Starting phenix.real_space_refine on Thu Feb 22 08:22:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufc_42192/02_2024/8ufc_42192.pdb" } resolution = 3.09 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= 0.001 sd= 0.059 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 8 9.91 5 S 240 5.16 5 C 21216 2.51 5 N 5828 2.21 5 O 6332 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33624 Number of models: 1 Model: "" Number of chains: 28 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: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "W" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} 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} Time building chain proxies: 17.98, per 1000 atoms: 0.53 Number of scatterers: 33624 At special positions: 0 Unit cell: (161.069, 171.879, 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 8 19.99 S 240 16.00 O 6332 8.00 N 5828 7.00 C 21216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 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=2.03 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=2.02 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=2.04 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 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=2.04 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=2.04 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 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: 12.51 Conformation dependent library (CDL) restraints added in 5.9 seconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 86 sheets defined 16.1% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 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: 3.685A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.525A pdb=" N ALA F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.392A 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 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: 3.692A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.856A 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 removed outlier: 3.516A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) 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: 3.603A 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 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: 4.536A 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: 4.429A 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: 3.568A pdb=" N LYS X 65 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 4.547A 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: 4.685A 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 sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.539A 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: 4.760A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.338A 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: 5.439A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.878A 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: 3.606A 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: 6.653A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 27.786A pdb=" N ARG B 46 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 22.803A pdb=" N ASN B 69 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 16.976A pdb=" N GLN B 48 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 13.745A pdb=" N PHE B 67 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N SER B 50 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N MET B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N MET B 52 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ALA B 63 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 54 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.608A 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: 4.377A 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 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: 6.378A pdb=" N PHE C 4 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR C 15 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 6 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 8.057A 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: 9.607A 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: 8.225A 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: 6.034A pdb=" N VAL C 117 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.586A 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: 6.450A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.279A 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 186 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 186 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: 4.938A pdb=" N ASP D 299 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS D 322 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (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: 4.625A pdb=" N ASN E 21 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 6.053A 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: 3.536A pdb=" N SER E 93 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 5.868A 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: 11.550A pdb=" N MET E 52 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA E 63 " --> pdb=" O MET E 52 " (cutoff:3.500A) removed outlier: 4.221A 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: 3.516A pdb=" N THR E 108 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.866A 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: 6.123A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.812A 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: 9.334A 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: 8.042A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.955A 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 Processing sheet with id=AE6, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.486A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE G 38 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR G 128 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR G 42 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL G 124 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR G 46 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 5.414A 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 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 184 through 186 current: chain 'G' and resid 268 through 270 Processing sheet with id=AE7, 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=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AF1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.772A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AF4, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF5, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.294A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.596A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR H 64 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LYS H 56 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N LEU H 62 " --> pdb=" O LYS H 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.695A pdb=" N THR H 108 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS H 126 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR H 110 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL H 124 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY H 112 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 122 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS H 114 " --> pdb=" O HIS H 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS H 120 " --> pdb=" O HIS H 114 " (cutoff:3.500A) 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: 3.703A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.992A 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: 9.812A 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: 8.853A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.854A 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: 3.560A 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: 6.564A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.310A 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: 6.047A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.794A 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: 3.639A 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: 8.478A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.552A 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: 3.549A pdb=" N THR K 108 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.846A 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: 3.743A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 3.530A 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: 8.984A 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: 9.040A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 6.996A 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 1135 hydrogen bonds defined for protein. 2853 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: 12.67 Time building geometry restraints manager: 13.63 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: 11000 1.35 - 1.47: 8258 1.47 - 1.59: 14962 1.59 - 1.71: 0 1.71 - 1.83: 284 Bond restraints: 34504 Sorted by residual: bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG H 501 " pdb=" O5 NAG H 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+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 2.89e+00 ... (remaining 34499 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 1524 106.74 - 113.58: 18966 113.58 - 120.41: 12060 120.41 - 127.25: 13864 127.25 - 134.08: 582 Bond angle restraints: 46996 Sorted by residual: angle pdb=" N ASN Y 66 " pdb=" CA ASN Y 66 " pdb=" C ASN Y 66 " ideal model delta sigma weight residual 112.90 117.67 -4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" N LYS Y 65 " pdb=" CA LYS Y 65 " pdb=" C LYS Y 65 " ideal model delta sigma weight residual 111.07 114.69 -3.62 1.07e+00 8.73e-01 1.15e+01 angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 108.15 111.01 -2.86 9.90e-01 1.02e+00 8.35e+00 angle pdb=" N ALA H 42 " pdb=" CA ALA H 42 " pdb=" C ALA H 42 " ideal model delta sigma weight residual 109.11 113.07 -3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" N TRP H 327 " pdb=" CA TRP H 327 " pdb=" C TRP H 327 " ideal model delta sigma weight residual 109.96 105.35 4.61 1.68e+00 3.54e-01 7.53e+00 ... (remaining 46991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20070 17.95 - 35.91: 592 35.91 - 53.86: 159 53.86 - 71.82: 39 71.82 - 89.77: 16 Dihedral angle restraints: 20876 sinusoidal: 8368 harmonic: 12508 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 93.00 148.40 -55.40 1 1.00e+01 1.00e-02 4.15e+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 93.00 142.94 -49.94 1 1.00e+01 1.00e-02 3.42e+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 93.00 137.69 -44.69 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3269 0.035 - 0.071: 1279 0.071 - 0.106: 460 0.106 - 0.141: 197 0.141 - 0.177: 19 Chirality restraints: 5224 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 7.79e-01 chirality pdb=" CA PRO B 286 " pdb=" N PRO B 286 " pdb=" C PRO B 286 " pdb=" CB PRO B 286 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA CYS D 371 " pdb=" N CYS D 371 " pdb=" C CYS D 371 " pdb=" CB CYS D 371 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 5221 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.274 9.50e-02 1.11e+02 1.23e-01 1.06e+01 pdb=" NE ARG B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.009 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 K 239 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.72e+00 pdb=" NE ARG K 239 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG K 239 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 239 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.240 9.50e-02 1.11e+02 1.08e-01 9.56e+00 pdb=" NE ARG D 110 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.000 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1990 2.73 - 3.27: 32508 3.27 - 3.81: 54575 3.81 - 4.36: 67618 4.36 - 4.90: 118904 Nonbonded interactions: 275595 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 201 " model vdw 2.186 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 201 " model vdw 2.206 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 202 " model vdw 2.254 2.510 nonbonded pdb=" O TRP Y 50 " pdb="CA CA Y 201 " model vdw 2.264 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.280 2.520 ... (remaining 275590 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 '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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.720 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 85.940 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.340 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 0.040 34504 Z= 0.173 Angle : 0.653 6.393 46996 Z= 0.369 Chirality : 0.046 0.177 5224 Planarity : 0.008 0.124 6080 Dihedral : 9.954 89.771 12616 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.74 (0.12), residues: 4304 helix: 0.73 (0.22), residues: 488 sheet: 0.62 (0.14), residues: 1320 loop : 0.51 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP Y 89 HIS 0.011 0.002 HIS B 253 PHE 0.022 0.002 PHE G 421 TYR 0.028 0.005 TYR D 309 ARG 0.027 0.003 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.244 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: B 168 GLN cc_start: 0.7746 (tt0) cc_final: 0.7514 (tt0) REVERT: E 4 THR cc_start: 0.8797 (t) cc_final: 0.8227 (p) REVERT: G 148 TYR cc_start: 0.7404 (m-80) cc_final: 0.6978 (m-80) REVERT: H 236 ASN cc_start: 0.8814 (p0) cc_final: 0.8581 (p0) REVERT: I 67 TYR cc_start: 0.6804 (p90) cc_final: 0.6570 (p90) REVERT: J 98 THR cc_start: 0.7919 (p) cc_final: 0.7634 (m) REVERT: K 52 MET cc_start: 0.7667 (mmm) cc_final: 0.7401 (mmm) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.4670 time to fit residues: 509.8827 Evaluate side-chains 442 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 20.0000 chunk 324 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 335 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 223 GLN A 236 GLN B 8 GLN B 213 HIS B 230 ASN B 236 ASN C 79 HIS D 176 ASN D 223 GLN D 356 HIS E 80 ASN E 120 HIS E 151 ASN E 175 HIS E 213 HIS F 37 GLN F 79 HIS G 28 HIS G 223 GLN H 114 HIS H 346 HIS I 11 GLN K 21 ASN K 213 HIS K 346 HIS V 42 ASN W 37 GLN Y 42 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 34504 Z= 0.391 Angle : 0.617 10.222 46996 Z= 0.329 Chirality : 0.049 0.220 5224 Planarity : 0.005 0.051 6080 Dihedral : 5.291 88.856 4840 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.91 % Allowed : 5.37 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.74 (0.13), residues: 4304 helix: 1.43 (0.24), residues: 492 sheet: 0.53 (0.14), residues: 1312 loop : 0.40 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.013 0.001 HIS K 213 PHE 0.022 0.002 PHE C 24 TYR 0.028 0.002 TYR J 309 ARG 0.006 0.001 ARG K 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 442 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.8002 (ttt90) REVERT: B 358 ASN cc_start: 0.7500 (m-40) cc_final: 0.7263 (m110) REVERT: E 213 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.6082 (t-90) REVERT: F 78 TRP cc_start: 0.6239 (OUTLIER) cc_final: 0.5223 (p-90) REVERT: G 148 TYR cc_start: 0.7360 (m-80) cc_final: 0.7138 (m-80) REVERT: H 129 GLU cc_start: 0.7588 (pt0) cc_final: 0.7283 (pt0) REVERT: H 376 MET cc_start: 0.5635 (mmp) cc_final: 0.5161 (mtp) REVERT: I 7 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4305 (mmt) REVERT: I 49 TYR cc_start: 0.6655 (m-80) cc_final: 0.6434 (m-80) REVERT: K 237 SER cc_start: 0.8538 (t) cc_final: 0.8334 (t) outliers start: 71 outliers final: 47 residues processed: 481 average time/residue: 0.4449 time to fit residues: 348.6567 Evaluate side-chains 457 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 407 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 0.6980 chunk 264 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 389 optimal weight: 6.9990 chunk 420 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN B 213 HIS B 230 ASN B 236 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN E 213 HIS G 77 GLN G 176 ASN G 223 GLN H 277 HIS K 21 ASN K 73 GLN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS K 346 HIS Y 42 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34504 Z= 0.292 Angle : 0.550 10.352 46996 Z= 0.290 Chirality : 0.046 0.196 5224 Planarity : 0.004 0.060 6080 Dihedral : 5.292 87.791 4840 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 6.74 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.63 (0.13), residues: 4304 helix: 1.86 (0.24), residues: 472 sheet: 0.39 (0.14), residues: 1280 loop : 0.26 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 327 HIS 0.022 0.001 HIS E 213 PHE 0.020 0.002 PHE C 24 TYR 0.025 0.002 TYR J 309 ARG 0.009 0.000 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 415 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7784 (ttt90) REVERT: B 339 GLU cc_start: 0.6758 (mp0) cc_final: 0.6363 (mp0) REVERT: B 358 ASN cc_start: 0.7536 (m-40) cc_final: 0.7324 (m110) REVERT: G 148 TYR cc_start: 0.7399 (m-80) cc_final: 0.7189 (m-80) REVERT: H 16 ILE cc_start: 0.8694 (mt) cc_final: 0.8470 (mt) REVERT: H 376 MET cc_start: 0.5646 (mmp) cc_final: 0.5212 (mtp) REVERT: I 7 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4442 (mmt) REVERT: K 236 ASN cc_start: 0.8872 (p0) cc_final: 0.8661 (p0) REVERT: K 237 SER cc_start: 0.8494 (t) cc_final: 0.8233 (t) REVERT: Y 92 ASP cc_start: 0.4751 (OUTLIER) cc_final: 0.3658 (m-30) outliers start: 77 outliers final: 55 residues processed: 464 average time/residue: 0.4418 time to fit residues: 333.8921 Evaluate side-chains 448 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 391 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 223 GLN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 413 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 370 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS B 168 GLN B 213 HIS B 230 ASN D 30 GLN D 176 ASN D 223 GLN E 213 HIS E 275 HIS G 223 GLN K 213 HIS L 80 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34504 Z= 0.227 Angle : 0.515 6.877 46996 Z= 0.272 Chirality : 0.045 0.195 5224 Planarity : 0.004 0.046 6080 Dihedral : 5.194 86.939 4840 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.86 % Allowed : 8.12 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.66 (0.13), residues: 4304 helix: 2.04 (0.24), residues: 480 sheet: 0.38 (0.14), residues: 1280 loop : 0.26 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 78 HIS 0.007 0.001 HIS K 213 PHE 0.018 0.001 PHE C 24 TYR 0.023 0.001 TYR J 309 ARG 0.005 0.000 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 405 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7791 (ttt90) REVERT: A 290 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7713 (mmt180) REVERT: B 339 GLU cc_start: 0.6891 (mp0) cc_final: 0.6434 (mp0) REVERT: D 440 ARG cc_start: 0.6629 (ttm-80) cc_final: 0.6362 (ttm-80) REVERT: G 226 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8167 (mm110) REVERT: G 421 PHE cc_start: 0.5151 (OUTLIER) cc_final: 0.4291 (t80) REVERT: H 16 ILE cc_start: 0.8734 (mt) cc_final: 0.8483 (mt) REVERT: J 343 ASN cc_start: 0.7436 (m-40) cc_final: 0.7228 (m-40) REVERT: K 237 SER cc_start: 0.8338 (t) cc_final: 0.8082 (t) REVERT: L 78 TRP cc_start: 0.7242 (p-90) cc_final: 0.6841 (p-90) REVERT: Y 92 ASP cc_start: 0.4594 (OUTLIER) cc_final: 0.3555 (m-30) outliers start: 69 outliers final: 54 residues processed: 444 average time/residue: 0.4513 time to fit residues: 328.8881 Evaluate side-chains 438 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 382 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 344 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 308 optimal weight: 0.7980 chunk 170 optimal weight: 0.0870 chunk 353 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 213 HIS D 176 ASN D 223 GLN D 369 GLN G 223 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34504 Z= 0.236 Angle : 0.510 6.999 46996 Z= 0.268 Chirality : 0.045 0.182 5224 Planarity : 0.004 0.043 6080 Dihedral : 5.110 85.859 4840 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.40 % Allowed : 8.33 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.64 (0.13), residues: 4304 helix: 2.15 (0.24), residues: 480 sheet: 0.34 (0.14), residues: 1280 loop : 0.23 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 134 HIS 0.008 0.001 HIS B 213 PHE 0.018 0.001 PHE C 24 TYR 0.028 0.001 TYR K 197 ARG 0.005 0.000 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 399 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7832 (ttt90) REVERT: B 339 GLU cc_start: 0.6982 (mp0) cc_final: 0.6489 (mp0) REVERT: G 421 PHE cc_start: 0.5231 (OUTLIER) cc_final: 0.4365 (t80) REVERT: H 16 ILE cc_start: 0.8744 (mt) cc_final: 0.8490 (mt) REVERT: J 343 ASN cc_start: 0.7517 (m-40) cc_final: 0.7306 (m-40) REVERT: L 78 TRP cc_start: 0.7308 (p-90) cc_final: 0.6826 (p-90) REVERT: Y 92 ASP cc_start: 0.4591 (OUTLIER) cc_final: 0.3546 (m-30) outliers start: 89 outliers final: 73 residues processed: 452 average time/residue: 0.4322 time to fit residues: 318.6819 Evaluate side-chains 453 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 378 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 9.9990 chunk 372 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 414 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 213 HIS D 176 ASN D 223 GLN E 21 ASN E 230 ASN G 223 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34504 Z= 0.176 Angle : 0.488 6.655 46996 Z= 0.257 Chirality : 0.044 0.181 5224 Planarity : 0.004 0.041 6080 Dihedral : 4.990 85.005 4840 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.08 % Allowed : 9.25 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.65 (0.13), residues: 4304 helix: 2.05 (0.24), residues: 504 sheet: 0.42 (0.15), residues: 1240 loop : 0.20 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 134 HIS 0.005 0.001 HIS G 28 PHE 0.015 0.001 PHE C 24 TYR 0.026 0.001 TYR K 197 ARG 0.005 0.000 ARG E 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 397 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7785 (ttt90) REVERT: A 421 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5636 (t80) REVERT: B 339 GLU cc_start: 0.6973 (mp0) cc_final: 0.6457 (mp0) REVERT: D 146 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7257 (t0) REVERT: D 440 ARG cc_start: 0.6482 (ttm-80) cc_final: 0.6200 (ttm-80) REVERT: E 171 LEU cc_start: 0.8452 (mt) cc_final: 0.8243 (mt) REVERT: G 421 PHE cc_start: 0.5173 (OUTLIER) cc_final: 0.4535 (t80) REVERT: H 16 ILE cc_start: 0.8739 (mt) cc_final: 0.8471 (mt) REVERT: J 343 ASN cc_start: 0.7533 (m-40) cc_final: 0.7317 (m-40) REVERT: K 64 TYR cc_start: 0.7275 (m-10) cc_final: 0.7024 (m-80) REVERT: L 78 TRP cc_start: 0.7309 (p-90) cc_final: 0.6683 (p-90) REVERT: Y 92 ASP cc_start: 0.4483 (OUTLIER) cc_final: 0.3528 (m-30) outliers start: 77 outliers final: 61 residues processed: 442 average time/residue: 0.4416 time to fit residues: 320.8474 Evaluate side-chains 432 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 367 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 223 GLN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 328 ASN Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 412 optimal weight: 0.0370 chunk 258 optimal weight: 0.6980 chunk 251 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 168 GLN D 223 GLN E 140 HIS G 219 ASN G 223 GLN I 84 GLN K 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34504 Z= 0.225 Angle : 0.501 7.642 46996 Z= 0.262 Chirality : 0.045 0.171 5224 Planarity : 0.004 0.049 6080 Dihedral : 4.938 83.867 4840 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.18 % Allowed : 9.57 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.59 (0.13), residues: 4304 helix: 2.10 (0.24), residues: 496 sheet: 0.35 (0.14), residues: 1304 loop : 0.15 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 142 HIS 0.007 0.001 HIS G 28 PHE 0.017 0.001 PHE C 24 TYR 0.026 0.001 TYR K 197 ARG 0.004 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 385 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7808 (ttt90) REVERT: A 421 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.5645 (t80) REVERT: B 339 GLU cc_start: 0.7026 (mp0) cc_final: 0.6504 (mp0) REVERT: D 37 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8182 (mtm110) REVERT: D 146 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7228 (t0) REVERT: D 440 ARG cc_start: 0.6603 (ttm-80) cc_final: 0.6320 (ttm-80) REVERT: E 171 LEU cc_start: 0.8468 (mt) cc_final: 0.8262 (mt) REVERT: G 421 PHE cc_start: 0.5145 (OUTLIER) cc_final: 0.4571 (t80) REVERT: H 16 ILE cc_start: 0.8748 (mt) cc_final: 0.8477 (mt) REVERT: J 343 ASN cc_start: 0.7544 (m-40) cc_final: 0.7324 (m-40) REVERT: L 78 TRP cc_start: 0.7328 (p-90) cc_final: 0.6692 (p-90) REVERT: Y 92 ASP cc_start: 0.4461 (OUTLIER) cc_final: 0.3544 (m-30) outliers start: 81 outliers final: 72 residues processed: 433 average time/residue: 0.4533 time to fit residues: 319.8108 Evaluate side-chains 469 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 393 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 203 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN G 223 GLN I 84 GLN J 32 GLN J 328 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34504 Z= 0.251 Angle : 0.512 7.343 46996 Z= 0.268 Chirality : 0.045 0.171 5224 Planarity : 0.004 0.045 6080 Dihedral : 4.953 81.800 4840 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.32 % Allowed : 9.68 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.50 (0.13), residues: 4304 helix: 2.08 (0.24), residues: 496 sheet: 0.29 (0.14), residues: 1304 loop : 0.08 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 142 HIS 0.005 0.001 HIS G 28 PHE 0.018 0.001 PHE C 24 TYR 0.027 0.001 TYR K 197 ARG 0.004 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 401 time to evaluate : 3.628 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: A 224 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7768 (ttt90) REVERT: A 421 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.5653 (t80) REVERT: B 339 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.5863 (mt-10) REVERT: D 37 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8199 (mtm110) REVERT: D 146 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7241 (t0) REVERT: D 440 ARG cc_start: 0.6650 (ttm-80) cc_final: 0.6402 (ttm-80) REVERT: G 421 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4598 (t80) REVERT: H 16 ILE cc_start: 0.8738 (mt) cc_final: 0.8468 (mt) REVERT: H 68 MET cc_start: 0.8653 (mmt) cc_final: 0.8306 (mmt) REVERT: J 343 ASN cc_start: 0.7526 (m-40) cc_final: 0.7300 (m-40) REVERT: K 237 SER cc_start: 0.8205 (t) cc_final: 0.7986 (t) REVERT: L 78 TRP cc_start: 0.7365 (p-90) cc_final: 0.6721 (p-90) REVERT: V 38 PHE cc_start: 0.8370 (t80) cc_final: 0.8075 (t80) REVERT: Y 92 ASP cc_start: 0.4193 (OUTLIER) cc_final: 0.3384 (m-30) outliers start: 86 outliers final: 74 residues processed: 454 average time/residue: 0.4382 time to fit residues: 325.0582 Evaluate side-chains 456 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 377 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 328 ASN Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 375 optimal weight: 2.9990 chunk 395 optimal weight: 10.0000 chunk 360 optimal weight: 4.9990 chunk 384 optimal weight: 0.0870 chunk 231 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 347 optimal weight: 0.0020 chunk 363 optimal weight: 7.9990 chunk 383 optimal weight: 0.8980 overall best weight: 1.7970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN F 37 GLN G 223 GLN I 11 GLN J 328 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34504 Z= 0.235 Angle : 0.511 8.115 46996 Z= 0.267 Chirality : 0.045 0.169 5224 Planarity : 0.004 0.044 6080 Dihedral : 4.928 80.187 4840 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.35 % Allowed : 9.82 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.47 (0.13), residues: 4304 helix: 2.10 (0.24), residues: 496 sheet: 0.27 (0.14), residues: 1304 loop : 0.06 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 142 HIS 0.007 0.001 HIS G 28 PHE 0.017 0.001 PHE C 24 TYR 0.025 0.001 TYR K 197 ARG 0.005 0.000 ARG K 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 378 time to evaluate : 4.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7763 (ttt90) REVERT: A 421 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.5637 (t80) REVERT: D 37 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8204 (mtm110) REVERT: D 146 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7247 (t0) REVERT: D 440 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6560 (ttm-80) REVERT: G 421 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.4593 (t80) REVERT: H 68 MET cc_start: 0.8688 (mmt) cc_final: 0.8342 (mmt) REVERT: H 376 MET cc_start: 0.5199 (mmp) cc_final: 0.4968 (mmt) REVERT: K 237 SER cc_start: 0.8184 (t) cc_final: 0.7974 (t) REVERT: V 38 PHE cc_start: 0.8339 (t80) cc_final: 0.8060 (t80) REVERT: Y 92 ASP cc_start: 0.4181 (OUTLIER) cc_final: 0.3404 (m-30) outliers start: 87 outliers final: 77 residues processed: 434 average time/residue: 0.4464 time to fit residues: 316.7520 Evaluate side-chains 460 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 379 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 426 optimal weight: 0.5980 chunk 392 optimal weight: 1.9990 chunk 339 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 213 HIS ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN Y 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34504 Z= 0.178 Angle : 0.492 7.873 46996 Z= 0.258 Chirality : 0.044 0.179 5224 Planarity : 0.004 0.044 6080 Dihedral : 4.841 78.501 4840 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.05 % Allowed : 10.30 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.53 (0.13), residues: 4304 helix: 2.18 (0.24), residues: 496 sheet: 0.31 (0.14), residues: 1304 loop : 0.08 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 142 HIS 0.029 0.001 HIS B 213 PHE 0.015 0.001 PHE C 24 TYR 0.024 0.001 TYR K 197 ARG 0.005 0.000 ARG K 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 384 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7729 (ttt90) REVERT: A 421 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5612 (t80) REVERT: B 339 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: D 37 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8188 (mtm110) REVERT: D 146 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7232 (t0) REVERT: D 440 ARG cc_start: 0.6718 (ttm-80) cc_final: 0.6463 (ttm-80) REVERT: E 171 LEU cc_start: 0.8497 (mt) cc_final: 0.8290 (mt) REVERT: G 421 PHE cc_start: 0.5154 (OUTLIER) cc_final: 0.4584 (t80) REVERT: H 68 MET cc_start: 0.8622 (mmt) cc_final: 0.8366 (mmt) REVERT: H 376 MET cc_start: 0.5188 (mmp) cc_final: 0.4968 (mmt) REVERT: J 394 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7263 (mm-40) REVERT: K 237 SER cc_start: 0.8110 (t) cc_final: 0.7864 (t) REVERT: V 38 PHE cc_start: 0.8335 (t80) cc_final: 0.8066 (t80) REVERT: Y 92 ASP cc_start: 0.4081 (OUTLIER) cc_final: 0.3306 (m-30) outliers start: 76 outliers final: 68 residues processed: 432 average time/residue: 0.4379 time to fit residues: 309.4817 Evaluate side-chains 446 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 373 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 7 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 176 ASN Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Chi-restraints excluded: chain Y residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 269 optimal weight: 3.9990 chunk 361 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 349 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 213 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 223 GLN K 80 ASN K 114 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.182387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130769 restraints weight = 37059.235| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.57 r_work: 0.3290 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 34504 Z= 0.370 Angle : 0.572 8.171 46996 Z= 0.299 Chirality : 0.047 0.182 5224 Planarity : 0.005 0.046 6080 Dihedral : 5.098 75.891 4840 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.21 % Allowed : 10.52 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.32 (0.13), residues: 4304 helix: 1.99 (0.24), residues: 496 sheet: 0.21 (0.14), residues: 1296 loop : -0.07 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 142 HIS 0.030 0.001 HIS B 213 PHE 0.022 0.002 PHE C 24 TYR 0.027 0.002 TYR J 309 ARG 0.007 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8055.91 seconds wall clock time: 147 minutes 9.77 seconds (8829.77 seconds total)