Starting phenix.real_space_refine on Mon Sep 30 05:10:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihs_35454/09_2024/8ihs_35454.cif" } resolution = 2.5 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= 0.058 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: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 Cl 8 4.86 5 C 15272 2.51 5 N 4432 2.21 5 O 4552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24352 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 14.19, per 1000 atoms: 0.58 Number of scatterers: 24352 At special positions: 0 Unit cell: (147.05, 147.05, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 72 16.00 O 4552 8.00 N 4432 7.00 C 15272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.04 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.04 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.01 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 41.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.584A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.723A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.601A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 303 removed outlier: 3.723A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 363 removed outlier: 3.983A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS H 106 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 303 removed outlier: 3.724A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 363 removed outlier: 3.982A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 Processing helix chain 'H' and resid 408 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.344A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.987A pdb=" N VAL A 248 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU A 270 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 250 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 269 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.653A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 248 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU B 270 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 250 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 269 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 248 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU C 270 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 250 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 269 " --> pdb=" O VAL C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL D 248 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU D 270 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 250 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 269 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL E 248 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU E 270 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA E 250 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 269 " --> pdb=" O VAL E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.621A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 248 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU F 270 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 250 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 269 " --> pdb=" O VAL F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 38 removed outlier: 13.872A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.720A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL G 248 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU G 270 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA G 250 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE G 269 " --> pdb=" O VAL G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 removed outlier: 13.873A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.675A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL H 248 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 270 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 250 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 269 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 999 hydrogen bonds defined for protein. 2685 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: 7.99 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8421 1.34 - 1.46: 5485 1.46 - 1.58: 10806 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 24848 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.385 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 24843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 33328 2.63 - 5.25: 343 5.25 - 7.88: 41 7.88 - 10.51: 0 10.51 - 13.13: 8 Bond angle restraints: 33720 Sorted by residual: angle pdb=" CAH 97U D 503 " pdb=" OAI 97U D 503 " pdb=" CAJ 97U D 503 " ideal model delta sigma weight residual 120.79 107.66 13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAH 97U C 503 " pdb=" OAI 97U C 503 " pdb=" CAJ 97U C 503 " ideal model delta sigma weight residual 120.79 107.68 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAH 97U A 503 " pdb=" OAI 97U A 503 " pdb=" CAJ 97U A 503 " ideal model delta sigma weight residual 120.79 107.71 13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAH 97U B 503 " pdb=" OAI 97U B 503 " pdb=" CAJ 97U B 503 " ideal model delta sigma weight residual 120.79 107.81 12.98 3.00e+00 1.11e-01 1.87e+01 angle pdb=" N THR H 301 " pdb=" CA THR H 301 " pdb=" C THR H 301 " ideal model delta sigma weight residual 113.55 108.10 5.45 1.26e+00 6.30e-01 1.87e+01 ... (remaining 33715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12769 17.83 - 35.65: 1457 35.65 - 53.48: 424 53.48 - 71.30: 77 71.30 - 89.12: 73 Dihedral angle restraints: 14800 sinusoidal: 5840 harmonic: 8960 Sorted by residual: dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.14 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 27 " pdb=" SG CYS A 27 " pdb=" SG CYS A 75 " pdb=" CB CYS A 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 14797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3291 0.073 - 0.146: 377 0.146 - 0.219: 12 0.219 - 0.292: 0 0.292 - 0.364: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" C 97U H 503 " pdb=" CB 97U H 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" C 97U G 503 " pdb=" CB 97U G 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA 97U E 503 " pdb=" N 97U E 503 " pdb=" C 97U E 503 " pdb=" CB 97U E 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3685 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 298 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ARG G 298 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG G 298 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE G 299 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 102 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO G 103 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 291 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 292 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 292 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 292 " -0.023 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 23 2.15 - 2.84: 7699 2.84 - 3.52: 30872 3.52 - 4.21: 58985 4.21 - 4.90: 105021 Nonbonded interactions: 202600 Sorted by model distance: nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.460 2.230 nonbonded pdb=" OQ1 KCX H 210 " pdb="ZN ZN H 502 " model vdw 1.528 2.230 nonbonded pdb="ZN ZN G 502 " pdb=" OAX 97U G 503 " model vdw 1.769 2.230 nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.789 2.230 nonbonded pdb="ZN ZN A 502 " pdb=" OAX 97U A 503 " model vdw 1.825 2.230 ... (remaining 202595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.200 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 24848 Z= 0.357 Angle : 0.647 13.133 33720 Z= 0.339 Chirality : 0.047 0.364 3688 Planarity : 0.005 0.041 4488 Dihedral : 17.351 89.125 9096 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.37 % Allowed : 19.66 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.15), residues: 3136 helix: 0.67 (0.15), residues: 1256 sheet: -0.58 (0.25), residues: 448 loop : -0.66 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 79 HIS 0.011 0.001 HIS G 251 PHE 0.013 0.002 PHE H 294 TYR 0.011 0.001 TYR C 333 ARG 0.008 0.000 ARG H 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 457 time to evaluate : 2.571 Fit side-chains REVERT: E 44 LEU cc_start: 0.8128 (mp) cc_final: 0.7892 (mm) REVERT: E 172 GLU cc_start: 0.7459 (pt0) cc_final: 0.7085 (tt0) REVERT: E 174 LEU cc_start: 0.7722 (mt) cc_final: 0.7512 (mt) REVERT: E 281 ARG cc_start: 0.7358 (mtp180) cc_final: 0.7134 (mtm110) REVERT: E 327 GLN cc_start: 0.6857 (mp-120) cc_final: 0.6452 (mm-40) REVERT: F 44 LEU cc_start: 0.8116 (mp) cc_final: 0.7894 (mm) REVERT: F 155 LYS cc_start: 0.8035 (tptp) cc_final: 0.7828 (tptp) REVERT: F 172 GLU cc_start: 0.7454 (pt0) cc_final: 0.6935 (mm-30) REVERT: F 174 LEU cc_start: 0.7628 (mt) cc_final: 0.7409 (mt) REVERT: F 281 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7145 (mtm110) REVERT: F 327 GLN cc_start: 0.6872 (mp-120) cc_final: 0.6475 (mm-40) REVERT: G 44 LEU cc_start: 0.8140 (mp) cc_final: 0.7901 (mm) REVERT: G 155 LYS cc_start: 0.8043 (tptp) cc_final: 0.7839 (tptp) REVERT: G 172 GLU cc_start: 0.7450 (pt0) cc_final: 0.7064 (tt0) REVERT: G 174 LEU cc_start: 0.7697 (mt) cc_final: 0.7480 (mt) REVERT: G 207 ASP cc_start: 0.8386 (m-30) cc_final: 0.8139 (m-30) REVERT: G 281 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7191 (mtm110) REVERT: G 327 GLN cc_start: 0.6797 (mp-120) cc_final: 0.6399 (mm-40) REVERT: H 44 LEU cc_start: 0.8119 (mp) cc_final: 0.7873 (mm) REVERT: H 155 LYS cc_start: 0.8013 (tptp) cc_final: 0.7807 (tptp) REVERT: H 174 LEU cc_start: 0.7662 (mt) cc_final: 0.7458 (mt) REVERT: H 281 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7146 (mtm110) REVERT: H 327 GLN cc_start: 0.6826 (mp-120) cc_final: 0.6437 (mm-40) outliers start: 9 outliers final: 9 residues processed: 465 average time/residue: 1.4678 time to fit residues: 776.4309 Evaluate side-chains 374 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 365 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN E 26 GLN E 53 GLN E 93 GLN E 404 ASN F 26 GLN F 53 GLN F 93 GLN F 404 ASN G 26 GLN G 53 GLN G 93 GLN G 404 ASN H 26 GLN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24848 Z= 0.342 Angle : 0.610 8.836 33720 Z= 0.328 Chirality : 0.049 0.228 3688 Planarity : 0.006 0.047 4488 Dihedral : 10.461 85.891 3771 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.64 % Allowed : 16.31 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.15), residues: 3136 helix: 0.75 (0.15), residues: 1264 sheet: -0.02 (0.25), residues: 472 loop : -0.85 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.008 0.001 HIS C 251 PHE 0.016 0.002 PHE F 294 TYR 0.016 0.002 TYR G 244 ARG 0.004 0.001 ARG F 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 342 time to evaluate : 2.904 Fit side-chains REVERT: A 52 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6683 (mpt-90) REVERT: A 270 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8476 (mm-30) REVERT: B 270 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: C 270 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: D 270 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: E 44 LEU cc_start: 0.8462 (mp) cc_final: 0.8135 (mm) REVERT: E 131 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: E 172 GLU cc_start: 0.7498 (pt0) cc_final: 0.7239 (pt0) REVERT: E 173 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.5437 (ttm-80) REVERT: E 281 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7022 (mtm110) REVERT: E 414 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7509 (t70) REVERT: F 44 LEU cc_start: 0.8456 (mp) cc_final: 0.8131 (mm) REVERT: F 131 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: F 172 GLU cc_start: 0.7499 (pt0) cc_final: 0.7242 (pt0) REVERT: F 173 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.5965 (ttm170) REVERT: F 281 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7022 (mtm110) REVERT: F 414 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7510 (t70) REVERT: G 44 LEU cc_start: 0.8462 (mp) cc_final: 0.8157 (mm) REVERT: G 131 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: G 172 GLU cc_start: 0.7487 (pt0) cc_final: 0.7249 (pt0) REVERT: G 173 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.5436 (ttm-80) REVERT: G 281 ARG cc_start: 0.7398 (mtp180) cc_final: 0.7032 (mtm110) REVERT: G 414 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7506 (t70) REVERT: H 44 LEU cc_start: 0.8461 (mp) cc_final: 0.8147 (mm) REVERT: H 131 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: H 173 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5445 (ttm-80) REVERT: H 281 ARG cc_start: 0.7387 (mtp180) cc_final: 0.7024 (mtm110) REVERT: H 414 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7503 (t70) outliers start: 88 outliers final: 39 residues processed: 401 average time/residue: 1.4512 time to fit residues: 663.1032 Evaluate side-chains 374 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 319 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 0.0370 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 53 GLN G 93 GLN H 53 GLN H 93 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 24848 Z= 0.397 Angle : 0.639 10.325 33720 Z= 0.343 Chirality : 0.051 0.228 3688 Planarity : 0.006 0.049 4488 Dihedral : 10.200 83.688 3771 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.39 % Allowed : 15.15 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.15), residues: 3136 helix: 0.60 (0.14), residues: 1272 sheet: 0.07 (0.25), residues: 472 loop : -0.94 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.008 0.001 HIS A 251 PHE 0.018 0.002 PHE H 294 TYR 0.016 0.003 TYR D 333 ARG 0.005 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 336 time to evaluate : 2.910 Fit side-chains REVERT: A 52 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6682 (mpt-90) REVERT: A 270 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: B 270 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8509 (mm-30) REVERT: C 270 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: D 270 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: E 44 LEU cc_start: 0.8490 (mp) cc_final: 0.8162 (mm) REVERT: E 55 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6998 (mt) REVERT: E 131 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: E 173 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5409 (ttm-80) REVERT: E 281 ARG cc_start: 0.7378 (mtp180) cc_final: 0.7035 (mtm110) REVERT: E 404 ASN cc_start: 0.8540 (t0) cc_final: 0.8327 (t0) REVERT: E 414 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7475 (t70) REVERT: F 44 LEU cc_start: 0.8499 (mp) cc_final: 0.8171 (mm) REVERT: F 55 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6999 (mt) REVERT: F 131 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: F 173 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.5421 (ttm-80) REVERT: F 404 ASN cc_start: 0.8543 (t0) cc_final: 0.8329 (t0) REVERT: F 414 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7472 (t70) REVERT: G 44 LEU cc_start: 0.8509 (mp) cc_final: 0.8182 (mm) REVERT: G 55 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7026 (mt) REVERT: G 131 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: G 173 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.5977 (ttm170) REVERT: G 404 ASN cc_start: 0.8537 (t0) cc_final: 0.8323 (t0) REVERT: G 414 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7475 (t70) REVERT: H 44 LEU cc_start: 0.8507 (mp) cc_final: 0.8180 (mm) REVERT: H 55 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6935 (mt) REVERT: H 131 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: H 173 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.5429 (ttm-80) REVERT: H 404 ASN cc_start: 0.8527 (t0) cc_final: 0.8310 (t0) REVERT: H 414 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7473 (t70) outliers start: 106 outliers final: 42 residues processed: 401 average time/residue: 1.5000 time to fit residues: 684.3392 Evaluate side-chains 392 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 330 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 8.9990 chunk 213 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN D 26 GLN D 53 GLN D 404 ASN E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 53 GLN G 93 GLN H 53 GLN H 93 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24848 Z= 0.209 Angle : 0.512 7.098 33720 Z= 0.273 Chirality : 0.045 0.225 3688 Planarity : 0.005 0.046 4488 Dihedral : 9.349 81.241 3771 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.73 % Allowed : 15.36 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.15), residues: 3136 helix: 0.90 (0.14), residues: 1264 sheet: 0.22 (0.25), residues: 472 loop : -0.91 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.006 0.001 HIS A 251 PHE 0.013 0.002 PHE G 294 TYR 0.011 0.001 TYR B 333 ARG 0.003 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 328 time to evaluate : 2.868 Fit side-chains REVERT: A 52 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6744 (mpt-90) REVERT: A 173 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5345 (ttm-80) REVERT: B 173 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.5344 (ttm-80) REVERT: C 173 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.5345 (ttm-80) REVERT: D 173 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.5345 (ttm-80) REVERT: E 26 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: E 44 LEU cc_start: 0.8490 (mp) cc_final: 0.8185 (mm) REVERT: E 55 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6955 (mt) REVERT: E 131 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: E 174 LEU cc_start: 0.7644 (mt) cc_final: 0.7410 (mt) REVERT: E 281 ARG cc_start: 0.7349 (mtp180) cc_final: 0.7076 (mtm-85) REVERT: E 404 ASN cc_start: 0.8426 (t0) cc_final: 0.8221 (t0) REVERT: E 414 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (t70) REVERT: F 26 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7489 (mt0) REVERT: F 44 LEU cc_start: 0.8489 (mp) cc_final: 0.8183 (mm) REVERT: F 55 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6939 (mt) REVERT: F 131 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: F 174 LEU cc_start: 0.7644 (mt) cc_final: 0.7404 (mt) REVERT: F 404 ASN cc_start: 0.8435 (t0) cc_final: 0.8226 (t0) REVERT: F 414 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7480 (t70) REVERT: G 26 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: G 44 LEU cc_start: 0.8498 (mp) cc_final: 0.8186 (mm) REVERT: G 55 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6954 (mt) REVERT: G 131 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: G 174 LEU cc_start: 0.7644 (mt) cc_final: 0.7410 (mt) REVERT: G 404 ASN cc_start: 0.8427 (t0) cc_final: 0.8222 (t0) REVERT: G 414 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7428 (t70) REVERT: H 26 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: H 44 LEU cc_start: 0.8496 (mp) cc_final: 0.8191 (mm) REVERT: H 55 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6964 (mt) REVERT: H 131 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: H 174 LEU cc_start: 0.7669 (mt) cc_final: 0.7436 (mt) REVERT: H 404 ASN cc_start: 0.8427 (t0) cc_final: 0.8219 (t0) REVERT: H 414 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (t70) outliers start: 90 outliers final: 39 residues processed: 383 average time/residue: 1.3346 time to fit residues: 591.3511 Evaluate side-chains 386 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 327 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 0.0370 chunk 124 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 53 GLN G 93 GLN H 53 GLN H 93 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24848 Z= 0.239 Angle : 0.528 7.245 33720 Z= 0.282 Chirality : 0.046 0.223 3688 Planarity : 0.005 0.045 4488 Dihedral : 9.260 79.653 3763 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.39 % Allowed : 14.11 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.15), residues: 3136 helix: 0.96 (0.15), residues: 1264 sheet: 0.28 (0.25), residues: 472 loop : -0.94 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.015 0.002 PHE H 294 TYR 0.012 0.002 TYR C 333 ARG 0.003 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 333 time to evaluate : 2.960 Fit side-chains REVERT: A 52 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6642 (mpt-90) REVERT: A 173 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5355 (ttm-80) REVERT: A 270 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: B 173 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.5355 (ttm-80) REVERT: B 270 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8400 (mm-30) REVERT: C 173 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5399 (ttm-80) REVERT: C 270 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: D 173 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.5353 (ttm-80) REVERT: D 270 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: E 26 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: E 44 LEU cc_start: 0.8470 (mp) cc_final: 0.8152 (mm) REVERT: E 55 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6871 (mt) REVERT: E 131 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: E 173 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5416 (ttm-80) REVERT: E 174 LEU cc_start: 0.7658 (mt) cc_final: 0.7418 (mt) REVERT: E 281 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7093 (mtm-85) REVERT: E 414 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7444 (t70) REVERT: F 26 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: F 44 LEU cc_start: 0.8483 (mp) cc_final: 0.8163 (mm) REVERT: F 55 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6860 (mt) REVERT: F 131 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: F 173 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5414 (ttm-80) REVERT: F 174 LEU cc_start: 0.7659 (mt) cc_final: 0.7419 (mt) REVERT: F 414 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7442 (t70) REVERT: G 26 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: G 44 LEU cc_start: 0.8481 (mp) cc_final: 0.8160 (mm) REVERT: G 55 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6920 (mt) REVERT: G 131 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: G 173 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.5414 (ttm-80) REVERT: G 174 LEU cc_start: 0.7658 (mt) cc_final: 0.7416 (mt) REVERT: G 414 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7445 (t70) REVERT: H 26 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: H 44 LEU cc_start: 0.8480 (mp) cc_final: 0.8162 (mm) REVERT: H 55 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6933 (mt) REVERT: H 131 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: H 173 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.5930 (ttm170) REVERT: H 414 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7443 (t70) outliers start: 106 outliers final: 49 residues processed: 406 average time/residue: 1.3428 time to fit residues: 628.9788 Evaluate side-chains 405 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 328 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.9990 chunk 271 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN H 53 GLN H 404 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24848 Z= 0.186 Angle : 0.489 6.115 33720 Z= 0.260 Chirality : 0.044 0.222 3688 Planarity : 0.005 0.044 4488 Dihedral : 8.531 74.654 3760 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.27 % Allowed : 15.31 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.15), residues: 3136 helix: 1.09 (0.15), residues: 1264 sheet: 0.35 (0.25), residues: 472 loop : -0.88 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 289 HIS 0.005 0.001 HIS A 251 PHE 0.013 0.001 PHE H 294 TYR 0.010 0.001 TYR D 333 ARG 0.005 0.000 ARG G 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 333 time to evaluate : 2.803 Fit side-chains REVERT: A 52 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6669 (mpt-90) REVERT: A 173 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.5415 (ttm-80) REVERT: A 270 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: B 53 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: B 173 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.5409 (ttm-80) REVERT: B 270 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: C 53 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: C 173 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.5407 (ttm-80) REVERT: C 270 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: D 53 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: D 173 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.5406 (ttm-80) REVERT: D 270 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: E 55 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6821 (mt) REVERT: E 131 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: E 281 ARG cc_start: 0.7350 (mtp180) cc_final: 0.7106 (mtm-85) REVERT: E 414 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7426 (t70) REVERT: F 55 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6860 (mt) REVERT: F 131 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: F 414 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7427 (t70) REVERT: G 131 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: H 44 LEU cc_start: 0.8444 (mp) cc_final: 0.8127 (mm) REVERT: H 131 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: H 173 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.5380 (ttm-80) REVERT: H 313 VAL cc_start: 0.5638 (OUTLIER) cc_final: 0.5214 (p) REVERT: H 414 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7425 (t70) outliers start: 79 outliers final: 41 residues processed: 387 average time/residue: 1.3441 time to fit residues: 601.1588 Evaluate side-chains 382 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 319 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 404 ASN B 26 GLN B 53 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 53 GLN D 26 GLN D 53 GLN D 404 ASN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN H 53 GLN H 404 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24848 Z= 0.291 Angle : 0.558 7.915 33720 Z= 0.300 Chirality : 0.047 0.223 3688 Planarity : 0.005 0.046 4488 Dihedral : 9.297 78.169 3760 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.52 % Allowed : 15.65 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.15), residues: 3136 helix: 0.99 (0.15), residues: 1264 sheet: 0.38 (0.25), residues: 472 loop : -0.97 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 289 HIS 0.008 0.001 HIS A 251 PHE 0.016 0.002 PHE H 294 TYR 0.014 0.002 TYR D 333 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 330 time to evaluate : 2.714 Fit side-chains REVERT: A 52 ARG cc_start: 0.7357 (mtm180) cc_final: 0.6663 (mpt-90) REVERT: A 173 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.5441 (ttm-80) REVERT: A 270 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8446 (mm-30) REVERT: B 173 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5433 (ttm-80) REVERT: B 270 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: C 173 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5406 (ttm-80) REVERT: C 270 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: D 173 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.5406 (ttm-80) REVERT: D 270 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8451 (mm-30) REVERT: E 55 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6847 (mt) REVERT: E 131 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: E 173 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5954 (ttm170) REVERT: E 281 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7151 (mtm-85) REVERT: E 414 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7450 (t70) REVERT: F 55 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6859 (mt) REVERT: F 131 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: F 173 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5954 (ttm170) REVERT: F 414 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7451 (t70) REVERT: G 131 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: G 173 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5955 (ttm170) REVERT: H 44 LEU cc_start: 0.8484 (mp) cc_final: 0.8154 (mm) REVERT: H 131 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: H 173 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5906 (ttm170) REVERT: H 313 VAL cc_start: 0.5661 (OUTLIER) cc_final: 0.5219 (p) REVERT: H 414 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7450 (t70) outliers start: 85 outliers final: 47 residues processed: 394 average time/residue: 1.3764 time to fit residues: 623.0651 Evaluate side-chains 395 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 326 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 191 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24848 Z= 0.256 Angle : 0.535 7.457 33720 Z= 0.287 Chirality : 0.046 0.224 3688 Planarity : 0.005 0.044 4488 Dihedral : 9.153 77.974 3760 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.31 % Allowed : 15.77 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.15), residues: 3136 helix: 1.01 (0.14), residues: 1264 sheet: 0.38 (0.25), residues: 472 loop : -0.97 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.015 0.002 PHE H 294 TYR 0.013 0.002 TYR B 333 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 322 time to evaluate : 2.799 Fit side-chains REVERT: A 52 ARG cc_start: 0.7376 (mtm180) cc_final: 0.6672 (mpt-90) REVERT: A 173 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.5399 (ttm-80) REVERT: A 270 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8389 (mm-30) REVERT: B 53 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: B 173 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.5367 (ttm-80) REVERT: B 270 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8414 (mm-30) REVERT: C 53 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: C 173 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5391 (ttm-80) REVERT: C 270 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: D 53 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: D 173 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.5391 (ttm-80) REVERT: D 270 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8409 (mm-30) REVERT: E 55 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6849 (mt) REVERT: E 131 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: E 173 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5393 (ttm-80) REVERT: E 281 ARG cc_start: 0.7410 (mtp180) cc_final: 0.7205 (mtm-85) REVERT: E 313 VAL cc_start: 0.5688 (OUTLIER) cc_final: 0.5248 (p) REVERT: E 414 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7450 (t70) REVERT: F 55 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6844 (mt) REVERT: F 131 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: F 173 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.5951 (ttm170) REVERT: F 313 VAL cc_start: 0.5690 (OUTLIER) cc_final: 0.5251 (p) REVERT: F 414 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7448 (t70) REVERT: G 55 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6812 (mt) REVERT: G 131 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: G 173 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5392 (ttm-80) REVERT: G 313 VAL cc_start: 0.5688 (OUTLIER) cc_final: 0.5248 (p) REVERT: H 44 LEU cc_start: 0.8484 (mp) cc_final: 0.8143 (mm) REVERT: H 131 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: H 173 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.5928 (ttm170) REVERT: H 313 VAL cc_start: 0.5688 (OUTLIER) cc_final: 0.5252 (p) REVERT: H 414 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7448 (t70) outliers start: 80 outliers final: 50 residues processed: 383 average time/residue: 1.2757 time to fit residues: 566.2506 Evaluate side-chains 399 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 320 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 0.7980 chunk 262 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 0.4980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 26 GLN E 53 GLN F 26 GLN F 53 GLN F 404 ASN G 26 GLN G 53 GLN G 404 ASN H 53 GLN H 404 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24848 Z= 0.281 Angle : 0.554 7.853 33720 Z= 0.297 Chirality : 0.047 0.224 3688 Planarity : 0.005 0.046 4488 Dihedral : 9.282 78.477 3760 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.52 % Allowed : 15.60 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.15), residues: 3136 helix: 0.98 (0.15), residues: 1264 sheet: 0.38 (0.25), residues: 472 loop : -1.01 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 289 HIS 0.007 0.001 HIS A 251 PHE 0.015 0.002 PHE H 294 TYR 0.013 0.002 TYR D 333 ARG 0.004 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 314 time to evaluate : 2.632 Fit side-chains REVERT: A 52 ARG cc_start: 0.7392 (mtm180) cc_final: 0.6631 (mpt-90) REVERT: A 173 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.5431 (ttm-80) REVERT: A 270 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: B 53 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: B 173 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5402 (ttm-80) REVERT: B 270 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8433 (mm-30) REVERT: C 53 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: C 173 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5431 (ttm-80) REVERT: C 270 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8433 (mm-30) REVERT: D 53 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: D 173 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.5403 (ttm-80) REVERT: D 270 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8434 (mm-30) REVERT: E 55 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6837 (mt) REVERT: E 131 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: E 173 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.5918 (ttm170) REVERT: E 281 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7208 (mtm-85) REVERT: E 414 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7450 (t70) REVERT: F 55 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6847 (mt) REVERT: F 131 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: F 173 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5919 (ttm170) REVERT: F 313 VAL cc_start: 0.5734 (OUTLIER) cc_final: 0.5278 (p) REVERT: F 414 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7449 (t70) REVERT: G 55 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6807 (mt) REVERT: G 131 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: G 173 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5919 (ttm170) REVERT: G 313 VAL cc_start: 0.5738 (OUTLIER) cc_final: 0.5283 (p) REVERT: G 414 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7505 (t70) REVERT: H 44 LEU cc_start: 0.8491 (mp) cc_final: 0.8157 (mm) REVERT: H 131 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: H 173 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.5891 (ttm170) REVERT: H 313 VAL cc_start: 0.5699 (OUTLIER) cc_final: 0.5246 (p) REVERT: H 414 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7449 (t70) outliers start: 85 outliers final: 53 residues processed: 377 average time/residue: 1.2987 time to fit residues: 567.1606 Evaluate side-chains 395 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 313 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 8.9990 chunk 296 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 310 optimal weight: 0.1980 chunk 286 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 151 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN D 404 ASN E 404 ASN G 53 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24848 Z= 0.125 Angle : 0.442 5.136 33720 Z= 0.234 Chirality : 0.043 0.219 3688 Planarity : 0.004 0.043 4488 Dihedral : 7.376 63.445 3760 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.24 % Allowed : 16.76 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.15), residues: 3136 helix: 1.61 (0.15), residues: 1208 sheet: 0.37 (0.26), residues: 432 loop : -0.83 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 289 HIS 0.005 0.000 HIS H 251 PHE 0.011 0.001 PHE H 294 TYR 0.007 0.001 TYR B 333 ARG 0.005 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 316 time to evaluate : 2.611 Fit side-chains REVERT: A 37 GLN cc_start: 0.6894 (mm110) cc_final: 0.6691 (OUTLIER) REVERT: A 52 ARG cc_start: 0.7421 (mtm180) cc_final: 0.6604 (mpt-90) REVERT: A 173 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.5388 (ttm-80) REVERT: A 313 VAL cc_start: 0.5999 (OUTLIER) cc_final: 0.5737 (p) REVERT: B 37 GLN cc_start: 0.6893 (mm110) cc_final: 0.6689 (OUTLIER) REVERT: B 173 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5133 (ttm-80) REVERT: C 173 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.5387 (ttm-80) REVERT: D 37 GLN cc_start: 0.6894 (mm110) cc_final: 0.6692 (OUTLIER) REVERT: D 173 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.5387 (ttm-80) REVERT: E 131 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: E 173 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.5774 (ttm170) REVERT: E 281 ARG cc_start: 0.7405 (mtp180) cc_final: 0.7190 (mtm-85) REVERT: E 327 GLN cc_start: 0.6777 (mp10) cc_final: 0.6471 (mm-40) REVERT: F 131 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: F 173 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.5777 (ttm170) REVERT: G 131 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: G 173 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.5776 (ttm170) REVERT: H 131 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: H 173 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.5218 (ttm-80) outliers start: 54 outliers final: 27 residues processed: 356 average time/residue: 1.4278 time to fit residues: 582.1769 Evaluate side-chains 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 26 GLN E 404 ASN F 26 GLN F 404 ASN G 26 GLN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104541 restraints weight = 23974.293| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.60 r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24848 Z= 0.429 Angle : 0.644 8.796 33720 Z= 0.347 Chirality : 0.051 0.226 3688 Planarity : 0.006 0.049 4488 Dihedral : 9.562 80.752 3752 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.44 % Allowed : 16.97 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.15), residues: 3136 helix: 0.90 (0.14), residues: 1264 sheet: 0.39 (0.25), residues: 472 loop : -1.05 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 289 HIS 0.008 0.001 HIS C 251 PHE 0.019 0.003 PHE G 294 TYR 0.017 0.003 TYR B 333 ARG 0.005 0.001 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9800.63 seconds wall clock time: 170 minutes 53.89 seconds (10253.89 seconds total)