Starting phenix.real_space_refine on Thu Feb 22 16:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufb_42190/02_2024/8ufb_42190.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 264 5.16 5 C 21816 2.51 5 N 6012 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34656 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "C" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "E" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "F" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "H" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "I" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "K" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "L" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "V" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "W" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "R" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "S" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "T" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "U" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.32, per 1000 atoms: 0.53 Number of scatterers: 34656 At special positions: 0 Unit cell: (162.15, 182.689, 202.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 264 16.00 O 6552 8.00 N 6012 7.00 C 21816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=96, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.04 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 413 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 413 " distance=2.04 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.03 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=2.03 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 413 " distance=2.03 Simple disulfide: pdb=" SG CYS V 33 " - pdb=" SG CYS V 45 " distance=2.03 Simple disulfide: pdb=" SG CYS V 40 " - pdb=" SG CYS V 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 52 " - pdb=" SG CYS V 67 " distance=2.03 Simple disulfide: pdb=" SG CYS V 72 " - pdb=" SG CYS V 84 " distance=2.03 Simple disulfide: pdb=" SG CYS V 79 " - pdb=" SG CYS V 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 91 " - pdb=" SG CYS V 108 " distance=2.03 Simple disulfide: pdb=" SG CYS W 33 " - pdb=" SG CYS W 45 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 58 " distance=2.03 Simple disulfide: pdb=" SG CYS W 52 " - pdb=" SG CYS W 67 " distance=2.03 Simple disulfide: pdb=" SG CYS W 72 " - pdb=" SG CYS W 84 " distance=2.03 Simple disulfide: pdb=" SG CYS W 79 " - pdb=" SG CYS W 97 " distance=2.04 Simple disulfide: pdb=" SG CYS W 91 " - pdb=" SG CYS W 108 " distance=2.03 Simple disulfide: pdb=" SG CYS X 33 " - pdb=" SG CYS X 45 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 67 " distance=2.03 Simple disulfide: pdb=" SG CYS X 72 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 79 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 33 " - pdb=" SG CYS Y 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 40 " - pdb=" SG CYS Y 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 52 " - pdb=" SG CYS Y 67 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 72 " - pdb=" SG CYS Y 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 79 " - pdb=" SG CYS Y 97 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 91 " - pdb=" SG CYS Y 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 239 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS R 246 " - pdb=" SG CYS R 264 " distance=2.04 Simple disulfide: pdb=" SG CYS R 258 " - pdb=" SG CYS R 273 " distance=2.03 Simple disulfide: pdb=" SG CYS S 239 " - pdb=" SG CYS S 251 " distance=2.03 Simple disulfide: pdb=" SG CYS S 246 " - pdb=" SG CYS S 264 " distance=2.03 Simple disulfide: pdb=" SG CYS S 258 " - pdb=" SG CYS S 273 " distance=2.03 Simple disulfide: pdb=" SG CYS T 239 " - pdb=" SG CYS T 251 " distance=2.03 Simple disulfide: pdb=" SG CYS T 246 " - pdb=" SG CYS T 264 " distance=2.04 Simple disulfide: pdb=" SG CYS T 258 " - pdb=" SG CYS T 273 " distance=2.03 Simple disulfide: pdb=" SG CYS U 239 " - pdb=" SG CYS U 251 " distance=2.03 Simple disulfide: pdb=" SG CYS U 246 " - pdb=" SG CYS U 264 " distance=2.03 Simple disulfide: pdb=" SG CYS U 258 " - pdb=" SG CYS U 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " Time building additional restraints: 11.94 Conformation dependent library (CDL) restraints added in 6.7 seconds 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 90 sheets defined 16.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 404 through 441 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 360 through 399 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 404 through 441 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 348 through 360 Processing helix chain 'E' and resid 360 through 399 Proline residue: E 396 - end of helix Processing helix chain 'E' and resid 406 through 413 removed outlier: 3.664A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.382A pdb=" N SER F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 239 through 248 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 257 through 260 Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 404 through 441 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 348 through 360 Processing helix chain 'H' and resid 360 through 399 Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 406 through 413 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.702A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE I 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 41' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.572A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 8 through 12 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 348 through 360 Processing helix chain 'K' and resid 360 through 399 Proline residue: K 396 - end of helix Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'V' and resid 61 through 66 removed outlier: 4.163A pdb=" N ASN V 66 " --> pdb=" O SER V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 90 No H-bonds generated for 'chain 'V' and resid 88 through 90' Processing helix chain 'V' and resid 99 through 104 removed outlier: 4.540A pdb=" N ASP V 102 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 51 No H-bonds generated for 'chain 'W' and resid 49 through 51' Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'W' and resid 100 through 108 Proline residue: W 105 - end of helix Processing helix chain 'X' and resid 49 through 52 removed outlier: 4.440A pdb=" N CYS X 52 " --> pdb=" O LEU X 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 49 through 52' Processing helix chain 'X' and resid 61 through 66 removed outlier: 3.610A pdb=" N LYS X 65 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN X 66 " --> pdb=" O SER X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 66' Processing helix chain 'X' and resid 88 through 90 No H-bonds generated for 'chain 'X' and resid 88 through 90' Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'Y' and resid 49 through 51 No H-bonds generated for 'chain 'Y' and resid 49 through 51' Processing helix chain 'Y' and resid 61 through 66 removed outlier: 4.686A pdb=" N ASN Y 66 " --> pdb=" O SER Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing helix chain 'R' and resid 255 through 257 No H-bonds generated for 'chain 'R' and resid 255 through 257' Processing helix chain 'R' and resid 269 through 273 removed outlier: 3.577A pdb=" N CYS R 273 " --> pdb=" O GLU R 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 255 through 257 No H-bonds generated for 'chain 'S' and resid 255 through 257' Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'T' and resid 255 through 257 No H-bonds generated for 'chain 'T' and resid 255 through 257' Processing helix chain 'T' and resid 269 through 273 removed outlier: 3.558A pdb=" N CYS T 273 " --> pdb=" O GLU T 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 269 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.548A pdb=" N LYS A 161 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.494A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 186 current: chain 'A' and resid 268 through 270 Processing sheet with id=AA3, 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 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 306 removed outlier: 5.392A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'A' and resid 365 through 368 Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.642A pdb=" N CYS B 27 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.753A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS B 56 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LEU B 62 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.472A pdb=" N ASP B 107 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB6, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.523A pdb=" N VAL B 172 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 205 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB9, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.382A pdb=" N PHE C 4 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR C 15 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 6 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR C 15 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 74 through 78 removed outlier: 9.579A pdb=" N ALA C 82 " --> pdb=" O PRO C 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 89 through 93 current: chain 'C' and resid 113 through 123 removed outlier: 8.217A pdb=" N ALA C 115 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N TRP C 134 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 117 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 132 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.470A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 148 current: chain 'D' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 187 current: chain 'D' and resid 268 through 270 Processing sheet with id=AC5, 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=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AC8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 306 removed outlier: 4.277A pdb=" N LEU D 300 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 320 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 302 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR D 318 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE D 304 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 316 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AD2, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD3, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.630A pdb=" N ASN E 21 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.568A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 93 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU E 91 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 52 through 56 removed outlier: 11.496A pdb=" N MET E 52 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ALA E 63 " --> pdb=" O MET E 52 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY E 54 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.593A pdb=" N THR E 108 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS E 120 " --> pdb=" O HIS E 114 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AE1, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE2, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AE3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.166A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR F 15 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 66 through 67 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 67 current: chain 'F' and resid 81 through 86 removed outlier: 9.311A pdb=" N ALA F 82 " --> pdb=" O PRO F 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 89 through 93 current: chain 'F' and resid 112 through 122 removed outlier: 8.058A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 132 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.531A pdb=" N LYS G 161 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.494A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER G 141 " --> pdb=" O TYR G 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 148 current: chain 'G' and resid 268 through 270 Processing sheet with id=AE7, first strand: chain 'G' and resid 41 through 48 removed outlier: 6.962A pdb=" N ALA G 121 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE G 47 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA G 119 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AF1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AF2, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF3, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.789A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AF5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.345A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.611A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 35 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR H 64 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N LYS H 56 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N LEU H 62 " --> pdb=" O LYS H 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 77 current: chain 'H' and resid 88 through 102 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 88 through 102 current: chain 'H' and resid 118 through 128 Processing sheet with id=AF8, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AF9, first strand: chain 'H' and resid 234 through 235 Processing sheet with id=AG1, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AG2, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AG3, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AG4, first strand: chain 'I' and resid 32 through 33 removed outlier: 3.725A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR I 15 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 74 through 78 removed outlier: 9.764A pdb=" N ALA I 82 " --> pdb=" O PRO I 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 89 through 93 current: chain 'I' and resid 113 through 122 removed outlier: 8.829A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG I 126 " --> pdb=" O ASN I 122 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.571A pdb=" N LYS J 161 " --> pdb=" O ASP J 282 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.597A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 140 through 148 current: chain 'J' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 186 current: chain 'J' and resid 268 through 270 Processing sheet with id=AG8, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 101 through 110 No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AH1, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AH2, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'J' and resid 296 through 306 removed outlier: 6.048A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 344 through 346 Processing sheet with id=AH5, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AH6, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.695A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.477A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N LEU K 62 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 82 through 84 removed outlier: 3.595A pdb=" N THR K 108 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS K 120 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AI1, first strand: chain 'K' and resid 234 through 235 Processing sheet with id=AI2, first strand: chain 'K' and resid 172 through 173 Processing sheet with id=AI3, first strand: chain 'K' and resid 178 through 179 Processing sheet with id=AI4, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AI5, first strand: chain 'L' and resid 32 through 33 removed outlier: 3.764A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY L 54 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 74 through 78 removed outlier: 8.960A pdb=" N ALA L 82 " --> pdb=" O PRO L 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 89 through 93 current: chain 'L' and resid 113 through 122 removed outlier: 9.027A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ARG L 126 " --> pdb=" O ASN L 122 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 37 through 39 Processing sheet with id=AI8, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AI9, first strand: chain 'W' and resid 37 through 39 Processing sheet with id=AJ1, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AJ2, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AJ3, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 37 through 39 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 76 through 78 Processing sheet with id=AJ6, first strand: chain 'R' and resid 243 through 245 Processing sheet with id=AJ7, first strand: chain 'S' and resid 243 through 245 Processing sheet with id=AJ8, first strand: chain 'T' and resid 243 through 245 Processing sheet with id=AJ9, first strand: chain 'U' and resid 243 through 245 1150 hydrogen bonds defined for protein. 2880 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: 12.51 Time building geometry restraints manager: 13.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11372 1.35 - 1.47: 8362 1.47 - 1.59: 15506 1.59 - 1.71: 0 1.71 - 1.83: 308 Bond restraints: 35548 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" N ALA V 31 " pdb=" CA ALA V 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N ALA Y 31 " pdb=" CA ALA Y 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA W 31 " pdb=" CA ALA W 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 35543 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 1508 106.85 - 113.65: 19755 113.65 - 120.44: 12585 120.44 - 127.24: 13945 127.24 - 134.04: 599 Bond angle restraints: 48392 Sorted by residual: angle pdb=" N GLU B 244 " pdb=" CA GLU B 244 " pdb=" C GLU B 244 " ideal model delta sigma weight residual 110.23 114.32 -4.09 1.45e+00 4.76e-01 7.94e+00 angle pdb=" C GLY B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta sigma weight residual 120.71 124.54 -3.83 1.42e+00 4.96e-01 7.29e+00 angle pdb=" CA TYR J 309 " pdb=" CB TYR J 309 " pdb=" CG TYR J 309 " ideal model delta sigma weight residual 113.90 118.59 -4.69 1.80e+00 3.09e-01 6.78e+00 angle pdb=" CB ARG B 239 " pdb=" CG ARG B 239 " pdb=" CD ARG B 239 " ideal model delta sigma weight residual 111.30 117.04 -5.74 2.30e+00 1.89e-01 6.22e+00 angle pdb=" N TYR B 98 " pdb=" CA TYR B 98 " pdb=" C TYR B 98 " ideal model delta sigma weight residual 109.24 113.24 -4.00 1.63e+00 3.76e-01 6.03e+00 ... (remaining 48387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20625 17.67 - 35.34: 701 35.34 - 53.02: 172 53.02 - 70.69: 40 70.69 - 88.36: 14 Dihedral angle restraints: 21552 sinusoidal: 8660 harmonic: 12892 Sorted by residual: dihedral pdb=" CB CYS J 329 " pdb=" SG CYS J 329 " pdb=" SG CYS J 371 " pdb=" CB CYS J 371 " ideal model delta sinusoidal sigma weight residual 93.00 146.87 -53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS X 52 " pdb=" SG CYS X 52 " pdb=" SG CYS X 67 " pdb=" CB CYS X 67 " ideal model delta sinusoidal sigma weight residual 93.00 141.92 -48.92 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS V 52 " pdb=" SG CYS V 52 " pdb=" SG CYS V 67 " pdb=" CB CYS V 67 " ideal model delta sinusoidal sigma weight residual 93.00 137.29 -44.29 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3563 0.037 - 0.074: 1172 0.074 - 0.110: 452 0.110 - 0.147: 169 0.147 - 0.184: 4 Chirality restraints: 5360 Sorted by residual: chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 315 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE B 31 " pdb=" CA ILE B 31 " pdb=" CG1 ILE B 31 " pdb=" CG2 ILE B 31 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE H 99 " pdb=" N ILE H 99 " pdb=" C ILE H 99 " pdb=" CB ILE H 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 5357 not shown) Planarity restraints: 6280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.28e+01 pdb=" NE ARG B 239 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.50e+00 pdb=" NE ARG B 84 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 84 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.211 9.50e-02 1.11e+02 9.54e-02 6.93e+00 pdb=" NE ARG D 110 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 6277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3193 2.75 - 3.28: 33573 3.28 - 3.82: 56654 3.82 - 4.36: 68302 4.36 - 4.90: 120066 Nonbonded interactions: 281788 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 801 " model vdw 2.207 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 801 " model vdw 2.238 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 802 " model vdw 2.247 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.255 2.520 nonbonded pdb=" OG SER U 248 " pdb=" OE1 GLU U 250 " model vdw 2.269 2.440 ... (remaining 281783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.810 Check model and map are aligned: 0.440 Set scattering table: 0.300 Process input model: 88.890 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.410 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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 : 0.003 0.036 35548 Z= 0.178 Angle : 0.572 6.008 48392 Z= 0.311 Chirality : 0.045 0.184 5360 Planarity : 0.007 0.142 6272 Dihedral : 10.017 88.359 13008 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4436 helix: 0.99 (0.23), residues: 508 sheet: 0.61 (0.14), residues: 1332 loop : 0.49 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 89 HIS 0.007 0.001 HIS I 80 PHE 0.023 0.001 PHE G 421 TYR 0.019 0.003 TYR A 309 ARG 0.021 0.003 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1000 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.7043 (m-80) cc_final: 0.6839 (m-80) REVERT: A 132 MET cc_start: 0.8063 (tpp) cc_final: 0.7804 (tpp) REVERT: A 171 TRP cc_start: 0.6890 (t60) cc_final: 0.6188 (t-100) REVERT: A 304 ILE cc_start: 0.8661 (mm) cc_final: 0.8249 (mt) REVERT: A 380 ASP cc_start: 0.6017 (m-30) cc_final: 0.5736 (m-30) REVERT: B 230 ASN cc_start: 0.7878 (m-40) cc_final: 0.7649 (m-40) REVERT: D 111 SER cc_start: 0.8854 (p) cc_final: 0.8650 (t) REVERT: D 136 THR cc_start: 0.8308 (t) cc_final: 0.7984 (m) REVERT: D 252 LEU cc_start: 0.8129 (tp) cc_final: 0.7798 (tp) REVERT: D 333 SER cc_start: 0.8838 (t) cc_final: 0.8326 (p) REVERT: E 64 TYR cc_start: 0.7857 (m-80) cc_final: 0.7390 (m-80) REVERT: E 136 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 266 THR cc_start: 0.7532 (p) cc_final: 0.7286 (p) REVERT: E 291 LEU cc_start: 0.8949 (tp) cc_final: 0.8743 (tp) REVERT: E 302 ASN cc_start: 0.8083 (t0) cc_final: 0.7879 (t0) REVERT: E 326 THR cc_start: 0.9120 (m) cc_final: 0.8787 (p) REVERT: E 334 ARG cc_start: 0.8312 (mtt180) cc_final: 0.8039 (mtt90) REVERT: F 65 LEU cc_start: 0.5560 (mt) cc_final: 0.5305 (mt) REVERT: G 174 PHE cc_start: 0.6821 (m-80) cc_final: 0.6382 (m-80) REVERT: G 277 ILE cc_start: 0.8266 (mt) cc_final: 0.8017 (mt) REVERT: G 299 ASP cc_start: 0.6747 (t0) cc_final: 0.6499 (t0) REVERT: J 11 VAL cc_start: 0.8664 (t) cc_final: 0.8059 (t) REVERT: J 134 ASN cc_start: 0.7093 (t0) cc_final: 0.6791 (t0) REVERT: K 219 ASP cc_start: 0.7101 (t0) cc_final: 0.6756 (t0) REVERT: K 307 TRP cc_start: 0.7721 (m100) cc_final: 0.7179 (m100) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.4732 time to fit residues: 781.6661 Evaluate side-chains 577 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 344 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 256 optimal weight: 9.9990 chunk 399 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 79 HIS C 87 ASN D 73 HIS D 439 HIS E 275 HIS F 37 GLN F 80 HIS G 73 HIS ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN H 114 HIS H 160 GLN H 168 GLN ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN J 236 GLN J 271 ASN K 114 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 222 GLN K 402 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35548 Z= 0.196 Angle : 0.583 7.709 48392 Z= 0.310 Chirality : 0.046 0.211 5360 Planarity : 0.004 0.048 6272 Dihedral : 4.594 51.964 4976 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.32 % Allowed : 8.44 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4436 helix: 2.33 (0.25), residues: 456 sheet: 0.58 (0.14), residues: 1336 loop : 0.82 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 336 HIS 0.014 0.001 HIS B 277 PHE 0.021 0.002 PHE G 421 TYR 0.021 0.002 TYR E 325 ARG 0.007 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 662 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8076 (tpp) cc_final: 0.7725 (tpp) REVERT: A 171 TRP cc_start: 0.7014 (t60) cc_final: 0.6172 (t-100) REVERT: A 271 ASN cc_start: 0.8012 (m-40) cc_final: 0.7761 (m-40) REVERT: B 270 GLU cc_start: 0.7747 (tp30) cc_final: 0.7515 (mm-30) REVERT: C 60 MET cc_start: 0.4363 (mmm) cc_final: 0.3654 (mmm) REVERT: C 86 GLU cc_start: 0.5148 (tp30) cc_final: 0.4945 (tp30) REVERT: D 30 GLN cc_start: 0.8418 (tt0) cc_final: 0.7976 (tt0) REVERT: D 100 ASN cc_start: 0.7325 (m-40) cc_final: 0.6634 (m-40) REVERT: D 252 LEU cc_start: 0.8149 (tp) cc_final: 0.7784 (tp) REVERT: E 291 LEU cc_start: 0.9010 (tp) cc_final: 0.8653 (tp) REVERT: G 206 SER cc_start: 0.9073 (t) cc_final: 0.8677 (m) REVERT: H 253 HIS cc_start: 0.7391 (p90) cc_final: 0.7003 (p90) REVERT: H 339 GLU cc_start: 0.7243 (mp0) cc_final: 0.7006 (mp0) REVERT: K 219 ASP cc_start: 0.7376 (t0) cc_final: 0.7154 (t0) REVERT: K 256 PHE cc_start: 0.8248 (m-80) cc_final: 0.7877 (m-10) outliers start: 89 outliers final: 49 residues processed: 715 average time/residue: 0.4398 time to fit residues: 542.6269 Evaluate side-chains 596 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 547 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 1 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 130 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 400 optimal weight: 2.9990 chunk 432 optimal weight: 4.9990 chunk 356 optimal weight: 0.8980 chunk 396 optimal weight: 3.9990 chunk 136 optimal weight: 0.0020 chunk 321 optimal weight: 0.6980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN E 120 HIS E 167 HIS F 80 HIS F 88 ASN F 136 GLN ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS H 285 HIS ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 35548 Z= 0.170 Angle : 0.530 9.796 48392 Z= 0.280 Chirality : 0.045 0.200 5360 Planarity : 0.004 0.044 6272 Dihedral : 4.415 54.028 4976 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 10.82 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4436 helix: 2.51 (0.25), residues: 456 sheet: 0.73 (0.14), residues: 1344 loop : 0.81 (0.13), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 336 HIS 0.017 0.001 HIS B 350 PHE 0.027 0.002 PHE K 113 TYR 0.020 0.001 TYR G 76 ARG 0.009 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 579 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8068 (tpp) cc_final: 0.7655 (tpp) REVERT: A 171 TRP cc_start: 0.6747 (t60) cc_final: 0.5879 (t-100) REVERT: A 271 ASN cc_start: 0.8096 (m-40) cc_final: 0.7774 (m110) REVERT: B 229 ASP cc_start: 0.4031 (t0) cc_final: 0.3773 (t0) REVERT: B 235 TYR cc_start: 0.6884 (t80) cc_final: 0.6619 (t80) REVERT: B 270 GLU cc_start: 0.7794 (tp30) cc_final: 0.7592 (mm-30) REVERT: C 60 MET cc_start: 0.4297 (mmm) cc_final: 0.3495 (mmm) REVERT: D 30 GLN cc_start: 0.8299 (tt0) cc_final: 0.7806 (tt0) REVERT: D 152 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6609 (mm-30) REVERT: D 252 LEU cc_start: 0.8176 (tp) cc_final: 0.7877 (tp) REVERT: E 291 LEU cc_start: 0.9053 (tp) cc_final: 0.8725 (tp) REVERT: G 37 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7239 (mtm-85) REVERT: G 192 GLU cc_start: 0.8250 (tp30) cc_final: 0.6639 (tt0) REVERT: G 206 SER cc_start: 0.9070 (t) cc_final: 0.8716 (m) REVERT: G 283 ILE cc_start: 0.8078 (mm) cc_final: 0.7850 (mt) REVERT: H 61 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6538 (m-30) REVERT: H 290 THR cc_start: 0.8732 (m) cc_final: 0.8230 (p) REVERT: H 355 TYR cc_start: 0.7105 (t80) cc_final: 0.6786 (t80) REVERT: K 197 TYR cc_start: 0.7379 (p90) cc_final: 0.7018 (p90) REVERT: K 219 ASP cc_start: 0.7375 (t0) cc_final: 0.7150 (t0) REVERT: K 256 PHE cc_start: 0.8419 (m-80) cc_final: 0.8056 (m-10) REVERT: L 67 TYR cc_start: 0.5864 (p90) cc_final: 0.5634 (p90) outliers start: 101 outliers final: 67 residues processed: 636 average time/residue: 0.3933 time to fit residues: 431.6444 Evaluate side-chains 588 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 520 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 155 HIS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 376 MET Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 159 ASP Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain L residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 0.0270 chunk 300 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 268 optimal weight: 0.0770 chunk 401 optimal weight: 4.9990 chunk 425 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN B 95 HIS B 167 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS E 95 HIS ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 79 HIS F 88 ASN G 28 HIS ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 ASN G 231 HIS H 162 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN K 253 HIS ** L 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN X 42 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 35548 Z= 0.385 Angle : 0.676 9.846 48392 Z= 0.358 Chirality : 0.049 0.238 5360 Planarity : 0.005 0.051 6272 Dihedral : 5.268 56.300 4976 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.68 % Allowed : 10.55 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4436 helix: 2.37 (0.24), residues: 456 sheet: 0.42 (0.13), residues: 1356 loop : 0.41 (0.13), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 336 HIS 0.011 0.002 HIS E 126 PHE 0.027 0.002 PHE G 95 TYR 0.030 0.003 TYR J 89 ARG 0.007 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 578 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8007 (pm20) cc_final: 0.7751 (pm20) REVERT: A 171 TRP cc_start: 0.7523 (t60) cc_final: 0.6370 (t-100) REVERT: A 271 ASN cc_start: 0.8579 (m-40) cc_final: 0.8129 (m110) REVERT: B 187 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6686 (mt) REVERT: B 270 GLU cc_start: 0.7947 (tp30) cc_final: 0.7653 (mm-30) REVERT: B 300 ASP cc_start: 0.6636 (t0) cc_final: 0.6428 (t0) REVERT: C 60 MET cc_start: 0.4381 (mmm) cc_final: 0.3667 (mmm) REVERT: C 86 GLU cc_start: 0.5262 (tp30) cc_final: 0.4848 (tp30) REVERT: D 30 GLN cc_start: 0.8353 (tt0) cc_final: 0.7957 (tt0) REVERT: D 252 LEU cc_start: 0.8443 (tp) cc_final: 0.8159 (tp) REVERT: E 302 ASN cc_start: 0.8458 (t0) cc_final: 0.8188 (t0) REVERT: E 327 TRP cc_start: 0.8564 (t-100) cc_final: 0.7285 (t-100) REVERT: F 15 TYR cc_start: 0.5694 (m-80) cc_final: 0.5189 (m-80) REVERT: F 88 ASN cc_start: 0.4445 (OUTLIER) cc_final: 0.4231 (m-40) REVERT: G 37 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7148 (mtm-85) REVERT: G 206 SER cc_start: 0.9174 (t) cc_final: 0.8803 (m) REVERT: H 251 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7731 (ttpt) REVERT: H 290 THR cc_start: 0.8900 (m) cc_final: 0.8539 (p) REVERT: H 355 TYR cc_start: 0.7408 (t80) cc_final: 0.7188 (t80) REVERT: I 7 MET cc_start: 0.2535 (tmm) cc_final: 0.2278 (ttt) REVERT: J 247 ASP cc_start: 0.6191 (t70) cc_final: 0.5933 (t70) REVERT: K 177 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7128 (mt) REVERT: K 197 TYR cc_start: 0.7685 (p90) cc_final: 0.7362 (p90) REVERT: K 256 PHE cc_start: 0.8777 (m-80) cc_final: 0.8535 (m-10) REVERT: K 262 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.8028 (mttp) outliers start: 179 outliers final: 126 residues processed: 685 average time/residue: 0.4101 time to fit residues: 475.4363 Evaluate side-chains 626 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 496 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 302 ASN Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 362 optimal weight: 0.5980 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 381 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS E 114 HIS E 118 ASN E 194 GLN F 136 GLN G 28 HIS G 187 ASN G 219 ASN H 120 HIS ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 35548 Z= 0.186 Angle : 0.541 9.960 48392 Z= 0.284 Chirality : 0.045 0.305 5360 Planarity : 0.004 0.050 6272 Dihedral : 4.946 59.867 4976 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.74 % Allowed : 13.66 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.13), residues: 4436 helix: 2.27 (0.25), residues: 472 sheet: 0.62 (0.14), residues: 1276 loop : 0.36 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 336 HIS 0.008 0.001 HIS B 350 PHE 0.030 0.001 PHE E 113 TYR 0.024 0.002 TYR A 46 ARG 0.008 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 537 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7355 (t60) cc_final: 0.6196 (t-100) REVERT: B 163 TYR cc_start: 0.8029 (m-80) cc_final: 0.7799 (m-10) REVERT: B 270 GLU cc_start: 0.7940 (tp30) cc_final: 0.7725 (mm-30) REVERT: B 300 ASP cc_start: 0.6686 (t0) cc_final: 0.6477 (t0) REVERT: C 7 MET cc_start: 0.3966 (mpp) cc_final: 0.0649 (tmm) REVERT: C 60 MET cc_start: 0.4357 (mmm) cc_final: 0.3500 (mmm) REVERT: D 30 GLN cc_start: 0.8342 (tt0) cc_final: 0.7893 (tt0) REVERT: D 252 LEU cc_start: 0.8385 (tp) cc_final: 0.8040 (tp) REVERT: E 302 ASN cc_start: 0.8431 (t0) cc_final: 0.8145 (t0) REVERT: E 327 TRP cc_start: 0.8457 (t-100) cc_final: 0.7246 (t-100) REVERT: F 15 TYR cc_start: 0.5736 (m-80) cc_final: 0.5099 (m-80) REVERT: G 75 ASP cc_start: 0.8370 (t0) cc_final: 0.7998 (t0) REVERT: G 206 SER cc_start: 0.9038 (t) cc_final: 0.8729 (m) REVERT: H 115 ASP cc_start: 0.7826 (t0) cc_final: 0.7612 (t0) REVERT: H 290 THR cc_start: 0.8961 (m) cc_final: 0.8701 (p) REVERT: H 355 TYR cc_start: 0.7156 (t80) cc_final: 0.6916 (t80) REVERT: J 247 ASP cc_start: 0.6391 (t70) cc_final: 0.6049 (t0) REVERT: J 321 TYR cc_start: 0.7298 (p90) cc_final: 0.6990 (p90) REVERT: K 35 GLU cc_start: 0.7646 (tt0) cc_final: 0.7423 (tt0) REVERT: K 52 MET cc_start: 0.6464 (ttm) cc_final: 0.6226 (ttp) REVERT: K 262 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7947 (mttm) outliers start: 105 outliers final: 78 residues processed: 602 average time/residue: 0.3975 time to fit residues: 407.7373 Evaluate side-chains 577 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 498 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 262 LYS Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 10.0000 chunk 383 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 425 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 80 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS K 80 ASN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35548 Z= 0.261 Angle : 0.568 8.980 48392 Z= 0.298 Chirality : 0.046 0.341 5360 Planarity : 0.005 0.046 6272 Dihedral : 4.886 57.131 4976 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.47 % Allowed : 13.43 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4436 helix: 2.24 (0.24), residues: 472 sheet: 0.31 (0.14), residues: 1360 loop : 0.29 (0.13), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 336 HIS 0.010 0.001 HIS G 28 PHE 0.023 0.002 PHE E 113 TYR 0.024 0.002 TYR A 46 ARG 0.005 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 523 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7463 (t60) cc_final: 0.6851 (t-100) REVERT: A 342 GLU cc_start: 0.7665 (mp0) cc_final: 0.7161 (tt0) REVERT: B 270 GLU cc_start: 0.7987 (tp30) cc_final: 0.7677 (mm-30) REVERT: B 300 ASP cc_start: 0.6776 (t0) cc_final: 0.6567 (t0) REVERT: B 313 THR cc_start: 0.7634 (p) cc_final: 0.7368 (p) REVERT: C 7 MET cc_start: 0.3754 (mpp) cc_final: 0.0420 (tmm) REVERT: C 60 MET cc_start: 0.4447 (mmm) cc_final: 0.3664 (mmm) REVERT: D 30 GLN cc_start: 0.8331 (tt0) cc_final: 0.7827 (tt0) REVERT: D 252 LEU cc_start: 0.8448 (tp) cc_final: 0.8126 (tp) REVERT: D 385 LYS cc_start: 0.7245 (tppt) cc_final: 0.6938 (tppt) REVERT: E 302 ASN cc_start: 0.8520 (t0) cc_final: 0.8240 (t0) REVERT: E 327 TRP cc_start: 0.8573 (t-100) cc_final: 0.7268 (t-100) REVERT: F 15 TYR cc_start: 0.5747 (m-80) cc_final: 0.5195 (m-80) REVERT: G 37 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7171 (mtm-85) REVERT: G 75 ASP cc_start: 0.8474 (t0) cc_final: 0.8046 (t0) REVERT: G 206 SER cc_start: 0.9012 (t) cc_final: 0.8760 (m) REVERT: H 290 THR cc_start: 0.8972 (m) cc_final: 0.8574 (p) REVERT: H 355 TYR cc_start: 0.7239 (t80) cc_final: 0.7023 (t80) REVERT: J 32 GLN cc_start: 0.8094 (tt0) cc_final: 0.7292 (tt0) REVERT: J 247 ASP cc_start: 0.6555 (t70) cc_final: 0.6187 (t70) REVERT: K 35 GLU cc_start: 0.7702 (tt0) cc_final: 0.7488 (tt0) REVERT: K 52 MET cc_start: 0.6655 (ttm) cc_final: 0.6401 (ttp) REVERT: K 327 TRP cc_start: 0.8830 (t-100) cc_final: 0.8342 (t-100) REVERT: K 356 TYR cc_start: 0.6739 (m-10) cc_final: 0.6524 (m-80) outliers start: 133 outliers final: 114 residues processed: 603 average time/residue: 0.4074 time to fit residues: 414.5641 Evaluate side-chains 603 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 489 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 242 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 358 optimal weight: 0.3980 chunk 237 optimal weight: 6.9990 chunk 424 optimal weight: 0.0370 chunk 265 optimal weight: 30.0000 chunk 258 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 80 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 35548 Z= 0.143 Angle : 0.515 9.192 48392 Z= 0.269 Chirality : 0.044 0.402 5360 Planarity : 0.004 0.048 6272 Dihedral : 4.670 55.716 4976 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.19 % Allowed : 15.28 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4436 helix: 2.47 (0.24), residues: 472 sheet: 0.53 (0.14), residues: 1292 loop : 0.27 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 336 HIS 0.023 0.001 HIS B 213 PHE 0.018 0.001 PHE G 421 TYR 0.027 0.001 TYR B 235 ARG 0.005 0.000 ARG H 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 531 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7905 (tp30) cc_final: 0.7703 (mm-30) REVERT: C 7 MET cc_start: 0.3875 (mpp) cc_final: 0.0511 (tmm) REVERT: C 60 MET cc_start: 0.4404 (mmm) cc_final: 0.3632 (mmm) REVERT: D 30 GLN cc_start: 0.8164 (tt0) cc_final: 0.7841 (tt0) REVERT: D 113 GLU cc_start: 0.7168 (mp0) cc_final: 0.6934 (mp0) REVERT: D 252 LEU cc_start: 0.8379 (tp) cc_final: 0.8031 (tp) REVERT: D 385 LYS cc_start: 0.7331 (tppt) cc_final: 0.6886 (tppt) REVERT: E 302 ASN cc_start: 0.8510 (t0) cc_final: 0.8187 (t0) REVERT: E 325 TYR cc_start: 0.8869 (p90) cc_final: 0.8568 (p90) REVERT: E 327 TRP cc_start: 0.8515 (t-100) cc_final: 0.7291 (t-100) REVERT: F 15 TYR cc_start: 0.5894 (m-80) cc_final: 0.5220 (m-80) REVERT: G 37 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7149 (mtm-85) REVERT: G 75 ASP cc_start: 0.8311 (t0) cc_final: 0.7963 (t0) REVERT: G 206 SER cc_start: 0.8997 (t) cc_final: 0.8748 (m) REVERT: G 231 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8036 (p-80) REVERT: H 290 THR cc_start: 0.8950 (m) cc_final: 0.8528 (p) REVERT: J 32 GLN cc_start: 0.8129 (tt0) cc_final: 0.7920 (tt0) REVERT: J 247 ASP cc_start: 0.6720 (t70) cc_final: 0.6340 (t70) REVERT: K 52 MET cc_start: 0.6637 (ttm) cc_final: 0.6404 (ttp) REVERT: K 90 SER cc_start: 0.7671 (OUTLIER) cc_final: 0.7309 (p) REVERT: K 302 ASN cc_start: 0.7210 (p0) cc_final: 0.6981 (p0) REVERT: L 67 TYR cc_start: 0.6568 (p90) cc_final: 0.6268 (p90) outliers start: 84 outliers final: 69 residues processed: 586 average time/residue: 0.4078 time to fit residues: 407.0050 Evaluate side-chains 570 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 499 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 269 optimal weight: 0.0670 chunk 288 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN W 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 35548 Z= 0.379 Angle : 0.635 10.771 48392 Z= 0.336 Chirality : 0.048 0.700 5360 Planarity : 0.005 0.048 6272 Dihedral : 5.097 58.796 4976 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 3.27 % Allowed : 14.79 % Favored : 81.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4436 helix: 2.33 (0.24), residues: 468 sheet: 0.34 (0.14), residues: 1368 loop : -0.02 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP K 233 HIS 0.009 0.001 HIS K 213 PHE 0.021 0.002 PHE K 113 TYR 0.030 0.002 TYR A 46 ARG 0.007 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 505 time to evaluate : 4.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7575 (ptm) cc_final: 0.7314 (ptp) REVERT: A 75 ASP cc_start: 0.8112 (t70) cc_final: 0.7789 (t70) REVERT: A 171 TRP cc_start: 0.7399 (t60) cc_final: 0.6451 (t-100) REVERT: A 342 GLU cc_start: 0.7818 (mp0) cc_final: 0.7159 (tt0) REVERT: A 367 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7669 (mtpp) REVERT: B 270 GLU cc_start: 0.7971 (tp30) cc_final: 0.7575 (mm-30) REVERT: B 339 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6638 (mm-30) REVERT: C 7 MET cc_start: 0.3804 (mpp) cc_final: 0.0571 (tmm) REVERT: C 60 MET cc_start: 0.4443 (mmm) cc_final: 0.3792 (mmm) REVERT: D 75 ASP cc_start: 0.8592 (t0) cc_final: 0.8281 (t70) REVERT: D 252 LEU cc_start: 0.8464 (tp) cc_final: 0.8198 (tp) REVERT: E 302 ASN cc_start: 0.8594 (t0) cc_final: 0.8270 (t0) REVERT: E 325 TYR cc_start: 0.9002 (p90) cc_final: 0.8770 (p90) REVERT: E 327 TRP cc_start: 0.8624 (t-100) cc_final: 0.7279 (t-100) REVERT: F 15 TYR cc_start: 0.5947 (m-80) cc_final: 0.5334 (m-80) REVERT: G 37 ARG cc_start: 0.7476 (mtm110) cc_final: 0.7167 (mtm-85) REVERT: G 206 SER cc_start: 0.9075 (t) cc_final: 0.8737 (m) REVERT: H 166 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6763 (mtp) REVERT: H 290 THR cc_start: 0.8961 (m) cc_final: 0.8208 (p) REVERT: H 327 TRP cc_start: 0.8813 (t-100) cc_final: 0.7460 (t-100) REVERT: J 247 ASP cc_start: 0.6851 (t70) cc_final: 0.6537 (t70) REVERT: K 52 MET cc_start: 0.6703 (ttm) cc_final: 0.6428 (ttp) REVERT: K 302 ASN cc_start: 0.7397 (p0) cc_final: 0.7178 (p0) REVERT: K 327 TRP cc_start: 0.8908 (t-100) cc_final: 0.8379 (t-100) REVERT: L 67 TYR cc_start: 0.6609 (p90) cc_final: 0.6349 (p90) outliers start: 125 outliers final: 103 residues processed: 585 average time/residue: 0.4437 time to fit residues: 444.5293 Evaluate side-chains 587 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 482 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain K residue 340 SER Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 chunk 370 optimal weight: 0.7980 chunk 395 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 357 optimal weight: 0.9990 chunk 373 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 35548 Z= 0.233 Angle : 0.563 9.709 48392 Z= 0.294 Chirality : 0.047 1.007 5360 Planarity : 0.004 0.049 6272 Dihedral : 4.948 59.844 4976 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 2.72 % Allowed : 16.07 % Favored : 81.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 4436 helix: 2.14 (0.24), residues: 492 sheet: 0.39 (0.14), residues: 1300 loop : 0.02 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP E 336 HIS 0.013 0.001 HIS K 213 PHE 0.017 0.002 PHE F 24 TYR 0.027 0.002 TYR J 137 ARG 0.008 0.000 ARG H 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 513 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7502 (ptm) cc_final: 0.7266 (ptp) REVERT: A 75 ASP cc_start: 0.8086 (t70) cc_final: 0.7813 (t70) REVERT: A 171 TRP cc_start: 0.7325 (t60) cc_final: 0.6433 (t-100) REVERT: A 342 GLU cc_start: 0.7694 (mp0) cc_final: 0.7245 (tt0) REVERT: B 270 GLU cc_start: 0.7945 (tp30) cc_final: 0.7590 (mm-30) REVERT: C 7 MET cc_start: 0.3561 (mpp) cc_final: 0.0543 (tmm) REVERT: C 60 MET cc_start: 0.4490 (mmm) cc_final: 0.3803 (mmm) REVERT: D 30 GLN cc_start: 0.8329 (tt0) cc_final: 0.8080 (tt0) REVERT: D 75 ASP cc_start: 0.8546 (t0) cc_final: 0.8279 (t70) REVERT: D 252 LEU cc_start: 0.8533 (tp) cc_final: 0.8219 (tp) REVERT: D 385 LYS cc_start: 0.7415 (tppt) cc_final: 0.7071 (tppt) REVERT: D 386 ASP cc_start: 0.7505 (m-30) cc_final: 0.7255 (m-30) REVERT: E 302 ASN cc_start: 0.8558 (t0) cc_final: 0.8231 (t0) REVERT: E 327 TRP cc_start: 0.8623 (t-100) cc_final: 0.7314 (t-100) REVERT: F 15 TYR cc_start: 0.5841 (m-80) cc_final: 0.5242 (m-80) REVERT: G 206 SER cc_start: 0.8944 (t) cc_final: 0.8669 (m) REVERT: H 166 MET cc_start: 0.7316 (ttm) cc_final: 0.6842 (mtp) REVERT: H 290 THR cc_start: 0.8927 (m) cc_final: 0.8488 (p) REVERT: J 32 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: J 247 ASP cc_start: 0.6843 (t70) cc_final: 0.6528 (t70) REVERT: K 52 MET cc_start: 0.6590 (ttm) cc_final: 0.6354 (ttp) REVERT: K 302 ASN cc_start: 0.7450 (p0) cc_final: 0.7189 (p0) REVERT: K 327 TRP cc_start: 0.8848 (t-100) cc_final: 0.8413 (t-100) REVERT: L 60 MET cc_start: 0.6366 (mpp) cc_final: 0.6133 (mpp) REVERT: L 67 TYR cc_start: 0.6377 (p90) cc_final: 0.6165 (p90) outliers start: 104 outliers final: 96 residues processed: 580 average time/residue: 0.4003 time to fit residues: 397.2947 Evaluate side-chains 591 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 494 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 5.9990 chunk 417 optimal weight: 40.0000 chunk 255 optimal weight: 5.9990 chunk 198 optimal weight: 0.0670 chunk 290 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 403 optimal weight: 4.9990 chunk 349 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 214 optimal weight: 0.4980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 35548 Z= 0.184 Angle : 0.546 8.717 48392 Z= 0.285 Chirality : 0.047 0.979 5360 Planarity : 0.004 0.060 6272 Dihedral : 4.793 57.841 4976 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 16.98 % Favored : 80.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 4436 helix: 2.22 (0.24), residues: 492 sheet: 0.34 (0.14), residues: 1300 loop : 0.05 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E 336 HIS 0.014 0.001 HIS B 213 PHE 0.019 0.001 PHE F 24 TYR 0.036 0.002 TYR E 325 ARG 0.009 0.000 ARG H 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 501 time to evaluate : 4.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7428 (ptm) cc_final: 0.7218 (ptp) REVERT: A 171 TRP cc_start: 0.7292 (t60) cc_final: 0.6442 (t-100) REVERT: A 342 GLU cc_start: 0.7598 (mp0) cc_final: 0.7130 (tt0) REVERT: B 270 GLU cc_start: 0.7940 (tp30) cc_final: 0.7548 (mm-30) REVERT: C 7 MET cc_start: 0.3828 (mpp) cc_final: 0.0819 (tmm) REVERT: C 60 MET cc_start: 0.4490 (mmm) cc_final: 0.3758 (mmm) REVERT: D 30 GLN cc_start: 0.8322 (tt0) cc_final: 0.8030 (tt0) REVERT: D 75 ASP cc_start: 0.8531 (t0) cc_final: 0.8274 (t70) REVERT: D 252 LEU cc_start: 0.8523 (tp) cc_final: 0.8194 (tp) REVERT: D 385 LYS cc_start: 0.7444 (tppt) cc_final: 0.7077 (tppt) REVERT: D 386 ASP cc_start: 0.7501 (m-30) cc_final: 0.7230 (m-30) REVERT: E 302 ASN cc_start: 0.8553 (t0) cc_final: 0.8230 (t0) REVERT: E 327 TRP cc_start: 0.8584 (t-100) cc_final: 0.7322 (t-100) REVERT: F 15 TYR cc_start: 0.5869 (m-80) cc_final: 0.5238 (m-80) REVERT: G 206 SER cc_start: 0.8918 (t) cc_final: 0.8641 (m) REVERT: H 166 MET cc_start: 0.7255 (ttm) cc_final: 0.6822 (mtp) REVERT: H 290 THR cc_start: 0.8902 (m) cc_final: 0.8176 (p) REVERT: H 327 TRP cc_start: 0.8813 (t-100) cc_final: 0.7560 (t-100) REVERT: J 32 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: J 247 ASP cc_start: 0.6857 (t70) cc_final: 0.6644 (t70) REVERT: K 52 MET cc_start: 0.6618 (ttm) cc_final: 0.6347 (ttp) REVERT: K 90 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7618 (p) REVERT: K 302 ASN cc_start: 0.7420 (p0) cc_final: 0.7159 (p0) REVERT: K 327 TRP cc_start: 0.8866 (t-100) cc_final: 0.8449 (t-100) outliers start: 85 outliers final: 80 residues processed: 554 average time/residue: 0.4161 time to fit residues: 396.3359 Evaluate side-chains 561 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 479 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 GLN Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 349 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.202153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149716 restraints weight = 46417.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153041 restraints weight = 30278.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154996 restraints weight = 18025.584| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 35548 Z= 0.301 Angle : 0.593 8.304 48392 Z= 0.311 Chirality : 0.048 0.931 5360 Planarity : 0.005 0.052 6272 Dihedral : 4.925 56.399 4976 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 2.64 % Allowed : 16.61 % Favored : 80.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4436 helix: 2.22 (0.24), residues: 492 sheet: 0.27 (0.14), residues: 1308 loop : -0.06 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 336 HIS 0.013 0.001 HIS B 213 PHE 0.020 0.002 PHE K 113 TYR 0.031 0.002 TYR E 325 ARG 0.008 0.001 ARG H 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8061.35 seconds wall clock time: 147 minutes 1.29 seconds (8821.29 seconds total)