 (mp10) cc_final: 0.7761 (pm20) REVERT: W 15 PHE cc_start: 0.5994 (p90) cc_final: 0.5194 (p90) REVERT: W 49 GLN cc_start: 0.8402 (mp10) cc_final: 0.8006 (mp10) REVERT: X 7 MET cc_start: 0.6056 (tpp) cc_final: 0.5295 (tpp) REVERT: X 49 GLN cc_start: 0.8632 (mp10) cc_final: 0.8146 (mp10) outliers start: 93 outliers final: 75 residues processed: 570 average time/residue: 0.2193 time to fit residues: 200.9077 Evaluate side-chains 583 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 503 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 41 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 127 HIS Chi-restraints excluded: chain H residue 235 TRP Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 156 ARG Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain X residue 52 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 266 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN D 264 ASN E 72 ASN F 195 GLN H 127 HIS I 180 HIS ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.085649 restraints weight = 54207.102| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.47 r_work: 0.2863 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33919 Z= 0.229 Angle : 0.599 17.299 46296 Z= 0.301 Chirality : 0.046 0.439 5260 Planarity : 0.004 0.049 5915 Dihedral : 5.242 84.676 5130 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.81 % Allowed : 11.94 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 4201 helix: 1.87 (0.22), residues: 556 sheet: 0.47 (0.14), residues: 1264 loop : 0.07 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 119 TYR 0.023 0.002 TYR U 27 PHE 0.018 0.001 PHE L 218 TRP 0.014 0.001 TRP H 64 HIS 0.013 0.001 HIS H 127 Details of bonding type rmsd covalent geometry : bond 0.00537 (33824) covalent geometry : angle 0.58650 (46078) SS BOND : bond 0.00420 ( 67) SS BOND : angle 1.18549 ( 134) hydrogen bonds : bond 0.03430 ( 1164) hydrogen bonds : angle 5.16482 ( 2976) link_BETA1-4 : bond 0.00462 ( 16) link_BETA1-4 : angle 1.90433 ( 48) link_BETA1-6 : bond 0.00232 ( 4) link_BETA1-6 : angle 1.33046 ( 12) link_NAG-ASN : bond 0.00373 ( 8) link_NAG-ASN : angle 4.04095 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 514 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6948 (p90) cc_final: 0.6456 (p90) REVERT: U 30 GLU cc_start: 0.7354 (tt0) cc_final: 0.7102 (tt0) REVERT: U 32 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7961 (tm-30) REVERT: U 36 ARG cc_start: 0.7361 (ttm110) cc_final: 0.6851 (ptm-80) REVERT: U 52 GLN cc_start: 0.8171 (mm110) cc_final: 0.7944 (mm110) REVERT: A 344 ILE cc_start: 0.8720 (pt) cc_final: 0.8369 (tp) REVERT: B 88 MET cc_start: 0.8363 (mmm) cc_final: 0.8057 (mtp) REVERT: B 212 ASP cc_start: 0.8405 (t0) cc_final: 0.7338 (p0) REVERT: B 279 SER cc_start: 0.9130 (m) cc_final: 0.8630 (p) REVERT: C 2 GLU cc_start: 0.8636 (tt0) cc_final: 0.8275 (tp30) REVERT: C 247 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.7553 (mtm-85) REVERT: C 298 ASP cc_start: 0.8865 (t0) cc_final: 0.8599 (t0) REVERT: C 324 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8020 (mttp) REVERT: C 338 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8889 (p) REVERT: D 229 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8339 (t) REVERT: D 295 SER cc_start: 0.9306 (t) cc_final: 0.9086 (p) REVERT: D 407 MET cc_start: 0.8661 (tpt) cc_final: 0.8294 (tpt) REVERT: E 70 MET cc_start: 0.8614 (mmm) cc_final: 0.8259 (tpt) REVERT: E 251 ARG cc_start: 0.6369 (ttm170) cc_final: 0.5905 (ttm170) REVERT: E 381 MET cc_start: 0.7707 (mmm) cc_final: 0.7369 (mmm) REVERT: F 166 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8037 (mm-30) REVERT: F 168 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: F 215 LYS cc_start: 0.7469 (mttt) cc_final: 0.7029 (mtpt) REVERT: F 252 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7889 (mtmm) REVERT: F 366 MET cc_start: 0.8752 (tpt) cc_final: 0.7743 (ttp) REVERT: G 70 MET cc_start: 0.8936 (mmm) cc_final: 0.8332 (tpp) REVERT: G 178 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.8011 (mmp80) REVERT: G 224 GLN cc_start: 0.8938 (mt0) cc_final: 0.8684 (mt0) REVERT: G 307 GLN cc_start: 0.8951 (mt0) cc_final: 0.8713 (mt0) REVERT: G 342 LEU cc_start: 0.8730 (mt) cc_final: 0.8489 (mp) REVERT: H 74 MET cc_start: 0.8279 (mmm) cc_final: 0.8068 (mmm) REVERT: H 158 GLN cc_start: 0.8674 (mm110) cc_final: 0.8057 (mm-40) REVERT: H 181 MET cc_start: 0.8019 (mmt) cc_final: 0.7676 (mmp) REVERT: H 235 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.7704 (m-10) REVERT: H 314 LYS cc_start: 0.7996 (mttt) cc_final: 0.6894 (mttt) REVERT: I 161 ASP cc_start: 0.8524 (t0) cc_final: 0.8066 (t0) REVERT: I 190 HIS cc_start: 0.8580 (t-90) cc_final: 0.8349 (t-90) REVERT: I 219 ASP cc_start: 0.7773 (p0) cc_final: 0.7196 (p0) REVERT: I 223 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7293 (mtm-85) REVERT: J 141 LYS cc_start: 0.7023 (tmtt) cc_final: 0.6817 (tmtt) REVERT: J 151 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8983 (mttt) REVERT: J 161 ASP cc_start: 0.7987 (t0) cc_final: 0.7600 (t0) REVERT: J 163 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7742 (mt-10) REVERT: J 172 LYS cc_start: 0.9608 (ttmt) cc_final: 0.8758 (ttmm) REVERT: J 190 HIS cc_start: 0.9070 (t-90) cc_final: 0.8657 (t-90) REVERT: J 241 SER cc_start: 0.8674 (m) cc_final: 0.8202 (p) REVERT: J 252 LYS cc_start: 0.9183 (ttpp) cc_final: 0.8928 (tttm) REVERT: J 260 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7419 (tp30) REVERT: K 151 LYS cc_start: 0.9138 (pttp) cc_final: 0.8820 (pttm) REVERT: K 161 ASP cc_start: 0.8360 (t70) cc_final: 0.7891 (t0) REVERT: K 180 HIS cc_start: 0.9221 (p-80) cc_final: 0.8927 (p-80) REVERT: K 187 TYR cc_start: 0.7967 (m-80) cc_final: 0.7440 (m-80) REVERT: K 221 LYS cc_start: 0.8498 (mmtt) cc_final: 0.7940 (tptp) REVERT: L 161 ASP cc_start: 0.9105 (t0) cc_final: 0.8864 (t0) REVERT: L 173 SER cc_start: 0.8860 (p) cc_final: 0.8453 (m) REVERT: L 219 ASP cc_start: 0.7920 (p0) cc_final: 0.7507 (p0) REVERT: L 223 ARG cc_start: 0.7736 (mpp80) cc_final: 0.6947 (mtm180) REVERT: L 234 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8678 (mt-10) REVERT: V 49 GLN cc_start: 0.8203 (mp10) cc_final: 0.7975 (mp10) REVERT: W 15 PHE cc_start: 0.6095 (p90) cc_final: 0.5335 (p90) REVERT: W 49 GLN cc_start: 0.8540 (mp10) cc_final: 0.8131 (mp10) REVERT: X 7 MET cc_start: 0.6161 (tpp) cc_final: 0.5685 (tpp) REVERT: X 49 GLN cc_start: 0.8727 (mp10) cc_final: 0.8256 (mp10) outliers start: 102 outliers final: 84 residues processed: 572 average time/residue: 0.2197 time to fit residues: 202.0419 Evaluate side-chains 591 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 501 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 41 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 235 TRP Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain X residue 52 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 166 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 292 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN D 264 ASN E 72 ASN F 158 GLN F 195 GLN F 349 HIS H 127 HIS ** X 41 ASN ** 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 = 0.3652 r_free = 0.3652 target = 0.129130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.086173 restraints weight = 54049.061| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.46 r_work: 0.2873 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33919 Z= 0.186 Angle : 0.589 16.293 46296 Z= 0.294 Chirality : 0.046 0.421 5260 Planarity : 0.004 0.090 5915 Dihedral : 5.184 83.921 5130 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.90 % Allowed : 12.25 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.54 (0.13), residues: 4201 helix: 1.86 (0.22), residues: 556 sheet: 0.46 (0.14), residues: 1264 loop : 0.03 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 223 TYR 0.020 0.001 TYR U 27 PHE 0.017 0.001 PHE L 218 TRP 0.016 0.001 TRP H 64 HIS 0.007 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00436 (33824) covalent geometry : angle 0.57593 (46078) SS BOND : bond 0.00357 ( 67) SS BOND : angle 1.26605 ( 134) hydrogen bonds : bond 0.03349 ( 1164) hydrogen bonds : angle 5.12839 ( 2976) link_BETA1-4 : bond 0.00464 ( 16) link_BETA1-4 : angle 1.80438 ( 48) link_BETA1-6 : bond 0.00261 ( 4) link_BETA1-6 : angle 1.33245 ( 12) link_NAG-ASN : bond 0.00346 ( 8) link_NAG-ASN : angle 4.01234 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 506 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 PHE cc_start: 0.6835 (p90) cc_final: 0.6238 (p90) REVERT: U 30 GLU cc_start: 0.7367 (tt0) cc_final: 0.7107 (tt0) REVERT: U 32 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8117 (tm-30) REVERT: U 36 ARG cc_start: 0.7400 (ttm110) cc_final: 0.6761 (mtp-110) REVERT: A 187 MET cc_start: 0.8767 (ttm) cc_final: 0.8490 (ttm) REVERT: A 344 ILE cc_start: 0.8712 (pt) cc_final: 0.8342 (tp) REVERT: B 88 MET cc_start: 0.8382 (mmm) cc_final: 0.7994 (mtp) REVERT: B 212 ASP cc_start: 0.8395 (t0) cc_final: 0.7347 (p0) REVERT: B 279 SER cc_start: 0.9092 (m) cc_final: 0.8582 (p) REVERT: B 319 LYS cc_start: 0.8778 (mttp) cc_final: 0.8310 (mtpp) REVERT: C 2 GLU cc_start: 0.8619 (tt0) cc_final: 0.8261 (tp30) REVERT: C 247 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7558 (mtm-85) REVERT: C 298 ASP cc_start: 0.8833 (t0) cc_final: 0.8603 (t0) REVERT: C 324 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8051 (mttp) REVERT: C 338 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8886 (p) REVERT: D 295 SER cc_start: 0.9301 (t) cc_final: 0.9078 (p) REVERT: D 407 MET cc_start: 0.8646 (tpt) cc_final: 0.8310 (tpt) REVERT: E 70 MET cc_start: 0.8600 (mmm) cc_final: 0.8251 (tpt) REVERT: E 251 ARG cc_start: 0.6421 (ttm170) cc_final: 0.5845 (ttm170) REVERT: E 381 MET cc_start: 0.7704 (mmm) cc_final: 0.7336 (mmm) REVERT: E 394 ARG cc_start: 0.6502 (ttp-170) cc_final: 0.6242 (tmm-80) REVERT: F 166 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8151 (mm-30) REVERT: F 215 LYS cc_start: 0.7502 (mttt) cc_final: 0.7056 (mtpt) REVERT: F 366 MET cc_start: 0.8746 (tpt) cc_final: 0.7780 (ttp) REVERT: G 70 MET cc_start: 0.8955 (mmm) cc_final: 0.8688 (tpt) REVERT: G 178 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.8003 (mmp80) REVERT: G 224 GLN cc_start: 0.8932 (mt0) cc_final: 0.8687 (mt0) REVERT: G 307 GLN cc_start: 0.8944 (mt0) cc_final: 0.8709 (mt0) REVERT: G 342 LEU cc_start: 0.8732 (mt) cc_final: 0.8377 (mp) REVERT: H 64 TRP cc_start: 0.8956 (p-90) cc_final: 0.8599 (p-90) REVERT: H 74 MET cc_start: 0.8401 (mmm) cc_final: 0.8156 (mmm) REVERT: H 181 MET cc_start: 0.8200 (mmt) cc_final: 0.7906 (mmp) REVERT: H 235 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (m-10) REVERT: H 314 LYS cc_start: 0.7910 (mttt) cc_final: 0.6830 (mttt) REVERT: I 161 ASP cc_start: 0.8524 (t0) cc_final: 0.8057 (t0) REVERT: I 190 HIS cc_start: 0.8538 (t-90) cc_final: 0.8307 (t-90) REVERT: I 219 ASP cc_start: 0.7741 (p0) cc_final: 0.7219 (p0) REVERT: I 223 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7359 (mtm-85) REVERT: J 161 ASP cc_start: 0.8036 (t0) cc_final: 0.7659 (t0) REVERT: J 163 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7738 (mt-10) REVERT: J 172 LYS cc_start: 0.9607 (ttmt) cc_final: 0.8761 (ttmm) REVERT: J 190 HIS cc_start: 0.9070 (t-90) cc_final: 0.8697 (t-90) REVERT: J 215 ARG cc_start: 0.8966 (mmt90) cc_final: 0.8329 (mmt90) REVERT: J 219 ASP cc_start: 0.7754 (p0) cc_final: 0.7509 (p0) REVERT: J 223 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7624 (mtm110) REVERT: J 241 SER cc_start: 0.8681 (m) cc_final: 0.8200 (p) REVERT: J 252 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8929 (tttm) REVERT: J 260 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7500 (tp30) REVERT: K 151 LYS cc_start: 0.9163 (pttp) cc_final: 0.8819 (pttm) REVERT: K 161 ASP cc_start: 0.8345 (t70) cc_final: 0.7838 (t0) REVERT: K 180 HIS cc_start: 0.9270 (p-80) cc_final: 0.8941 (p-80) REVERT: K 218 PHE cc_start: 0.8321 (m-80) cc_final: 0.8062 (m-80) REVERT: K 221 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7948 (tptp) REVERT: K 245 TRP cc_start: 0.8510 (p90) cc_final: 0.7755 (p90) REVERT: L 161 ASP cc_start: 0.9110 (t0) cc_final: 0.8861 (t0) REVERT: L 173 SER cc_start: 0.8732 (p) cc_final: 0.8372 (m) REVERT: L 219 ASP cc_start: 0.7954 (p0) cc_final: 0.7579 (p0) REVERT: L 223 ARG cc_start: 0.7775 (mpp80) cc_final: 0.7157 (mtm180) REVERT: L 234 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8683 (mt-10) REVERT: V 49 GLN cc_start: 0.8206 (mp10) cc_final: 0.7967 (mp10) REVERT: W 15 PHE cc_start: 0.6071 (p90) cc_final: 0.5269 (p90) REVERT: W 49 GLN cc_start: 0.8321 (mp10) cc_final: 0.7932 (mp10) REVERT: X 37 MET cc_start: 0.8812 (ptm) cc_final: 0.8608 (ppp) REVERT: X 49 GLN cc_start: 0.8736 (mp10) cc_final: 0.8262 (mp10) outliers start: 105 outliers final: 86 residues processed: 562 average time/residue: 0.2211 time to fit residues: 199.5563 Evaluate side-chains 587 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 498 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain U residue 41 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 235 TRP Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 156 ARG Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain V residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 51 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 71 optimal weight: 0.0870 chunk 290 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 279 optimal weight: 30.0000 chunk 353 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 308 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN F 158 GLN F 195 GLN I 180 HIS ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.087816 restraints weight = 53965.380| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.44 r_work: 0.2878 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33919 Z= 0.173 Angle : 0.581 15.777 46296 Z= 0.290 Chirality : 0.046 0.409 5260 Planarity : 0.004 0.066 5915 Dihedral : 5.136 86.184 5130 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.81 % Allowed : 12.47 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.13), residues: 4201 helix: 1.96 (0.22), residues: 550 sheet: 0.46 (0.14), residues: 1309 loop : 0.00 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 36 TYR 0.020 0.001 TYR U 27 PHE 0.022 0.001 PHE L 218 TRP 0.016 0.001 TRP H 64 HIS 0.008 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00405 (33824) covalent geometry : angle 0.56875 (46078) SS BOND : bond 0.00332 ( 67) SS BOND : angle 1.19622 ( 134) hydrogen bonds : bond 0.03301 ( 1164) hydrogen bonds : angle 5.08132 ( 2976) link_BETA1-4 : bond 0.00459 ( 16) link_BETA1-4 : angle 1.72291 ( 48) link_BETA1-6 : bond 0.00256 ( 4) link_BETA1-6 : angle 1.34013 ( 12) link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 3.98885 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 513 time to evaluate : 1.360 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: U 30 GLU cc_start: 0.7296 (tt0) cc_final: 0.7013 (tt0) REVERT: U 32 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8270 (tm-30) REVERT: U 36 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6975 (ptm-80) REVERT: A 187 MET cc_start: 0.8796 (ttm) cc_final: 0.8538 (ttm) REVERT: A 344 ILE cc_start: 0.8720 (pt) cc_final: 0.8313 (tp) REVERT: B 88 MET cc_start: 0.8390 (mmm) cc_final: 0.7962 (mtp) REVERT: B 212 ASP cc_start: 0.8383 (t0) cc_final: 0.7341 (p0) REVERT: B 279 SER cc_start: 0.9086 (m) cc_final: 0.8526 (p) REVERT: B 319 LYS cc_start: 0.8809 (mttp) cc_final: 0.8426 (mtpp) REVERT: C 2 GLU cc_start: 0.8608 (tt0) cc_final: 0.8251 (tp30) REVERT: C 247 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7553 (mtm-85) REVERT: C 298 ASP cc_start: 0.8892 (t0) cc_final: 0.8658 (t0) REVERT: C 324 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8066 (mttp) REVERT: C 338 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (p) REVERT: D 295 SER cc_start: 0.9315 (t) cc_final: 0.9085 (p) REVERT: D 407 MET cc_start: 0.8661 (tpt) cc_final: 0.8317 (tpt) REVERT: E 70 MET cc_start: 0.8585 (mmm) cc_final: 0.8252 (tpt) REVERT: E 251 ARG cc_start: 0.6584 (ttm170) cc_final: 0.6189 (ttm170) REVERT: E 381 MET cc_start: 0.7723 (mmm) cc_final: 0.7350 (mmm) REVERT: E 394 ARG cc_start: 0.6525 (ttp-170) cc_final: 0.6251 (tmm-80) REVERT: F 9 TYR cc_start: 0.8348 (m-80) cc_final: 0.7912 (m-80) REVERT: F 215 LYS cc_start: 0.7534 (mttt) cc_final: 0.7074 (mtpt) REVERT: F 366 MET cc_start: 0.8772 (tpt) cc_final: 0.7834 (ttp) REVERT: G 70 MET cc_start: 0.8950 (mmm) cc_final: 0.8310 (tpp) REVERT: G 171 MET cc_start: 0.8542 (ttm) cc_final: 0.8023 (tmm) REVERT: G 178 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.8004 (mmp80) REVERT: G 199 TYR cc_start: 0.7624 (p90) cc_final: 0.7195 (p90) REVERT: G 224 GLN cc_start: 0.8926 (mt0) cc_final: 0.8672 (mt0) REVERT: G 256 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8286 (m170) REVERT: G 307 GLN cc_start: 0.8937 (mt0) cc_final: 0.8702 (mt0) REVERT: G 342 LEU cc_start: 0.8783 (mt) cc_final: 0.8458 (mp) REVERT: H 64 TRP cc_start: 0.8996 (p-90) cc_final: 0.8686 (p-90) REVERT: H 70 MET cc_start: 0.8499 (tpp) cc_final: 0.8162 (tpp) REVERT: H 74 MET cc_start: 0.8293 (mmm) cc_final: 0.7866 (mmm) REVERT: H 235 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: H 314 LYS cc_start: 0.7914 (mttt) cc_final: 0.6720 (mttt) REVERT: I 161 ASP cc_start: 0.8535 (t0) cc_final: 0.8054 (t0) REVERT: I 178 PHE cc_start: 0.9036 (p90) cc_final: 0.8716 (p90) REVERT: I 190 HIS cc_start: 0.8547 (t-90) cc_final: 0.8317 (t-90) REVERT: I 196 TYR cc_start: 0.8265 (t80) cc_final: 0.8040 (t80) REVERT: I 219 ASP cc_start: 0.7717 (p0) cc_final: 0.7183 (p0) REVERT: I 223 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7169 (mtm-85) REVERT: J 161 ASP cc_start: 0.8073 (t0) cc_final: 0.7694 (t0) REVERT: J 163 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8006 (mt-10) REVERT: J 172 LYS cc_start: 0.9601 (ttmt) cc_final: 0.9191 (ttmm) REVERT: J 190 HIS cc_start: 0.9089 (t-90) cc_final: 0.8731 (t-90) REVERT: J 215 ARG cc_start: 0.9051 (mmt90) cc_final: 0.8470 (mmt90) REVERT: J 219 ASP cc_start: 0.7711 (p0) cc_final: 0.7473 (p0) REVERT: J 223 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7615 (mtm110) REVERT: J 241 SER cc_start: 0.8719 (m) cc_final: 0.8238 (p) REVERT: J 252 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8941 (tttm) REVERT: K 151 LYS cc_start: 0.9150 (pttp) cc_final: 0.8782 (pttm) REVERT: K 161 ASP cc_start: 0.8345 (t70) cc_final: 0.7841 (t0) REVERT: K 180 HIS cc_start: 0.9294 (p-80) cc_final: 0.8952 (p-80) REVERT: K 221 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7950 (tptp) REVERT: K 245 TRP cc_start: 0.8488 (p90) cc_final: 0.7828 (p90) REVERT: L 141 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7568 (ptpp) REVERT: L 161 ASP cc_start: 0.9132 (t0) cc_final: 0.8883 (t0) REVERT: L 173 SER cc_start: 0.8678 (p) cc_final: 0.8295 (m) REVERT: L 219 ASP cc_start: 0.7962 (p0) cc_final: 0.7607 (p0) REVERT: L 223 ARG cc_start: 0.7823 (mpp80) cc_final: 0.7234 (mtm180) REVERT: V 37 MET cc_start: 0.7659 (ttp) cc_final: 0.7011 (tmm) REVERT: V 49 GLN cc_start: 0.8307 (mp10) cc_final: 0.8056 (mp10) REVERT: W 15 PHE cc_start: 0.6055 (p90) cc_final: 0.5272 (p90) REVERT: W 49 GLN cc_start: 0.8319 (mp10) cc_final: 0.7936 (mp10) REVERT: X 7 MET cc_start: 0.6245 (mmt) cc_final: 0.5638 (mmm) REVERT: X 37 MET cc_start: 0.8820 (ptm) cc_final: 0.8603 (ppp) REVERT: X 49 GLN cc_start: 0.8689 (mp10) cc_final: 0.8253 (mp10) outliers start: 102 outliers final: 87 residues processed: 571 average time/residue: 0.2083 time to fit residues: 191.5445 Evaluate side-chains 591 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 500 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain U residue 41 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 256 HIS Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 235 TRP Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain V residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 122 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 290 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 241 optimal weight: 0.0970 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 149 ASN C 375 HIS E 72 ASN F 195 GLN X 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.084825 restraints weight = 54314.809| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.47 r_work: 0.2845 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 33919 Z= 0.257 Angle : 0.632 15.550 46296 Z= 0.317 Chirality : 0.047 0.411 5260 Planarity : 0.004 0.064 5915 Dihedral : 5.300 86.182 5130 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.62 % Allowed : 12.86 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4201 helix: 2.03 (0.22), residues: 546 sheet: 0.35 (0.14), residues: 1311 loop : -0.13 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 36 TYR 0.023 0.002 TYR U 27 PHE 0.023 0.002 PHE L 218 TRP 0.015 0.001 TRP H 64 HIS 0.010 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00606 (33824) covalent geometry : angle 0.61990 (46078) SS BOND : bond 0.00458 ( 67) SS BOND : angle 1.28744 ( 134) hydrogen bonds : bond 0.03500 ( 1164) hydrogen bonds : angle 5.23552 ( 2976) link_BETA1-4 : bond 0.00468 ( 16) link_BETA1-4 : angle 1.77965 ( 48) link_BETA1-6 : bond 0.00196 ( 4) link_BETA1-6 : angle 1.40241 ( 12) link_NAG-ASN : bond 0.00475 ( 8) link_NAG-ASN : angle 4.12017 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8402 Ramachandran restraints generated. 4201 Oldfield, 0 Emsley, 4201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 500 time to evaluate : 1.367 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: U 30 GLU cc_start: 0.7279 (tt0) cc_final: 0.7001 (tt0) REVERT: U 32 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8067 (tm-30) REVERT: A 187 MET cc_start: 0.8880 (ttm) cc_final: 0.8642 (ttm) REVERT: B 88 MET cc_start: 0.8428 (mmm) cc_final: 0.8057 (mtp) REVERT: B 212 ASP cc_start: 0.8370 (t0) cc_final: 0.7339 (p0) REVERT: B 279 SER cc_start: 0.9051 (m) cc_final: 0.8517 (p) REVERT: B 319 LYS cc_start: 0.8797 (mttp) cc_final: 0.8415 (mtpp) REVERT: C 247 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7575 (mtm-85) REVERT: C 298 ASP cc_start: 0.8917 (t0) cc_final: 0.8707 (t0) REVERT: C 324 LYS cc_start: 0.8501 (mtmm) cc_final: 0.7990 (mttp) REVERT: C 338 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8870 (p) REVERT: D 295 SER cc_start: 0.9314 (t) cc_final: 0.9083 (p) REVERT: D 407 MET cc_start: 0.8642 (tpt) cc_final: 0.8307 (tpt) REVERT: E 70 MET cc_start: 0.8571 (mmm) cc_final: 0.8273 (tpt) REVERT: E 251 ARG cc_start: 0.6624 (ttm170) cc_final: 0.6206 (ttm170) REVERT: E 381 MET cc_start: 0.7663 (mmm) cc_final: 0.7276 (mmm) REVERT: E 394 ARG cc_start: 0.6508 (ttp-170) cc_final: 0.6245 (tmm-80) REVERT: F 9 TYR cc_start: 0.8362 (m-80) cc_final: 0.7961 (m-80) REVERT: F 366 MET cc_start: 0.8777 (tpt) cc_final: 0.7835 (ttp) REVERT: G 70 MET cc_start: 0.8943 (mmm) cc_final: 0.8388 (tpp) REVERT: G 178 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8059 (mmp80) REVERT: G 224 GLN cc_start: 0.8979 (mt0) cc_final: 0.8741 (mt0) REVERT: G 256 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8276 (m170) REVERT: G 342 LEU cc_start: 0.8827 (mt) cc_final: 0.8511 (mp) REVERT: H 64 TRP cc_start: 0.9070 (p-90) cc_final: 0.8813 (p-90) REVERT: H 70 MET cc_start: 0.8492 (tpp) cc_final: 0.8172 (tpp) REVERT: H 74 MET cc_start: 0.8311 (mmm) cc_final: 0.7894 (mmm) REVERT: H 168 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: H 235 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: H 314 LYS cc_start: 0.7635 (mttt) cc_final: 0.6544 (mttp) REVERT: I 161 ASP cc_start: 0.8535 (t0) cc_final: 0.8095 (t0) REVERT: I 178 PHE cc_start: 0.9041 (p90) cc_final: 0.8779 (p90) REVERT: I 190 HIS cc_start: 0.8420 (t-90) cc_final: 0.8214 (t70) REVERT: I 196 TYR cc_start: 0.8206 (t80) cc_final: 0.7945 (t80) REVERT: I 219 ASP cc_start: 0.7803 (p0) cc_final: 0.7142 (p0) REVERT: I 223 ARG cc_start: 0.7646 (mtm110) cc_final: 0.6976 (mtm-85) REVERT: J 151 LYS cc_start: 0.9279 (mmmm) cc_final: 0.8996 (mttt) REVERT: J 161 ASP cc_start: 0.8335 (t0) cc_final: 0.7923 (t0) REVERT: J 163 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7698 (mt-10) REVERT: J 172 LYS cc_start: 0.9608 (ttmt) cc_final: 0.9204 (ttmm) REVERT: J 177 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8660 (mmmt) REVERT: J 190 HIS cc_start: 0.9128 (t-90) cc_final: 0.8785 (t-90) REVERT: J 219 ASP cc_start: 0.7673 (p0) cc_final: 0.7432 (p0) REVERT: J 223 ARG cc_start: 0.8022 (mtm110) cc_final: 0.7649 (mtm110) REVERT: J 252 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8943 (tttm) REVERT: J 260 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7570 (tp30) REVERT: K 151 LYS cc_start: 0.9170 (pttp) cc_final: 0.8749 (pttm) REVERT: K 161 ASP cc_start: 0.8334 (t70) cc_final: 0.7844 (t0) REVERT: K 209 LYS cc_start: 0.9164 (pttm) cc_final: 0.8738 (mmtt) REVERT: K 221 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7950 (tptp) REVERT: L 141 LYS cc_start: 0.7910 (ptpp) cc_final: 0.7708 (ptpp) REVERT: L 161 ASP cc_start: 0.9082 (t0) cc_final: 0.8857 (t0) REVERT: L 173 SER cc_start: 0.8693 (p) cc_final: 0.8311 (m) REVERT: L 219 ASP cc_start: 0.7932 (p0) cc_final: 0.7510 (p0) REVERT: L 223 ARG cc_start: 0.7873 (mpp80) cc_final: 0.7107 (mtm180) REVERT: V 7 MET cc_start: 0.7463 (tpp) cc_final: 0.7161 (tpp) REVERT: V 49 GLN cc_start: 0.8297 (mp10) cc_final: 0.8051 (mp10) REVERT: W 15 PHE cc_start: 0.6130 (p90) cc_final: 0.5460 (p90) REVERT: W 49 GLN cc_start: 0.8337 (mp10) cc_final: 0.7935 (mp10) REVERT: X 7 MET cc_start: 0.6556 (mmt) cc_final: 0.6011 (mmm) REVERT: X 39 GLU cc_start: 0.5430 (pt0) cc_final: 0.5163 (pt0) REVERT: X 49 GLN cc_start: 0.8729 (mp10) cc_final: 0.8252 (mp10) outliers start: 95 outliers final: 85 residues processed: 558 average time/residue: 0.1994 time to fit residues: 179.8021 Evaluate side-chains 584 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 494 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 41 ASN Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 349 ASN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 236 GLN Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 6 PHE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 256 HIS Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 235 TRP Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 408 VAL Chi-restraints excluded: chain I residue 164 CYS Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 245 TRP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 213 SER Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain V residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 331 optimal weight: 0.0060 chunk 28 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 384 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN F 195 GLN ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.087095 restraints weight = 54005.017| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.47 r_work: 0.2889 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33919 Z= 0.135 Angle : 0.579 15.164 46296 Z= 0.288 Chirality : 0.045 0.384 5260 Planarity : 0.004 0.049 5915 Dihedral : 5.071 85.098 5130 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 13.54 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4201 helix: 1.98 (0.22), residues: 550 sheet: 0.39 (0.14), residues: 1295 loop : -0.07 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 119 TYR 0.020 0.001 TYR U 47 PHE 0.020 0.001 PHE L 218 TRP 0.017 0.001 TRP H 64 HIS 0.010 0.001 HIS K 180 Details of bonding type rmsd covalent geometry : bond 0.00313 (33824) covalent geometry : angle 0.56752 (46078) SS BOND : bond 0.00277 ( 67) SS BOND : angle 1.13925 ( 134) hydrogen bonds : bond 0.03217 ( 1164) hydrogen bonds : angle 5.04437 ( 2976) link_BETA1-4 : bond 0.00459 ( 16) link_BETA1-4 : angle 1.61743 ( 48) link_BETA1-6 : bond 0.00276 ( 4) link_BETA1-6 : angle 1.33321 ( 12) link_NAG-ASN : bond 0.00296 ( 8) link_NAG-ASN : angle 3.95840 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12748.11 seconds wall clock time: 217 minutes 50.61 seconds (13070.61 seconds total)