Starting phenix.real_space_refine on Fri Aug 9 00:19:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/08_2024/8j85_36060.cif" } resolution = 2.7 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= 0.040 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 15288 2.51 5 N 4432 2.21 5 O 4560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 407": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24376 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 13.94, per 1000 atoms: 0.57 Number of scatterers: 24376 At special positions: 0 Unit cell: (145.35, 145.35, 104.55, 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 4560 8.00 N 4432 7.00 C 15288 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=2.01 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.01 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.01 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.01 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.01 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 4.4 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 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " 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 85 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " 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: 128 helices and 32 sheets defined 44.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP A 98 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.587A pdb=" N ALA A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.740A 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 305 removed outlier: 3.751A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.971A 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: 3.650A 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 94 through 100 removed outlier: 3.586A pdb=" N ASP B 98 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.585A pdb=" N ALA B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.741A 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 305 removed outlier: 3.763A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.529A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.887A 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: 3.646A 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 94 through 100 removed outlier: 3.587A pdb=" N ASP C 98 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 99 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.741A 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 305 removed outlier: 3.763A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 322 removed outlier: 4.548A pdb=" N LYS C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.887A 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: 3.650A 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 94 through 100 removed outlier: 3.586A pdb=" N ASP D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.584A pdb=" N ALA D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.741A 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 305 removed outlier: 3.763A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 322 removed outlier: 4.535A pdb=" N LYS D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 354 through 364 removed outlier: 3.888A 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: 3.648A 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 94 through 100 removed outlier: 3.588A pdb=" N ASP E 98 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.588A pdb=" N ALA E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.740A 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 305 removed outlier: 3.751A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 354 through 364 removed outlier: 3.972A 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 removed outlier: 3.650A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP F 98 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.585A pdb=" N ALA F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.742A 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 305 removed outlier: 3.763A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.529A pdb=" N THR F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 364 removed outlier: 3.887A 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 removed outlier: 3.647A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP G 98 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 100 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.741A 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 305 removed outlier: 3.762A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 322 removed outlier: 4.549A pdb=" N LYS G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 Processing helix chain 'G' and resid 354 through 364 removed outlier: 3.887A 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 removed outlier: 3.650A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 94 through 100 removed outlier: 3.586A pdb=" N ASP H 98 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.163A 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 205 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.741A 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 305 removed outlier: 3.763A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 322 removed outlier: 4.536A pdb=" N LYS H 317 " --> pdb=" O VAL H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 Processing helix chain 'H' and resid 354 through 364 removed outlier: 3.887A 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 removed outlier: 3.649A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) 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: 3.577A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.577A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.721A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.378A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.877A 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: 6.554A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.581A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.652A 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: 3.581A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 13.343A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.380A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.882A 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: 6.555A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 6.651A 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: 3.582A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 13.331A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.784A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.707A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.379A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.554A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.582A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.708A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.379A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.878A 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: 6.555A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.577A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.577A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.720A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.377A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.877A 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: 6.553A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 6.653A 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: 3.582A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.343A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.684A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.379A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.882A 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: 6.554A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 6.651A 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: 3.582A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY G 28 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP G 72 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N LEU G 30 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL G 74 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N ASP G 32 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N LEU G 76 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.379A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.878A 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: 6.553A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.652A 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: 3.582A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.733A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.720A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.379A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.876A 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: 6.554A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 10.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4176 1.31 - 1.44: 6600 1.44 - 1.56: 13960 1.56 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 24872 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 24867 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 832 107.13 - 113.85: 13596 113.85 - 120.57: 10111 120.57 - 127.29: 8956 127.29 - 134.01: 257 Bond angle restraints: 33752 Sorted by residual: angle pdb=" N VAL E 132 " pdb=" CA VAL E 132 " pdb=" C VAL E 132 " ideal model delta sigma weight residual 113.53 105.76 7.77 9.80e-01 1.04e+00 6.29e+01 angle pdb=" N VAL A 132 " pdb=" CA VAL A 132 " pdb=" C VAL A 132 " ideal model delta sigma weight residual 113.53 105.81 7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" N VAL B 132 " pdb=" CA VAL B 132 " pdb=" C VAL B 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL F 132 " pdb=" CA VAL F 132 " pdb=" C VAL F 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 113.53 106.16 7.37 9.80e-01 1.04e+00 5.65e+01 ... (remaining 33747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12714 17.95 - 35.90: 1513 35.90 - 53.84: 418 53.84 - 71.79: 117 71.79 - 89.74: 54 Dihedral angle restraints: 14816 sinusoidal: 5856 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY H 346 " pdb=" C GLY H 346 " pdb=" N VAL H 347 " pdb=" CA VAL H 347 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLY C 346 " pdb=" C GLY C 346 " pdb=" N VAL C 347 " pdb=" CA VAL C 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3058 0.066 - 0.132: 535 0.132 - 0.198: 77 0.198 - 0.264: 10 0.264 - 0.330: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U F 503 " pdb=" N 97U F 503 " pdb=" C 97U F 503 " pdb=" CB 97U F 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA 97U A 503 " pdb=" N 97U A 503 " pdb=" C 97U A 503 " pdb=" CB 97U A 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA 97U B 503 " pdb=" N 97U B 503 " pdb=" C 97U B 503 " pdb=" CB 97U B 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 3685 not shown) Planarity restraints: 4496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 73 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C LYS E 73 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS E 73 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 73 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LYS G 73 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL G 74 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 73 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LYS H 73 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS H 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL H 74 " -0.013 2.00e-02 2.50e+03 ... (remaining 4493 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 24 2.35 - 2.99: 12002 2.99 - 3.62: 33794 3.62 - 4.26: 57610 4.26 - 4.90: 99220 Nonbonded interactions: 202650 Sorted by model distance: nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.711 2.230 nonbonded pdb="ZN ZN F 502 " pdb=" OAX 97U F 503 " model vdw 1.712 2.230 nonbonded pdb="ZN ZN D 502 " pdb=" OAX 97U D 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN H 502 " pdb=" OAX 97U H 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.743 2.230 ... (remaining 202645 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 69.410 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.110 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:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.006 0.119 24872 Z= 0.416 Angle : 0.749 10.908 33752 Z= 0.447 Chirality : 0.054 0.330 3688 Planarity : 0.005 0.040 4496 Dihedral : 17.827 89.739 9112 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 18.87 % Favored : 79.80 % 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: -0.55 (0.14), residues: 3136 helix: 0.69 (0.15), residues: 1208 sheet: 0.51 (0.26), residues: 400 loop : -1.51 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.007 0.001 HIS H 251 PHE 0.011 0.001 PHE F 299 TYR 0.009 0.001 TYR E 333 ARG 0.002 0.000 ARG G 199 *********************** 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 499 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 467 time to evaluate : 2.742 Fit side-chains REVERT: A 23 VAL cc_start: 0.7512 (t) cc_final: 0.7286 (p) REVERT: A 76 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 315 ARG cc_start: 0.7221 (ttt90) cc_final: 0.6972 (mtp-110) REVERT: B 76 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7027 (tt) REVERT: B 315 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6992 (mtp-110) REVERT: C 315 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6988 (mtp-110) REVERT: D 23 VAL cc_start: 0.7542 (t) cc_final: 0.7298 (p) REVERT: D 76 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 315 ARG cc_start: 0.7278 (ttt90) cc_final: 0.7017 (mtp-110) REVERT: E 23 VAL cc_start: 0.7401 (t) cc_final: 0.6840 (p) REVERT: E 93 GLN cc_start: 0.7613 (mp10) cc_final: 0.7241 (mm-40) REVERT: E 281 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7213 (ttm110) REVERT: E 385 ASP cc_start: 0.7465 (p0) cc_final: 0.7129 (p0) REVERT: E 397 ASP cc_start: 0.7632 (m-30) cc_final: 0.7389 (m-30) REVERT: F 23 VAL cc_start: 0.7642 (t) cc_final: 0.7063 (p) REVERT: F 93 GLN cc_start: 0.7566 (mp10) cc_final: 0.7214 (mm-40) REVERT: F 385 ASP cc_start: 0.7481 (p0) cc_final: 0.7180 (p0) REVERT: F 397 ASP cc_start: 0.7617 (m-30) cc_final: 0.7370 (m-30) REVERT: G 23 VAL cc_start: 0.7427 (t) cc_final: 0.6918 (p) REVERT: G 93 GLN cc_start: 0.7546 (mp10) cc_final: 0.7198 (mm-40) REVERT: G 275 MET cc_start: 0.9094 (ttm) cc_final: 0.8882 (ttp) REVERT: G 385 ASP cc_start: 0.7437 (p0) cc_final: 0.7127 (p0) REVERT: G 397 ASP cc_start: 0.7609 (m-30) cc_final: 0.7381 (m-30) REVERT: H 23 VAL cc_start: 0.7421 (t) cc_final: 0.6866 (p) REVERT: H 93 GLN cc_start: 0.7587 (mp10) cc_final: 0.7233 (mm-40) REVERT: H 385 ASP cc_start: 0.7475 (p0) cc_final: 0.7126 (p0) REVERT: H 397 ASP cc_start: 0.7616 (m-30) cc_final: 0.7381 (m-30) outliers start: 32 outliers final: 5 residues processed: 493 average time/residue: 1.8036 time to fit residues: 986.8270 Evaluate side-chains 249 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 353 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN F 163 HIS ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 HIS H 163 HIS ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 24872 Z= 0.179 Angle : 0.508 6.960 33752 Z= 0.266 Chirality : 0.045 0.229 3688 Planarity : 0.004 0.044 4496 Dihedral : 9.516 89.936 3767 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.90 % Allowed : 21.44 % Favored : 76.66 % 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: 0.02 (0.14), residues: 3136 helix: 1.26 (0.15), residues: 1224 sheet: 0.68 (0.25), residues: 400 loop : -1.26 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 79 HIS 0.007 0.001 HIS D 251 PHE 0.009 0.001 PHE F 294 TYR 0.009 0.001 TYR A 333 ARG 0.004 0.000 ARG C 355 *********************** 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 304 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 2.773 Fit side-chains REVERT: A 131 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6416 (pp20) REVERT: A 315 ARG cc_start: 0.7218 (ttt90) cc_final: 0.6899 (mtp-110) REVERT: B 172 GLU cc_start: 0.7527 (tp30) cc_final: 0.6913 (tm-30) REVERT: B 312 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7031 (tp30) REVERT: B 315 ARG cc_start: 0.7289 (ttt90) cc_final: 0.6941 (mtp-110) REVERT: C 31 PHE cc_start: 0.8298 (t80) cc_final: 0.7899 (t80) REVERT: C 315 ARG cc_start: 0.7244 (ttt90) cc_final: 0.6900 (mtp-110) REVERT: D 315 ARG cc_start: 0.7237 (ttt90) cc_final: 0.6884 (mtp-110) REVERT: E 93 GLN cc_start: 0.7514 (mp10) cc_final: 0.7126 (mm-40) REVERT: E 173 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6025 (ttm170) REVERT: E 338 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7202 (mtt180) REVERT: E 385 ASP cc_start: 0.7752 (p0) cc_final: 0.7510 (p0) REVERT: F 88 GLU cc_start: 0.7368 (pt0) cc_final: 0.7158 (pt0) REVERT: F 93 GLN cc_start: 0.7512 (mp10) cc_final: 0.7130 (mm-40) REVERT: F 173 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6143 (ttm170) REVERT: F 338 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7218 (mtt180) REVERT: F 385 ASP cc_start: 0.7757 (p0) cc_final: 0.7511 (p0) REVERT: G 93 GLN cc_start: 0.7537 (mp10) cc_final: 0.7148 (mm-40) REVERT: G 173 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6040 (ttm170) REVERT: G 275 MET cc_start: 0.9026 (ttm) cc_final: 0.8821 (ttp) REVERT: G 338 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7212 (mtt180) REVERT: G 385 ASP cc_start: 0.7745 (p0) cc_final: 0.7501 (p0) REVERT: H 93 GLN cc_start: 0.7497 (mp10) cc_final: 0.7123 (mm-40) REVERT: H 173 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6161 (ttm170) REVERT: H 338 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: H 385 ASP cc_start: 0.7739 (p0) cc_final: 0.7478 (p0) outliers start: 46 outliers final: 18 residues processed: 290 average time/residue: 1.4904 time to fit residues: 491.5958 Evaluate side-chains 244 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24872 Z= 0.323 Angle : 0.597 8.795 33752 Z= 0.314 Chirality : 0.049 0.228 3688 Planarity : 0.005 0.052 4496 Dihedral : 8.989 88.223 3758 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.06 % Allowed : 20.03 % Favored : 75.91 % 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: -0.12 (0.14), residues: 3136 helix: 1.02 (0.15), residues: 1232 sheet: 0.55 (0.25), residues: 400 loop : -1.20 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 79 HIS 0.006 0.002 HIS D 251 PHE 0.011 0.002 PHE G 294 TYR 0.014 0.002 TYR A 95 ARG 0.004 0.001 ARG C 355 *********************** 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 322 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 224 time to evaluate : 2.702 Fit side-chains REVERT: A 53 GLN cc_start: 0.7650 (mt0) cc_final: 0.7168 (tp40) REVERT: A 131 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6460 (pp20) REVERT: A 172 GLU cc_start: 0.7157 (tt0) cc_final: 0.6821 (tm-30) REVERT: A 259 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7702 (ttmp) REVERT: A 315 ARG cc_start: 0.7316 (ttt90) cc_final: 0.6931 (mtp-110) REVERT: B 53 GLN cc_start: 0.7624 (mt0) cc_final: 0.7097 (mm110) REVERT: B 131 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6616 (pp20) REVERT: B 172 GLU cc_start: 0.7425 (tp30) cc_final: 0.6828 (tm-30) REVERT: B 259 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7689 (ttmp) REVERT: B 312 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7230 (tp30) REVERT: B 315 ARG cc_start: 0.7304 (ttt90) cc_final: 0.6973 (mtp-110) REVERT: C 53 GLN cc_start: 0.7639 (mt0) cc_final: 0.7152 (tp40) REVERT: C 131 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6584 (pp20) REVERT: C 172 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: C 259 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7726 (ttmp) REVERT: C 315 ARG cc_start: 0.7313 (ttt90) cc_final: 0.6931 (mtp-110) REVERT: D 53 GLN cc_start: 0.7674 (mt0) cc_final: 0.7143 (tp40) REVERT: D 131 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: D 259 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7706 (ttmp) REVERT: D 315 ARG cc_start: 0.7331 (ttt90) cc_final: 0.6928 (mtp-110) REVERT: E 173 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6001 (ttm170) REVERT: E 338 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7017 (mtt180) REVERT: F 173 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5997 (ttm170) REVERT: F 338 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6985 (mtt180) REVERT: G 173 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6004 (ttm170) REVERT: G 338 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: G 385 ASP cc_start: 0.8090 (p0) cc_final: 0.7874 (p0) REVERT: H 173 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6044 (ttm170) REVERT: H 338 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6982 (mtt180) REVERT: H 385 ASP cc_start: 0.8080 (p0) cc_final: 0.7860 (p0) outliers start: 98 outliers final: 37 residues processed: 302 average time/residue: 1.6777 time to fit residues: 569.1307 Evaluate side-chains 272 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 218 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 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 E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 172 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 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 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 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 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 Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.277 > 50: distance: 49 - 78: 28.331 distance: 66 - 70: 22.899 distance: 70 - 71: 40.317 distance: 71 - 72: 66.277 distance: 71 - 74: 42.611 distance: 72 - 73: 42.217 distance: 72 - 78: 59.027 distance: 74 - 75: 12.179 distance: 74 - 76: 19.712 distance: 75 - 77: 20.714 distance: 78 - 79: 33.757 distance: 79 - 80: 12.018 distance: 79 - 82: 25.466 distance: 80 - 81: 18.059 distance: 80 - 89: 12.870 distance: 82 - 83: 16.082 distance: 83 - 84: 10.005 distance: 89 - 90: 13.441 distance: 90 - 91: 41.764 distance: 90 - 93: 15.869 distance: 91 - 92: 31.801 distance: 91 - 98: 49.337 distance: 93 - 94: 20.376 distance: 95 - 96: 6.887 distance: 95 - 97: 5.059 distance: 98 - 99: 31.115 distance: 99 - 100: 28.497 distance: 99 - 102: 25.392 distance: 100 - 101: 23.218 distance: 100 - 105: 28.144 distance: 102 - 103: 20.273 distance: 102 - 104: 24.051 distance: 105 - 106: 26.168 distance: 106 - 107: 49.533 distance: 106 - 109: 56.902 distance: 107 - 108: 26.793 distance: 107 - 113: 41.111 distance: 109 - 110: 57.967 distance: 110 - 111: 28.809 distance: 110 - 112: 24.239 distance: 113 - 114: 34.921 distance: 113 - 119: 19.790 distance: 114 - 115: 21.686 distance: 114 - 117: 21.302 distance: 115 - 116: 22.418 distance: 115 - 120: 16.725 distance: 117 - 118: 11.403 distance: 118 - 119: 9.432 distance: 120 - 121: 14.002 distance: 121 - 122: 14.305 distance: 122 - 123: 8.985 distance: 126 - 129: 3.211 distance: 129 - 130: 3.998 distance: 130 - 133: 5.342 distance: 131 - 132: 7.898 distance: 131 - 140: 8.105 distance: 133 - 134: 5.749 distance: 134 - 135: 4.753 distance: 140 - 141: 3.941 distance: 141 - 142: 8.832 distance: 141 - 144: 7.285 distance: 142 - 143: 4.978 distance: 142 - 147: 6.575 distance: 144 - 145: 3.163 distance: 144 - 146: 5.160