Starting phenix.real_space_refine on Sat Dec 28 07:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.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/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.map" model { file = "/net/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7taw_25788/12_2024/7taw_25788.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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 158 5.49 5 S 58 5.16 5 C 31800 2.51 5 N 9349 2.21 5 O 10034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51399 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "b" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "c" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "d" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "e" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "f" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "g" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "h" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "i" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "m" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 22.53, per 1000 atoms: 0.44 Number of scatterers: 51399 At special positions: 0 Unit cell: (159.154, 162.316, 239.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 158 15.00 O 10034 8.00 N 9349 7.00 C 31800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.09 Conformation dependent library (CDL) restraints added in 5.0 seconds 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11608 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 99 sheets defined 34.6% alpha, 19.6% beta 21 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 13.87 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.517A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.508A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.743A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.807A pdb=" N TRP A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 4.018A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.551A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.021A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.176A pdb=" N THR A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 385 through 398 removed outlier: 3.935A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.904A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.800A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.639A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.587A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.773A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.950A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.547A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 58 removed outlier: 5.265A pdb=" N GLN E 56 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.548A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.555A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN F 56 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.673A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.628A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 332 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 172 removed outlier: 6.502A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.518A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.515A pdb=" N ASP K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 199 Processing helix chain 'K' and resid 211 through 222 Processing helix chain 'a' and resid 9 through 33 removed outlier: 3.628A pdb=" N LEU a 13 " --> pdb=" O THR a 9 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN a 22 " --> pdb=" O GLU a 18 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG a 24 " --> pdb=" O PHE a 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU a 25 " --> pdb=" O ILE a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 44 Processing helix chain 'a' and resid 49 through 63 removed outlier: 4.091A pdb=" N LEU a 53 " --> pdb=" O ARG a 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG a 58 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY a 61 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN a 62 " --> pdb=" O ARG a 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 121 removed outlier: 3.844A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 136 removed outlier: 3.938A pdb=" N TRP a 133 " --> pdb=" O ASN a 129 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU a 134 " --> pdb=" O LEU a 130 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU a 136 " --> pdb=" O ASN a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 161 Processing helix chain 'a' and resid 196 through 211 removed outlier: 3.604A pdb=" N GLU a 208 " --> pdb=" O ALA a 204 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA a 209 " --> pdb=" O LEU a 205 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 224 Processing helix chain 'a' and resid 247 through 251 removed outlier: 3.523A pdb=" N ASN a 250 " --> pdb=" O LYS a 247 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 258 removed outlier: 3.773A pdb=" N GLU a 257 " --> pdb=" O GLN a 253 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG a 258 " --> pdb=" O LEU a 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 253 through 258' Processing helix chain 'a' and resid 269 through 274 removed outlier: 4.173A pdb=" N GLN a 273 " --> pdb=" O PRO a 270 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG a 274 " --> pdb=" O ASN a 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 309 removed outlier: 3.502A pdb=" N LEU a 300 " --> pdb=" O GLU a 296 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG a 302 " --> pdb=" O SER a 298 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR a 303 " --> pdb=" O ARG a 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU a 304 " --> pdb=" O LEU a 300 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA a 309 " --> pdb=" O GLN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 340 removed outlier: 3.887A pdb=" N GLN a 320 " --> pdb=" O LEU a 316 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG a 321 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE a 329 " --> pdb=" O LEU a 325 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS a 330 " --> pdb=" O VAL a 326 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP a 331 " --> pdb=" O ALA a 327 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU a 332 " --> pdb=" O GLN a 328 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 359 through 364 removed outlier: 3.582A pdb=" N ASP a 364 " --> pdb=" O GLN a 360 " (cutoff:3.500A) Processing helix chain 'a' and resid 366 through 371 removed outlier: 4.054A pdb=" N THR a 370 " --> pdb=" O LEU a 366 " (cutoff:3.500A) Processing helix chain 'a' and resid 375 through 383 Processing helix chain 'a' and resid 386 through 397 removed outlier: 3.696A pdb=" N ARG a 397 " --> pdb=" O ASN a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 402 through 408 Processing helix chain 'a' and resid 409 through 431 removed outlier: 3.666A pdb=" N GLN a 413 " --> pdb=" O PRO a 409 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET a 424 " --> pdb=" O LYS a 420 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU a 429 " --> pdb=" O PHE a 425 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU a 430 " --> pdb=" O LYS a 426 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP a 431 " --> pdb=" O GLU a 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 48 removed outlier: 3.801A pdb=" N PHE b 37 " --> pdb=" O SER b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 121 removed outlier: 3.656A pdb=" N ASP b 120 " --> pdb=" O ASP b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 135 removed outlier: 3.524A pdb=" N GLN b 131 " --> pdb=" O ALA b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 180 removed outlier: 3.715A pdb=" N ARG b 179 " --> pdb=" O ARG b 175 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU b 180 " --> pdb=" O LEU b 176 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 204 Processing helix chain 'b' and resid 208 through 216 removed outlier: 3.509A pdb=" N ALA b 212 " --> pdb=" O THR b 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 302 Processing helix chain 'c' and resid 16 through 36 removed outlier: 3.519A pdb=" N GLN c 30 " --> pdb=" O GLY c 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL c 33 " --> pdb=" O HIS c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 73 Processing helix chain 'c' and resid 74 through 77 Processing helix chain 'c' and resid 108 through 121 removed outlier: 3.696A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG c 118 " --> pdb=" O ARG c 114 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG c 119 " --> pdb=" O ARG c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 131 Processing helix chain 'c' and resid 132 through 136 removed outlier: 3.808A pdb=" N VAL c 135 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA c 136 " --> pdb=" O ASP c 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 132 through 136' Processing helix chain 'd' and resid 130 through 148 Processing helix chain 'd' and resid 150 through 163 Processing helix chain 'd' and resid 208 through 224 removed outlier: 3.769A pdb=" N LEU d 214 " --> pdb=" O GLU d 210 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA d 215 " --> pdb=" O LEU d 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU d 216 " --> pdb=" O ASP d 212 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU d 217 " --> pdb=" O ALA d 213 " (cutoff:3.500A) Processing helix chain 'd' and resid 275 through 284 removed outlier: 3.947A pdb=" N ALA d 282 " --> pdb=" O LYS d 278 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 306 removed outlier: 3.825A pdb=" N SER d 306 " --> pdb=" O PRO d 303 " (cutoff:3.500A) Processing helix chain 'd' and resid 322 through 332 Processing helix chain 'd' and resid 338 through 352 removed outlier: 4.120A pdb=" N TYR d 344 " --> pdb=" O GLU d 340 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL d 345 " --> pdb=" O GLN d 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE d 346 " --> pdb=" O GLN d 342 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA d 347 " --> pdb=" O HIS d 343 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG d 351 " --> pdb=" O ALA d 347 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 55 removed outlier: 3.552A pdb=" N SER e 55 " --> pdb=" O ARG e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 90 removed outlier: 3.796A pdb=" N ALA e 88 " --> pdb=" O ALA e 84 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE e 90 " --> pdb=" O LEU e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 148 Processing helix chain 'e' and resid 151 through 163 Processing helix chain 'e' and resid 208 through 223 Processing helix chain 'e' and resid 275 through 284 Processing helix chain 'e' and resid 322 through 332 removed outlier: 3.526A pdb=" N LEU e 326 " --> pdb=" O ASP e 322 " (cutoff:3.500A) Processing helix chain 'e' and resid 341 through 352 removed outlier: 3.630A pdb=" N ILE e 346 " --> pdb=" O GLN e 342 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 58 removed outlier: 3.846A pdb=" N SER f 55 " --> pdb=" O ARG f 52 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN f 56 " --> pdb=" O ASP f 53 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU f 57 " --> pdb=" O ALA f 54 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP f 58 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 92 Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 150 through 163 Processing helix chain 'f' and resid 208 through 224 removed outlier: 3.534A pdb=" N GLU f 216 " --> pdb=" O ASP f 212 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU f 217 " --> pdb=" O ALA f 213 " (cutoff:3.500A) Processing helix chain 'f' and resid 275 through 284 removed outlier: 3.591A pdb=" N ALA f 282 " --> pdb=" O LYS f 278 " (cutoff:3.500A) Processing helix chain 'f' and resid 302 through 304 No H-bonds generated for 'chain 'f' and resid 302 through 304' Processing helix chain 'f' and resid 316 through 320 Processing helix chain 'f' and resid 322 through 332 removed outlier: 3.503A pdb=" N LEU f 326 " --> pdb=" O ASP f 322 " (cutoff:3.500A) Processing helix chain 'f' and resid 338 through 352 Processing helix chain 'g' and resid 82 through 92 removed outlier: 4.284A pdb=" N LEU g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 151 through 163 removed outlier: 3.535A pdb=" N ASN g 160 " --> pdb=" O ARG g 156 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU g 161 " --> pdb=" O TYR g 157 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 223 removed outlier: 3.713A pdb=" N GLU g 216 " --> pdb=" O ASP g 212 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU g 217 " --> pdb=" O ALA g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 275 through 284 Processing helix chain 'g' and resid 302 through 306 removed outlier: 4.126A pdb=" N SER g 306 " --> pdb=" O PRO g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 322 through 330 removed outlier: 3.584A pdb=" N LEU g 326 " --> pdb=" O ASP g 322 " (cutoff:3.500A) Processing helix chain 'g' and resid 338 through 351 removed outlier: 3.513A pdb=" N TYR g 344 " --> pdb=" O GLU g 340 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG g 351 " --> pdb=" O ALA g 347 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 92 removed outlier: 3.720A pdb=" N SER h 92 " --> pdb=" O ALA h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 148 Processing helix chain 'h' and resid 151 through 163 removed outlier: 3.610A pdb=" N ASN h 160 " --> pdb=" O ARG h 156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU h 161 " --> pdb=" O TYR h 157 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 223 Processing helix chain 'h' and resid 275 through 284 Processing helix chain 'h' and resid 302 through 306 removed outlier: 4.387A pdb=" N SER h 306 " --> pdb=" O PRO h 303 " (cutoff:3.500A) Processing helix chain 'h' and resid 322 through 332 removed outlier: 4.518A pdb=" N ASP h 328 " --> pdb=" O TYR h 324 " (cutoff:3.500A) Processing helix chain 'h' and resid 338 through 352 removed outlier: 3.839A pdb=" N HIS h 343 " --> pdb=" O VAL h 339 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR h 344 " --> pdb=" O GLU h 340 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA h 347 " --> pdb=" O HIS h 343 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN h 348 " --> pdb=" O TYR h 344 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU h 349 " --> pdb=" O VAL h 345 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE h 350 " --> pdb=" O ILE h 346 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 92 removed outlier: 3.743A pdb=" N ILE i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER i 92 " --> pdb=" O ALA i 88 " (cutoff:3.500A) Processing helix chain 'i' and resid 130 through 148 Processing helix chain 'i' and resid 150 through 163 Processing helix chain 'i' and resid 167 through 174 removed outlier: 3.634A pdb=" N GLY i 173 " --> pdb=" O ASN i 170 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA i 174 " --> pdb=" O ARG i 171 " (cutoff:3.500A) Processing helix chain 'i' and resid 208 through 224 removed outlier: 3.810A pdb=" N LEU i 214 " --> pdb=" O GLU i 210 " (cutoff:3.500A) Processing helix chain 'i' and resid 275 through 284 removed outlier: 3.968A pdb=" N ALA i 282 " --> pdb=" O LYS i 278 " (cutoff:3.500A) Processing helix chain 'i' and resid 302 through 306 removed outlier: 3.872A pdb=" N SER i 306 " --> pdb=" O PRO i 303 " (cutoff:3.500A) Processing helix chain 'i' and resid 322 through 332 removed outlier: 3.622A pdb=" N ASP i 328 " --> pdb=" O TYR i 324 " (cutoff:3.500A) Processing helix chain 'i' and resid 338 through 352 removed outlier: 3.545A pdb=" N HIS i 343 " --> pdb=" O VAL i 339 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR i 344 " --> pdb=" O GLU i 340 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE i 346 " --> pdb=" O GLN i 342 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU i 349 " --> pdb=" O VAL i 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.423A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.351A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.541A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.728A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 61 removed outlier: 3.851A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.898A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 33 removed outlier: 3.838A pdb=" N PHE D 355 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.969A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.764A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.804A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.185A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA E 176 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL E 177 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP E 196 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 63 through 70 removed outlier: 3.627A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC8, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.723A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.530A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 176 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.519A pdb=" N GLN F 96 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.694A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.210A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.584A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE3, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.692A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 196 removed outlier: 5.000A pdb=" N VAL H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG H 185 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.763A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 262 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR H 97 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR H 264 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 99 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE8, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.754A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.511A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.281A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.963A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.560A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 38 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR J 32 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF6, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.699A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 85 through 90 removed outlier: 5.232A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.256A pdb=" N HIS K 26 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR K 41 " --> pdb=" O HIS K 26 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP K 28 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE K 39 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K 30 " --> pdb=" O MET K 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 19 through 20 removed outlier: 6.192A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR i 97 " --> pdb=" O HIS K 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN i 94 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 85 through 91 Processing sheet with id=AG2, first strand: chain 'K' and resid 99 through 100 Processing sheet with id=AG3, first strand: chain 'a' and resid 64 through 66 Processing sheet with id=AG4, first strand: chain 'a' and resid 68 through 69 Processing sheet with id=AG5, first strand: chain 'a' and resid 180 through 181 Processing sheet with id=AG6, first strand: chain 'a' and resid 191 through 192 removed outlier: 6.377A pdb=" N ALA a 191 " --> pdb=" O VAL b 280 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN b 282 " --> pdb=" O ALA a 191 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 191 through 192 removed outlier: 6.377A pdb=" N ALA a 191 " --> pdb=" O VAL b 280 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASN b 282 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE b 279 " --> pdb=" O ALA b 257 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA b 257 " --> pdb=" O PHE b 279 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU b 281 " --> pdb=" O TYR b 255 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR b 255 " --> pdb=" O GLU b 281 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU b 283 " --> pdb=" O ALA b 253 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA b 253 " --> pdb=" O TRP b 316 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 239 through 240 removed outlier: 3.665A pdb=" N PHE b 81 " --> pdb=" O ILE a 240 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'a' and resid 265 through 267 removed outlier: 6.307A pdb=" N LEU a 265 " --> pdb=" O TRP b 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'b' and resid 55 through 61 removed outlier: 3.866A pdb=" N GLY b 112 " --> pdb=" O ASP b 57 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL b 59 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU b 110 " --> pdb=" O VAL b 59 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 65 through 68 removed outlier: 4.616A pdb=" N LEU b 105 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN b 18 " --> pdb=" O LEU b 105 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL b 107 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER b 16 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER b 16 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 221 through 222 removed outlier: 3.717A pdb=" N GLU b 222 " --> pdb=" O GLN b 240 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN b 240 " --> pdb=" O GLU b 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'c' and resid 41 through 43 removed outlier: 4.033A pdb=" N ARG c 8 " --> pdb=" O GLN c 84 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN c 84 " --> pdb=" O ARG c 8 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 41 through 43 Processing sheet with id=AH6, first strand: chain 'c' and resid 143 through 146 removed outlier: 3.615A pdb=" N PHE c 155 " --> pdb=" O LEU c 146 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN c 99 " --> pdb=" O GLY c 162 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU c 164 " --> pdb=" O TYR c 97 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR c 97 " --> pdb=" O LEU c 164 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 31 through 32 removed outlier: 3.580A pdb=" N ALA d 127 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 42 through 43 Processing sheet with id=AH9, first strand: chain 'd' and resid 46 through 47 Processing sheet with id=AI1, first strand: chain 'd' and resid 64 through 66 removed outlier: 3.604A pdb=" N LYS d 66 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA d 101 " --> pdb=" O VAL d 244 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 113 through 118 removed outlier: 3.763A pdb=" N VAL d 228 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU d 229 " --> pdb=" O ILE d 184 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL d 177 " --> pdb=" O ASP d 196 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP d 196 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL d 179 " --> pdb=" O ARG d 194 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG d 194 " --> pdb=" O VAL d 179 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE d 181 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA d 192 " --> pdb=" O ILE d 181 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS d 183 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 248 through 249 removed outlier: 3.627A pdb=" N THR d 264 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 285 through 287 Processing sheet with id=AI5, first strand: chain 'e' and resid 42 through 43 Processing sheet with id=AI6, first strand: chain 'e' and resid 45 through 47 removed outlier: 4.320A pdb=" N VAL e 228 " --> pdb=" O VAL e 118 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'e' and resid 63 through 70 removed outlier: 3.935A pdb=" N ASN e 94 " --> pdb=" O GLY e 70 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA e 101 " --> pdb=" O VAL e 244 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'e' and resid 285 through 287 Processing sheet with id=AI9, first strand: chain 'f' and resid 31 through 32 Processing sheet with id=AJ1, first strand: chain 'f' and resid 38 through 39 removed outlier: 3.642A pdb=" N VAL f 118 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL f 228 " --> pdb=" O VAL f 118 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU f 229 " --> pdb=" O ILE f 184 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL f 177 " --> pdb=" O ASP f 196 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP f 196 " --> pdb=" O VAL f 177 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL f 179 " --> pdb=" O ARG f 194 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG f 194 " --> pdb=" O VAL f 179 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE f 181 " --> pdb=" O ALA f 192 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA f 192 " --> pdb=" O ILE f 181 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS f 183 " --> pdb=" O ALA f 190 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'f' and resid 38 through 39 Processing sheet with id=AJ3, first strand: chain 'f' and resid 64 through 70 removed outlier: 3.967A pdb=" N GLY f 70 " --> pdb=" O ASN f 94 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN f 94 " --> pdb=" O GLY f 70 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'f' and resid 285 through 287 Processing sheet with id=AJ5, first strand: chain 'f' and resid 306 through 307 removed outlier: 3.615A pdb=" N LYS f 312 " --> pdb=" O VAL f 307 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'g' and resid 31 through 33 removed outlier: 3.619A pdb=" N GLY g 353 " --> pdb=" O PHE g 33 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'g' and resid 38 through 39 removed outlier: 4.124A pdb=" N VAL g 228 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU g 229 " --> pdb=" O ILE g 184 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL g 177 " --> pdb=" O ASP g 196 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP g 196 " --> pdb=" O VAL g 177 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL g 179 " --> pdb=" O ARG g 194 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG g 194 " --> pdb=" O VAL g 179 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE g 181 " --> pdb=" O ALA g 192 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA g 192 " --> pdb=" O ILE g 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS g 183 " --> pdb=" O ALA g 190 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'g' and resid 38 through 39 Processing sheet with id=AJ9, first strand: chain 'g' and resid 63 through 70 removed outlier: 4.384A pdb=" N ALA g 101 " --> pdb=" O VAL g 244 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'g' and resid 285 through 287 Processing sheet with id=AK2, first strand: chain 'h' and resid 127 through 128 removed outlier: 3.605A pdb=" N ALA h 127 " --> pdb=" O ALA h 32 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE h 355 " --> pdb=" O LEU h 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY h 353 " --> pdb=" O PHE h 33 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'h' and resid 188 through 196 removed outlier: 4.958A pdb=" N VAL h 189 " --> pdb=" O ARG h 185 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG h 185 " --> pdb=" O VAL h 189 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG h 191 " --> pdb=" O HIS h 183 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU h 229 " --> pdb=" O ILE h 184 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL h 228 " --> pdb=" O VAL h 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA h 236 " --> pdb=" O LEU h 110 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.642A pdb=" N ARG h 64 " --> pdb=" O VAL h 100 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL h 100 " --> pdb=" O ARG h 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA h 101 " --> pdb=" O VAL h 244 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.642A pdb=" N ARG h 64 " --> pdb=" O VAL h 100 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL h 100 " --> pdb=" O ARG h 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS h 261 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR h 97 " --> pdb=" O LYS h 261 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS h 263 " --> pdb=" O THR h 97 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'h' and resid 285 through 287 Processing sheet with id=AK7, first strand: chain 'i' and resid 125 through 127 removed outlier: 6.599A pdb=" N ALA i 32 " --> pdb=" O SER i 126 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY i 353 " --> pdb=" O PHE i 33 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'i' and resid 189 through 196 removed outlier: 6.442A pdb=" N HIS i 183 " --> pdb=" O ALA i 190 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA i 192 " --> pdb=" O ILE i 181 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE i 181 " --> pdb=" O ALA i 192 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG i 194 " --> pdb=" O VAL i 179 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL i 179 " --> pdb=" O ARG i 194 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP i 196 " --> pdb=" O VAL i 177 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL i 177 " --> pdb=" O ASP i 196 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU i 229 " --> pdb=" O ILE i 184 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'i' and resid 285 through 287 2022 hydrogen bonds defined for protein. 5538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 20.58 Time building geometry restraints manager: 10.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 8356 1.30 - 1.43: 14459 1.43 - 1.56: 29571 1.56 - 1.68: 316 1.68 - 1.81: 90 Bond restraints: 52792 Sorted by residual: bond pdb=" CA ALA G 271 " pdb=" C ALA G 271 " ideal model delta sigma weight residual 1.521 1.456 0.065 1.19e-02 7.06e+03 3.02e+01 bond pdb=" C HIS G 159 " pdb=" O HIS G 159 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.61e+01 bond pdb=" CA HIS G 159 " pdb=" C HIS G 159 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.61e+01 bond pdb=" C ALA G 158 " pdb=" O ALA G 158 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.25e-02 6.40e+03 1.50e+01 bond pdb=" CA ARG G 269 " pdb=" C ARG G 269 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.44e-02 4.82e+03 1.48e+01 ... (remaining 52787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 71392 2.33 - 4.67: 937 4.67 - 7.00: 111 7.00 - 9.34: 18 9.34 - 11.67: 5 Bond angle restraints: 72463 Sorted by residual: angle pdb=" N LEU G 161 " pdb=" CA LEU G 161 " pdb=" C LEU G 161 " ideal model delta sigma weight residual 114.04 102.37 11.67 1.24e+00 6.50e-01 8.86e+01 angle pdb=" N ARG b 218 " pdb=" CA ARG b 218 " pdb=" C ARG b 218 " ideal model delta sigma weight residual 110.14 120.01 -9.87 1.55e+00 4.16e-01 4.05e+01 angle pdb=" O SER G 267 " pdb=" C SER G 267 " pdb=" N VAL G 268 " ideal model delta sigma weight residual 123.33 130.38 -7.05 1.21e+00 6.83e-01 3.40e+01 angle pdb=" C LEU G 161 " pdb=" N ALA G 162 " pdb=" CA ALA G 162 " ideal model delta sigma weight residual 120.68 111.68 9.00 1.70e+00 3.46e-01 2.80e+01 angle pdb=" N ILE D 286 " pdb=" CA ILE D 286 " pdb=" C ILE D 286 " ideal model delta sigma weight residual 113.20 108.25 4.95 9.60e-01 1.09e+00 2.66e+01 ... (remaining 72458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 30819 35.91 - 71.82: 809 71.82 - 107.72: 86 107.72 - 143.63: 3 143.63 - 179.54: 9 Dihedral angle restraints: 31726 sinusoidal: 13750 harmonic: 17976 Sorted by residual: dihedral pdb=" O4' U m 33 " pdb=" C1' U m 33 " pdb=" N1 U m 33 " pdb=" C2 U m 33 " ideal model delta sinusoidal sigma weight residual 200.00 46.76 153.24 1 1.50e+01 4.44e-03 8.08e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 55.75 144.25 1 1.50e+01 4.44e-03 7.73e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 57.79 142.21 1 1.50e+01 4.44e-03 7.64e+01 ... (remaining 31723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7015 0.058 - 0.116: 1033 0.116 - 0.173: 106 0.173 - 0.231: 6 0.231 - 0.289: 4 Chirality restraints: 8164 Sorted by residual: chirality pdb=" CA ARG b 218 " pdb=" N ARG b 218 " pdb=" C ARG b 218 " pdb=" CB ARG b 218 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB THR b 318 " pdb=" CA THR b 318 " pdb=" OG1 THR b 318 " pdb=" CG2 THR b 318 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASP G 270 " pdb=" N ASP G 270 " pdb=" C ASP G 270 " pdb=" CB ASP G 270 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 8161 not shown) Planarity restraints: 8966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP a 228 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO a 229 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO a 229 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO a 229 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO A 72 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 267 " 0.013 2.00e-02 2.50e+03 2.96e-02 8.79e+00 pdb=" C SER G 267 " -0.051 2.00e-02 2.50e+03 pdb=" O SER G 267 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL G 268 " 0.017 2.00e-02 2.50e+03 ... (remaining 8963 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8592 2.77 - 3.30: 47910 3.30 - 3.83: 89776 3.83 - 4.37: 108250 4.37 - 4.90: 179087 Nonbonded interactions: 433615 Sorted by model distance: nonbonded pdb=" OH TYR d 290 " pdb=" O GLY d 297 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" OD2 ASP B 272 " model vdw 2.236 3.040 nonbonded pdb=" O VAL K 170 " pdb=" OG1 THR K 177 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG h 69 " pdb=" O2' U m 21 " model vdw 2.244 3.120 nonbonded pdb=" O VAL c 100 " pdb=" OG SER c 179 " model vdw 2.245 3.040 ... (remaining 433610 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 1 through 174 or resid 176 through 187)) selection = (chain 'c' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = chain 'd' selection = (chain 'e' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'f' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'g' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'h' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'i' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'm' } 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=0.37 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: 0.010 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.040 Extract box with map and model: 1.440 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 98.150 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 52792 Z= 0.193 Angle : 0.669 11.672 72463 Z= 0.363 Chirality : 0.042 0.289 8164 Planarity : 0.005 0.078 8966 Dihedral : 16.069 179.540 20118 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.48 % 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: -1.53 (0.10), residues: 6192 helix: -0.94 (0.10), residues: 2006 sheet: 0.76 (0.16), residues: 988 loop : -1.66 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP f 58 HIS 0.009 0.001 HIS K 25 PHE 0.024 0.001 PHE e 205 TYR 0.039 0.001 TYR G 304 ARG 0.009 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 889 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.7233 (m-30) cc_final: 0.6935 (m-30) REVERT: C 28 LEU cc_start: 0.5414 (pp) cc_final: 0.4866 (mm) REVERT: K 155 ASP cc_start: 0.6825 (t0) cc_final: 0.6442 (t0) REVERT: e 314 TYR cc_start: 0.6729 (m-80) cc_final: 0.6504 (m-80) outliers start: 3 outliers final: 3 residues processed: 890 average time/residue: 1.3412 time to fit residues: 1490.4448 Evaluate side-chains 479 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 476 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain a residue 116 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 528 optimal weight: 0.9990 chunk 474 optimal weight: 30.0000 chunk 263 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 490 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 365 optimal weight: 10.0000 chunk 568 optimal weight: 20.0000 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 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS B 69 GLN B 72 GLN B 89 ASN B 168 GLN B 306 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 227 HIS F 242 GLN G 94 ASN G 163 ASN G 248 GLN G 260 GLN G 343 HIS I 183 HIS J 216 HIS a 255 ASN a 389 ASN ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 82 ASN ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** c 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN ** d 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 329 ASN ** e 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 ASN ** e 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 248 GLN e 316 GLN f 91 GLN f 139 GLN f 310 GLN ** g 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 242 GLN ** g 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 348 ASN ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN h 183 HIS h 319 GLN h 342 GLN h 343 HIS i 170 ASN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 52792 Z= 0.352 Angle : 0.647 12.445 72463 Z= 0.338 Chirality : 0.043 0.300 8164 Planarity : 0.005 0.082 8966 Dihedral : 15.696 179.174 9132 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.18 % Allowed : 11.69 % Favored : 86.13 % 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: -0.89 (0.10), residues: 6192 helix: 0.15 (0.11), residues: 1978 sheet: 0.65 (0.16), residues: 1010 loop : -1.50 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP e 289 HIS 0.012 0.001 HIS C 29 PHE 0.034 0.002 PHE C 155 TYR 0.038 0.002 TYR A 336 ARG 0.014 0.001 ARG c 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 496 time to evaluate : 4.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: C 133 ASP cc_start: 0.3887 (m-30) cc_final: 0.3075 (t70) REVERT: F 51 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6699 (mt0) REVERT: G 312 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7495 (tttp) REVERT: H 203 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7089 (mmm160) REVERT: a 268 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6607 (mm) REVERT: b 79 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7315 (ptpp) REVERT: c 21 MET cc_start: 0.3326 (tmm) cc_final: 0.2515 (ttp) REVERT: e 314 TYR cc_start: 0.6956 (m-80) cc_final: 0.6747 (m-80) outliers start: 106 outliers final: 36 residues processed: 567 average time/residue: 1.2364 time to fit residues: 894.4872 Evaluate side-chains 437 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 397 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 81 ASN Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 275 THR Chi-restraints excluded: chain d residue 25 LEU Chi-restraints excluded: chain d residue 163 ASN Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 202 LEU Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain h residue 139 GLN Chi-restraints excluded: chain h residue 146 ASN Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 315 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 473 optimal weight: 0.5980 chunk 387 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 569 optimal weight: 8.9990 chunk 615 optimal weight: 7.9990 chunk 507 optimal weight: 2.9990 chunk 564 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 456 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS G 148 GLN K 208 GLN a 201 HIS a 253 GLN ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 GLN ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS c 161 HIS d 129 ASN d 139 GLN ** d 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 329 ASN g 183 HIS ** g 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN i 146 ASN ** i 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 329 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 52792 Z= 0.183 Angle : 0.562 12.358 72463 Z= 0.292 Chirality : 0.040 0.301 8164 Planarity : 0.004 0.081 8966 Dihedral : 15.581 179.280 9128 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.10 % Allowed : 14.06 % Favored : 83.84 % 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: -0.65 (0.10), residues: 6192 helix: 0.54 (0.11), residues: 1998 sheet: 0.70 (0.16), residues: 996 loop : -1.47 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 414 HIS 0.012 0.001 HIS C 29 PHE 0.035 0.001 PHE C 155 TYR 0.024 0.001 TYR a 336 ARG 0.013 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 492 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TRP cc_start: 0.3660 (OUTLIER) cc_final: 0.2671 (m-10) REVERT: B 53 ASP cc_start: 0.6592 (t0) cc_final: 0.6382 (t0) REVERT: C 133 ASP cc_start: 0.4058 (m-30) cc_final: 0.3274 (t70) REVERT: a 336 TYR cc_start: 0.6375 (t80) cc_final: 0.6170 (t80) REVERT: d 269 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5201 (mmp-170) REVERT: e 314 TYR cc_start: 0.7006 (m-80) cc_final: 0.6778 (m-80) REVERT: f 284 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7896 (ttm170) REVERT: h 243 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6168 (tt0) outliers start: 102 outliers final: 33 residues processed: 560 average time/residue: 1.2305 time to fit residues: 884.1763 Evaluate side-chains 452 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 416 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 81 ASN Chi-restraints excluded: chain a residue 154 GLU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 208 THR Chi-restraints excluded: chain d residue 269 ARG Chi-restraints excluded: chain d residue 323 PHE Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 202 LEU Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain h residue 139 GLN Chi-restraints excluded: chain h residue 179 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 562 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 295 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 382 optimal weight: 7.9990 chunk 571 optimal weight: 6.9990 chunk 605 optimal weight: 30.0000 chunk 298 optimal weight: 0.9990 chunk 541 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN a 389 ASN ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS ** c 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN d 139 GLN ** d 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 329 ASN f 319 GLN ** g 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 ASN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52792 Z= 0.177 Angle : 0.559 12.754 72463 Z= 0.288 Chirality : 0.040 0.290 8164 Planarity : 0.004 0.113 8966 Dihedral : 15.517 179.143 9126 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.25 % Allowed : 15.25 % Favored : 82.50 % 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: -0.48 (0.10), residues: 6192 helix: 0.80 (0.12), residues: 1998 sheet: 0.70 (0.16), residues: 996 loop : -1.44 (0.10), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 289 HIS 0.033 0.001 HIS c 61 PHE 0.035 0.001 PHE C 155 TYR 0.021 0.001 TYR g 344 ARG 0.018 0.000 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 472 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: A 331 ASP cc_start: 0.7271 (m-30) cc_final: 0.6877 (m-30) REVERT: B 53 ASP cc_start: 0.6771 (t0) cc_final: 0.6546 (t0) REVERT: C 28 LEU cc_start: 0.5705 (pp) cc_final: 0.4782 (mm) REVERT: C 133 ASP cc_start: 0.4008 (m-30) cc_final: 0.3251 (t70) REVERT: K 155 ASP cc_start: 0.6842 (t0) cc_final: 0.6473 (t0) REVERT: b 251 ILE cc_start: 0.6293 (pp) cc_final: 0.5961 (tp) REVERT: c 21 MET cc_start: 0.4435 (tmm) cc_final: 0.4193 (tmm) REVERT: d 329 ASN cc_start: 0.6315 (t0) cc_final: 0.5399 (t0) REVERT: f 94 ASN cc_start: 0.7753 (p0) cc_final: 0.7158 (p0) REVERT: g 333 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7088 (ptp-170) REVERT: h 243 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6132 (tt0) REVERT: i 268 VAL cc_start: 0.7433 (OUTLIER) cc_final: 0.7229 (t) outliers start: 109 outliers final: 38 residues processed: 543 average time/residue: 1.2313 time to fit residues: 856.6410 Evaluate side-chains 445 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 403 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 81 ASN Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 208 THR Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 202 LEU Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 139 GLN Chi-restraints excluded: chain h residue 179 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 202 LEU Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 503 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 450 optimal weight: 7.9990 chunk 249 optimal weight: 0.5980 chunk 516 optimal weight: 9.9990 chunk 418 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 308 optimal weight: 0.8980 chunk 543 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS B 306 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 148 GLN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 HIS H 91 GLN ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS ** c 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN d 139 GLN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 242 GLN g 281 ASN ** g 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 ASN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 52792 Z= 0.444 Angle : 0.653 13.548 72463 Z= 0.338 Chirality : 0.044 0.216 8164 Planarity : 0.005 0.108 8966 Dihedral : 15.628 179.996 9126 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.58 % Allowed : 16.41 % Favored : 81.02 % 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: -0.57 (0.10), residues: 6192 helix: 0.73 (0.11), residues: 1988 sheet: 0.51 (0.16), residues: 1034 loop : -1.44 (0.11), residues: 3170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 289 HIS 0.023 0.001 HIS c 61 PHE 0.037 0.002 PHE C 155 TYR 0.031 0.002 TYR A 336 ARG 0.015 0.001 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 423 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7263 (tp) REVERT: B 53 ASP cc_start: 0.6916 (t0) cc_final: 0.6694 (t0) REVERT: C 133 ASP cc_start: 0.3895 (m-30) cc_final: 0.3196 (t70) REVERT: D 44 MET cc_start: 0.7783 (mtt) cc_final: 0.7369 (mtt) REVERT: G 51 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: H 51 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: I 77 LYS cc_start: 0.7474 (mtpp) cc_final: 0.7229 (mtpp) REVERT: b 251 ILE cc_start: 0.6182 (pp) cc_final: 0.5826 (tp) REVERT: g 333 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6939 (ptp-170) REVERT: h 243 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: i 268 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7307 (t) outliers start: 125 outliers final: 54 residues processed: 509 average time/residue: 1.2825 time to fit residues: 840.4794 Evaluate side-chains 439 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 379 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 81 ASN Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 199 VAL Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain d residue 330 TRP Chi-restraints excluded: chain e residue 62 THR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 262 SER Chi-restraints excluded: chain e residue 321 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 202 LEU Chi-restraints excluded: chain f residue 319 GLN Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain h residue 146 ASN Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 202 LEU Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 203 optimal weight: 2.9990 chunk 544 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 355 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 605 optimal weight: 6.9990 chunk 502 optimal weight: 6.9990 chunk 280 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 317 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS d 139 GLN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 281 ASN d 329 ASN ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 242 GLN ** g 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 139 GLN ** i 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 170 ASN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52792 Z= 0.199 Angle : 0.580 14.421 72463 Z= 0.299 Chirality : 0.040 0.316 8164 Planarity : 0.004 0.100 8966 Dihedral : 15.515 179.311 9126 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.21 % Allowed : 17.87 % Favored : 79.93 % 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: -0.43 (0.11), residues: 6192 helix: 0.96 (0.12), residues: 1974 sheet: 0.49 (0.16), residues: 1022 loop : -1.39 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP d 330 HIS 0.020 0.001 HIS c 61 PHE 0.037 0.001 PHE C 155 TYR 0.026 0.001 TYR a 336 ARG 0.012 0.000 ARG c 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 452 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6854 (mtmt) REVERT: C 28 LEU cc_start: 0.5831 (pp) cc_final: 0.4723 (mm) REVERT: C 133 ASP cc_start: 0.3933 (m-30) cc_final: 0.3225 (t70) REVERT: D 261 LYS cc_start: 0.6617 (tptm) cc_final: 0.6344 (tmtt) REVERT: E 203 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6718 (mmm160) REVERT: a 116 ASP cc_start: 0.4698 (m-30) cc_final: 0.4476 (m-30) REVERT: a 119 LYS cc_start: 0.5837 (pptt) cc_final: 0.5361 (pptt) REVERT: a 268 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6826 (mm) REVERT: b 219 ILE cc_start: 0.5709 (OUTLIER) cc_final: 0.5481 (pp) REVERT: b 251 ILE cc_start: 0.6143 (pp) cc_final: 0.5814 (tp) REVERT: d 314 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: f 94 ASN cc_start: 0.7823 (p0) cc_final: 0.7242 (p0) REVERT: g 147 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7148 (p0) REVERT: g 333 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7179 (ptp-170) REVERT: h 205 PHE cc_start: 0.6678 (m-80) cc_final: 0.6116 (m-80) REVERT: h 243 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: i 268 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7315 (t) outliers start: 107 outliers final: 49 residues processed: 519 average time/residue: 1.1922 time to fit residues: 794.1888 Evaluate side-chains 466 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 408 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 81 ASN Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain d residue 314 TYR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 202 LEU Chi-restraints excluded: chain f residue 319 GLN Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 147 ASP Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 139 GLN Chi-restraints excluded: chain h residue 189 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 202 LEU Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 583 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 345 optimal weight: 40.0000 chunk 442 optimal weight: 30.0000 chunk 342 optimal weight: 8.9990 chunk 509 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 603 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 GLN E 91 GLN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 ASN a 98 HIS ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS c 120 HIS d 96 GLN d 129 ASN d 139 GLN d 148 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 329 ASN ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 242 GLN ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 129 ASN ** h 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 ASN i 170 ASN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.096 52792 Z= 0.771 Angle : 0.820 12.561 72463 Z= 0.422 Chirality : 0.052 0.432 8164 Planarity : 0.006 0.102 8966 Dihedral : 15.812 177.738 9126 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.76 % Allowed : 18.65 % Favored : 78.59 % 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: -0.85 (0.10), residues: 6192 helix: 0.45 (0.11), residues: 1964 sheet: 0.26 (0.16), residues: 984 loop : -1.51 (0.10), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP i 330 HIS 0.020 0.002 HIS c 61 PHE 0.040 0.002 PHE C 155 TYR 0.035 0.003 TYR g 144 ARG 0.017 0.001 ARG a 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 396 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.3703 (p-90) cc_final: 0.3245 (p-90) REVERT: A 363 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7826 (mp) REVERT: A 389 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6827 (p0) REVERT: A 420 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7464 (ptpp) REVERT: D 310 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: E 38 ASP cc_start: 0.7676 (m-30) cc_final: 0.7450 (m-30) REVERT: H 38 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: H 51 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: K 16 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.7013 (mpp-170) REVERT: a 119 LYS cc_start: 0.6010 (pptt) cc_final: 0.5471 (pptt) REVERT: a 128 LYS cc_start: 0.2373 (OUTLIER) cc_final: 0.1940 (pptt) REVERT: a 386 GLU cc_start: 0.4613 (pp20) cc_final: 0.3967 (tm-30) REVERT: b 251 ILE cc_start: 0.6259 (pp) cc_final: 0.5969 (tp) REVERT: d 96 GLN cc_start: 0.5803 (OUTLIER) cc_final: 0.5392 (tm-30) REVERT: g 333 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6806 (ptp-170) REVERT: i 268 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7393 (t) outliers start: 134 outliers final: 54 residues processed: 494 average time/residue: 1.2126 time to fit residues: 765.6957 Evaluate side-chains 433 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 370 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 310 GLN Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 51 GLN Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 128 LYS Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain d residue 96 GLN Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain e residue 62 THR Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain e residue 288 THR Chi-restraints excluded: chain e residue 332 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 319 GLN Chi-restraints excluded: chain f residue 335 GLU Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 189 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Chi-restraints excluded: chain i residue 321 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 373 optimal weight: 50.0000 chunk 240 optimal weight: 0.6980 chunk 360 optimal weight: 0.1980 chunk 181 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 474 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN d 139 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 242 GLN h 139 GLN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 52792 Z= 0.187 Angle : 0.622 14.740 72463 Z= 0.318 Chirality : 0.041 0.352 8164 Planarity : 0.004 0.093 8966 Dihedral : 15.592 179.809 9126 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.61 % Allowed : 19.93 % Favored : 78.46 % 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: -0.55 (0.11), residues: 6192 helix: 0.85 (0.12), residues: 1976 sheet: 0.35 (0.16), residues: 1032 loop : -1.43 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP i 330 HIS 0.018 0.001 HIS c 61 PHE 0.037 0.001 PHE C 155 TYR 0.025 0.002 TYR g 344 ARG 0.012 0.001 ARG a 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 436 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.3953 (p-90) cc_final: 0.3644 (p-90) REVERT: A 287 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: A 363 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7350 (tp) REVERT: A 389 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6632 (p0) REVERT: K 16 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.6951 (tpp-160) REVERT: a 128 LYS cc_start: 0.2218 (OUTLIER) cc_final: 0.1797 (pptt) REVERT: a 386 GLU cc_start: 0.4616 (pp20) cc_final: 0.3884 (tm-30) REVERT: b 251 ILE cc_start: 0.6207 (pp) cc_final: 0.5927 (tp) REVERT: f 94 ASN cc_start: 0.7902 (p0) cc_final: 0.7332 (p0) REVERT: g 333 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7218 (ptp-170) REVERT: i 268 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7374 (t) outliers start: 78 outliers final: 36 residues processed: 491 average time/residue: 1.2528 time to fit residues: 784.4761 Evaluate side-chains 431 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 389 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 318 LYS Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain a residue 128 LYS Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 208 THR Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 189 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 252 LEU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Chi-restraints excluded: chain i residue 321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 548 optimal weight: 0.9990 chunk 578 optimal weight: 5.9990 chunk 527 optimal weight: 6.9990 chunk 562 optimal weight: 0.4980 chunk 577 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 441 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 508 optimal weight: 0.0060 chunk 531 optimal weight: 5.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 242 GLN h 91 GLN h 139 GLN ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 52792 Z= 0.267 Angle : 0.642 15.722 72463 Z= 0.326 Chirality : 0.042 0.428 8164 Planarity : 0.004 0.091 8966 Dihedral : 15.543 179.991 9126 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.32 % Allowed : 20.67 % Favored : 78.01 % 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: -0.48 (0.11), residues: 6192 helix: 0.94 (0.12), residues: 1964 sheet: 0.31 (0.16), residues: 1022 loop : -1.37 (0.11), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP i 330 HIS 0.018 0.001 HIS c 61 PHE 0.036 0.001 PHE C 155 TYR 0.050 0.002 TYR A 336 ARG 0.009 0.000 ARG a 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 418 time to evaluate : 4.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.3972 (p-90) cc_final: 0.3714 (p-90) REVERT: A 281 MET cc_start: 0.6747 (mmp) cc_final: 0.6409 (mmp) REVERT: A 287 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: A 389 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6670 (p0) REVERT: A 420 LYS cc_start: 0.7728 (ptpp) cc_final: 0.7262 (ptpp) REVERT: C 29 HIS cc_start: 0.5647 (OUTLIER) cc_final: 0.5446 (t-170) REVERT: K 16 ARG cc_start: 0.7263 (tpp-160) cc_final: 0.6948 (tpp-160) REVERT: a 71 LYS cc_start: 0.5141 (tppt) cc_final: 0.4920 (tmmt) REVERT: a 128 LYS cc_start: 0.2260 (OUTLIER) cc_final: 0.1826 (pptt) REVERT: a 386 GLU cc_start: 0.4517 (pp20) cc_final: 0.3910 (tm-30) REVERT: b 219 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6275 (pp) REVERT: b 251 ILE cc_start: 0.6203 (pp) cc_final: 0.5924 (tp) REVERT: f 94 ASN cc_start: 0.7843 (p0) cc_final: 0.7248 (p0) REVERT: g 333 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7231 (ptp-170) REVERT: i 268 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7362 (t) outliers start: 64 outliers final: 39 residues processed: 458 average time/residue: 1.2276 time to fit residues: 720.2319 Evaluate side-chains 430 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 384 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain a residue 128 LYS Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 208 THR Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 319 GLN Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 189 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 252 LEU Chi-restraints excluded: chain h residue 296 LEU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 137 LEU Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Chi-restraints excluded: chain i residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 560 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 chunk 594 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 413 optimal weight: 6.9990 chunk 623 optimal weight: 50.0000 chunk 574 optimal weight: 2.9990 chunk 496 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 383 optimal weight: 0.5980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN d 163 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 52792 Z= 0.272 Angle : 0.651 15.885 72463 Z= 0.331 Chirality : 0.042 0.421 8164 Planarity : 0.005 0.090 8966 Dihedral : 15.526 179.763 9126 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.36 % Allowed : 20.96 % Favored : 77.68 % 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: -0.47 (0.11), residues: 6192 helix: 0.97 (0.12), residues: 1966 sheet: 0.32 (0.16), residues: 1040 loop : -1.39 (0.11), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP i 330 HIS 0.024 0.001 HIS C 29 PHE 0.036 0.001 PHE C 155 TYR 0.030 0.002 TYR d 266 ARG 0.017 0.000 ARG a 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 407 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TRP cc_start: 0.3960 (p-90) cc_final: 0.3733 (p-90) REVERT: A 287 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6614 (m-80) REVERT: A 389 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6674 (p0) REVERT: A 420 LYS cc_start: 0.7806 (ptpp) cc_final: 0.7516 (ptpp) REVERT: H 80 ASP cc_start: 0.7282 (p0) cc_final: 0.7041 (p0) REVERT: a 128 LYS cc_start: 0.2265 (OUTLIER) cc_final: 0.1825 (pptt) REVERT: a 386 GLU cc_start: 0.4425 (pp20) cc_final: 0.3780 (tm-30) REVERT: a 424 MET cc_start: 0.6237 (pmm) cc_final: 0.5972 (pmm) REVERT: b 219 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6267 (pp) REVERT: b 251 ILE cc_start: 0.6223 (pp) cc_final: 0.5945 (tp) REVERT: f 94 ASN cc_start: 0.7851 (p0) cc_final: 0.7256 (p0) REVERT: g 333 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7217 (ptp-170) REVERT: i 268 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7375 (t) outliers start: 66 outliers final: 43 residues processed: 452 average time/residue: 1.2660 time to fit residues: 729.7904 Evaluate side-chains 445 residues out of total 5036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain a residue 128 LYS Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain b residue 208 THR Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 80 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 72 ILE Chi-restraints excluded: chain f residue 95 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 319 GLN Chi-restraints excluded: chain f residue 350 ILE Chi-restraints excluded: chain g residue 78 THR Chi-restraints excluded: chain g residue 333 ARG Chi-restraints excluded: chain h residue 33 PHE Chi-restraints excluded: chain h residue 189 VAL Chi-restraints excluded: chain h residue 214 LEU Chi-restraints excluded: chain h residue 252 LEU Chi-restraints excluded: chain h residue 296 LEU Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 268 VAL Chi-restraints excluded: chain i residue 296 LEU Chi-restraints excluded: chain i residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 626 random chunks: chunk 304 optimal weight: 0.9980 chunk 394 optimal weight: 9.9990 chunk 529 optimal weight: 3.9990 chunk 152 optimal weight: 0.0170 chunk 457 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 497 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 510 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 289 HIS ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.169350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104081 restraints weight = 110127.441| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.96 r_work: 0.3029 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 52792 Z= 0.186 Angle : 0.630 16.751 72463 Z= 0.319 Chirality : 0.041 0.441 8164 Planarity : 0.004 0.092 8966 Dihedral : 15.465 179.096 9126 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.15 % Allowed : 21.19 % Favored : 77.66 % 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: -0.37 (0.11), residues: 6192 helix: 1.08 (0.12), residues: 1966 sheet: 0.42 (0.16), residues: 1030 loop : -1.36 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP e 289 HIS 0.017 0.001 HIS c 61 PHE 0.036 0.001 PHE C 155 TYR 0.050 0.002 TYR A 336 ARG 0.017 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14252.24 seconds wall clock time: 248 minutes 9.71 seconds (14889.71 seconds total)