Starting phenix.real_space_refine on Mon Sep 30 06:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/09_2024/6caj_7442.cif" } resolution = 2.8 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= 0.055 sd= 1.469 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 122 5.16 5 Cl 4 4.86 5 C 15461 2.51 5 N 4238 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24295 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "J" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "I" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 15.68, per 1000 atoms: 0.65 Number of scatterers: 24295 At special positions: 0 Unit cell: (134.918, 171.79, 118.996, 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) Cl 4 17.00 S 122 16.00 O 4470 8.00 N 4238 7.00 C 15461 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: 6.27 Conformation dependent library (CDL) restraints added in 3.3 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 36 sheets defined 43.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.511A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 4.235A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.838A pdb=" N CYS B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.576A pdb=" N GLN B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.845A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.831A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.691A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.654A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 227 Processing helix chain 'J' and resid 283 through 288 removed outlier: 3.673A pdb=" N GLY J 287 " --> pdb=" O ASN J 283 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP J 288 " --> pdb=" O ALA J 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 283 through 288' Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.632A pdb=" N GLU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 36 removed outlier: 3.831A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 62 through 77 removed outlier: 3.878A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 106 Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.857A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 4.258A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 removed outlier: 3.790A pdb=" N MET H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.812A pdb=" N TYR H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 293 through 304 removed outlier: 4.542A pdb=" N SER H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.536A pdb=" N ASP C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.620A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 96 removed outlier: 4.542A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.624A pdb=" N GLN C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.587A pdb=" N HIS C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.809A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.621A pdb=" N GLU C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 304' Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.613A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.979A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.056A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.773A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.653A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 325 removed outlier: 5.619A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.574A pdb=" N GLU F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.179A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 395 removed outlier: 4.055A pdb=" N SER F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.614A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.961A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.511A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.234A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.845A pdb=" N CYS A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.566A pdb=" N GLN A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.847A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'I' and resid 36 through 46 removed outlier: 3.830A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 94 through 97 Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.691A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.654A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 283 through 288 removed outlier: 3.674A pdb=" N GLY I 287 " --> pdb=" O ASN I 283 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP I 288 " --> pdb=" O ALA I 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 283 through 288' Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.631A pdb=" N GLU G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 36 removed outlier: 3.831A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.878A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.857A pdb=" N LYS G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 4.258A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 removed outlier: 3.790A pdb=" N MET G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.813A pdb=" N TYR G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 293 through 304 removed outlier: 4.542A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 removed outlier: 3.537A pdb=" N ASP D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.620A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 96 removed outlier: 4.542A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.626A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.587A pdb=" N HIS D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 159 " --> pdb=" O LEU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 159' Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.808A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.622A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 304' Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.611A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.979A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 4.057A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 removed outlier: 3.774A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.655A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 325 removed outlier: 5.620A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.574A pdb=" N GLU E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 379 removed outlier: 4.178A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 395 removed outlier: 4.046A pdb=" N SER E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.613A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.962A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 520 Processing sheet with id=AA1, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER B 179 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS B 288 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.738A pdb=" N ARG B 211 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 202 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 216 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.738A pdb=" N ARG B 211 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE J 193 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.835A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.390A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.374A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 418 through 419 removed outlier: 7.696A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 76 through 78 removed outlier: 8.824A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 200 through 201 removed outlier: 6.312A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR J 272 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET J 132 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.955A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 199 through 200 removed outlier: 4.089A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.525A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.795A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 314 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 306 through 307 removed outlier: 6.461A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 502 " --> pdb=" O GLY F 505 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 407 through 408 removed outlier: 3.657A pdb=" N SER F 416 " --> pdb=" O ASP F 490 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP F 490 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 179 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS A 288 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.746A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 202 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.746A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE I 193 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AC7, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.835A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.389A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.375A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 418 through 419 removed outlier: 7.695A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 76 through 78 removed outlier: 8.826A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 200 through 201 removed outlier: 6.314A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.955A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 199 through 200 removed outlier: 4.088A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.527A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 217 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.792A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 314 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 306 through 307 removed outlier: 6.464A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 502 " --> pdb=" O GLY E 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.657A pdb=" N SER E 416 " --> pdb=" O ASP E 490 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP E 490 " --> pdb=" O SER E 416 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 9872 1.41 - 1.65: 14681 1.65 - 1.88: 190 1.88 - 2.11: 0 2.11 - 2.35: 1 Bond restraints: 24744 Sorted by residual: bond pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 1.329 2.346 -1.017 1.44e-02 4.82e+03 4.99e+03 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.439 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 33519 5.28 - 10.55: 109 10.55 - 15.83: 2 15.83 - 21.11: 0 21.11 - 26.39: 1 Bond angle restraints: 33631 Sorted by residual: angle pdb=" C ILE J 267 " pdb=" N THR J 272 " pdb=" CA THR J 272 " ideal model delta sigma weight residual 122.64 96.25 26.39 1.70e+00 3.46e-01 2.41e+02 angle pdb=" O ILE J 267 " pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 122.76 114.16 8.60 1.47e+00 4.63e-01 3.42e+01 angle pdb=" C LEU E 387 " pdb=" N ILE E 388 " pdb=" CA ILE E 388 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" C LEU F 387 " pdb=" N ILE F 388 " pdb=" CA ILE F 388 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.02e+01 angle pdb=" C THR A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.45e+01 ... (remaining 33626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 14853 34.00 - 68.00: 62 68.00 - 102.00: 14 102.00 - 136.00: 12 136.00 - 170.00: 2 Dihedral angle restraints: 14943 sinusoidal: 5582 harmonic: 9361 Sorted by residual: dihedral pdb=" CA GLN G 156 " pdb=" C GLN G 156 " pdb=" N PRO G 157 " pdb=" CA PRO G 157 " ideal model delta harmonic sigma weight residual 180.00 140.39 39.61 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA GLN H 156 " pdb=" C GLN H 156 " pdb=" N PRO H 157 " pdb=" CA PRO H 157 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA ALA C 195 " pdb=" C ALA C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 142.84 37.16 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 14940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 4003 1.018 - 2.036: 0 2.036 - 3.054: 0 3.054 - 4.072: 0 4.072 - 5.090: 4 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.50 4.97 2.00e-01 2.50e+01 6.18e+02 ... (remaining 4004 not shown) Planarity restraints: 4297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 267 " -0.079 2.00e-02 2.50e+03 1.31e-01 1.72e+02 pdb=" C ILE J 267 " 0.225 2.00e-02 2.50e+03 pdb=" O ILE J 267 " -0.100 2.00e-02 2.50e+03 pdb=" N THR J 272 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 156 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 157 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 156 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO G 157 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " -0.036 5.00e-02 4.00e+02 ... (remaining 4294 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 3 2.15 - 2.84: 7542 2.84 - 3.53: 31921 3.53 - 4.21: 56930 4.21 - 4.90: 97487 Nonbonded interactions: 193883 Sorted by model distance: nonbonded pdb=" CD2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.467 3.760 nonbonded pdb=" CE2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.474 3.760 nonbonded pdb=" O ILE I 267 " pdb=" CB THR I 272 " model vdw 2.063 3.470 nonbonded pdb=" CE2 PHE I 266 " pdb=" OG1 THR I 272 " model vdw 2.273 3.340 nonbonded pdb=" CE2 PHE I 266 " pdb=" CB THR I 272 " model vdw 2.292 3.770 ... (remaining 193878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.710 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1591 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 : 0.008 1.017 24744 Z= 0.331 Angle : 0.879 26.386 33631 Z= 0.490 Chirality : 0.167 5.090 4007 Planarity : 0.007 0.131 4297 Dihedral : 10.477 170.000 8853 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.24 % Allowed : 1.81 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -3.63 (0.12), residues: 3150 helix: -2.59 (0.10), residues: 1204 sheet: -2.05 (0.22), residues: 410 loop : -2.29 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 272 HIS 0.006 0.001 HIS F 274 PHE 0.019 0.002 PHE C 272 TYR 0.018 0.002 TYR A 78 ARG 0.005 0.001 ARG F 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 828 time to evaluate : 2.919 Fit side-chains revert: symmetry clash REVERT: B 53 ASP cc_start: 0.4412 (t0) cc_final: 0.4162 (p0) REVERT: B 104 GLU cc_start: 0.5600 (tt0) cc_final: 0.5291 (tm-30) REVERT: B 269 ARG cc_start: 0.1374 (ttp80) cc_final: 0.1152 (ttp-170) REVERT: B 339 ARG cc_start: 0.1236 (mtp85) cc_final: 0.1032 (ttm-80) REVERT: B 352 HIS cc_start: 0.5278 (m-70) cc_final: 0.5007 (t70) REVERT: J 99 THR cc_start: 0.0757 (t) cc_final: -0.0026 (t) REVERT: H 270 HIS cc_start: 0.3595 (m-70) cc_final: 0.3321 (m170) REVERT: H 292 THR cc_start: 0.1763 (t) cc_final: 0.1558 (p) REVERT: C 149 GLU cc_start: 0.5583 (mt-10) cc_final: 0.5264 (tm-30) REVERT: C 203 MET cc_start: 0.3078 (ttt) cc_final: 0.2629 (tpp) REVERT: C 206 ASN cc_start: 0.4851 (m-40) cc_final: 0.4529 (m110) REVERT: C 251 THR cc_start: 0.3240 (t) cc_final: 0.2800 (t) REVERT: C 309 HIS cc_start: 0.0332 (m90) cc_final: -0.0504 (m-70) REVERT: C 342 GLU cc_start: 0.5093 (mt-10) cc_final: 0.4836 (mt-10) REVERT: F 248 LEU cc_start: 0.3485 (tt) cc_final: 0.3276 (tp) REVERT: F 277 ILE cc_start: 0.4718 (mt) cc_final: 0.4367 (mt) REVERT: F 362 ASP cc_start: 0.4420 (t0) cc_final: 0.4099 (t0) REVERT: F 461 ASP cc_start: 0.2855 (m-30) cc_final: 0.2653 (m-30) REVERT: A 53 ASP cc_start: 0.4342 (t0) cc_final: 0.4010 (p0) REVERT: A 104 GLU cc_start: 0.5504 (tt0) cc_final: 0.5241 (tm-30) REVERT: A 264 PHE cc_start: 0.3768 (t80) cc_final: 0.3566 (t80) REVERT: A 269 ARG cc_start: 0.1298 (ttp80) cc_final: 0.1071 (ttp-170) REVERT: A 352 HIS cc_start: 0.5286 (m-70) cc_final: 0.5014 (t70) REVERT: I 1 MET cc_start: 0.4147 (mmm) cc_final: 0.3931 (ttp) REVERT: I 99 THR cc_start: 0.0479 (t) cc_final: -0.0843 (t) REVERT: G 270 HIS cc_start: 0.3603 (m-70) cc_final: 0.3339 (m170) REVERT: G 292 THR cc_start: 0.1850 (t) cc_final: 0.1641 (p) REVERT: D 149 GLU cc_start: 0.5607 (mt-10) cc_final: 0.5295 (tm-30) REVERT: D 203 MET cc_start: 0.2943 (ttt) cc_final: 0.2502 (tpp) REVERT: D 206 ASN cc_start: 0.4809 (m-40) cc_final: 0.4467 (m110) REVERT: D 251 THR cc_start: 0.3224 (t) cc_final: 0.2786 (t) REVERT: D 309 HIS cc_start: 0.0388 (m90) cc_final: -0.0487 (m-70) REVERT: D 342 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4816 (mt-10) REVERT: E 273 MET cc_start: 0.3322 (mtp) cc_final: 0.3028 (mtp) REVERT: E 324 TYR cc_start: 0.1569 (t80) cc_final: 0.1358 (t80) REVERT: E 362 ASP cc_start: 0.4382 (t0) cc_final: 0.4085 (t0) outliers start: 6 outliers final: 2 residues processed: 832 average time/residue: 1.3289 time to fit residues: 1269.7648 Evaluate side-chains 449 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 447 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain A residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.0970 chunk 239 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 101 GLN B 255 GLN B 258 GLN B 263 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS B 410 GLN J 196 HIS J 218 ASN H 213 ASN H 243 GLN H 244 GLN C 160 HIS C 252 HIS C 286 HIS F 275 ASN F 422 GLN A 63 GLN A 101 GLN A 255 GLN A 258 GLN A 263 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 410 GLN I 203 HIS I 218 ASN G 213 ASN G 243 GLN G 244 GLN D 160 HIS D 252 HIS D 286 HIS E 275 ASN E 422 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1492 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24744 Z= 0.279 Angle : 0.673 12.862 33631 Z= 0.339 Chirality : 0.047 0.208 4007 Planarity : 0.006 0.069 4297 Dihedral : 6.639 156.337 3483 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.61 % Allowed : 13.63 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.73 (0.14), residues: 3152 helix: -0.51 (0.14), residues: 1244 sheet: -1.68 (0.24), residues: 449 loop : -1.44 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 37 HIS 0.008 0.002 HIS A 105 PHE 0.022 0.002 PHE D 272 TYR 0.017 0.002 TYR B 78 ARG 0.009 0.001 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 477 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5539 (tt0) cc_final: 0.5295 (tm-30) REVERT: J 53 VAL cc_start: 0.4581 (OUTLIER) cc_final: 0.4367 (m) REVERT: H 292 THR cc_start: 0.1871 (t) cc_final: 0.1517 (p) REVERT: F 254 ASN cc_start: 0.5822 (m110) cc_final: 0.5613 (m-40) REVERT: A 62 ASP cc_start: 0.4765 (OUTLIER) cc_final: 0.4556 (m-30) REVERT: A 104 GLU cc_start: 0.5540 (tt0) cc_final: 0.5321 (tm-30) REVERT: I 53 VAL cc_start: 0.4362 (OUTLIER) cc_final: 0.4148 (m) REVERT: I 156 ASP cc_start: 0.5365 (m-30) cc_final: 0.5140 (m-30) REVERT: G 270 HIS cc_start: 0.3190 (m-70) cc_final: 0.2836 (m170) REVERT: G 292 THR cc_start: 0.1877 (t) cc_final: 0.1500 (p) outliers start: 117 outliers final: 37 residues processed: 552 average time/residue: 1.3067 time to fit residues: 829.5363 Evaluate side-chains 385 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 345 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 285 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN C 44 GLN C 158 HIS C 206 ASN F 406 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS F 431 ASN A 44 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN D 44 GLN D 158 HIS D 162 ASN D 206 ASN E 254 ASN E 406 HIS ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS E 431 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1429 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24744 Z= 0.322 Angle : 0.694 10.915 33631 Z= 0.348 Chirality : 0.049 0.204 4007 Planarity : 0.005 0.057 4297 Dihedral : 6.973 171.244 3481 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.63 % Allowed : 15.29 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.06 (0.15), residues: 3152 helix: 0.17 (0.14), residues: 1222 sheet: -1.49 (0.22), residues: 505 loop : -1.07 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 37 HIS 0.010 0.002 HIS A 288 PHE 0.021 0.002 PHE D 177 TYR 0.018 0.002 TYR I 231 ARG 0.007 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 364 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5561 (tt0) cc_final: 0.5339 (tm-30) REVERT: F 247 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4810 (mp0) REVERT: G 180 ASP cc_start: 0.3746 (t0) cc_final: 0.3540 (t0) outliers start: 143 outliers final: 61 residues processed: 460 average time/residue: 1.2993 time to fit residues: 690.0749 Evaluate side-chains 366 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 304 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 270 HIS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 467 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.1980 chunk 216 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 137 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 273 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 255 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN A 101 GLN A 255 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24744 Z= 0.196 Angle : 0.583 9.176 33631 Z= 0.292 Chirality : 0.045 0.204 4007 Planarity : 0.004 0.054 4297 Dihedral : 6.394 162.317 3481 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.77 % Allowed : 18.09 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.58 (0.15), residues: 3152 helix: 0.71 (0.15), residues: 1238 sheet: -1.50 (0.23), residues: 463 loop : -0.88 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 97 HIS 0.007 0.001 HIS B 352 PHE 0.015 0.002 PHE C 177 TYR 0.018 0.001 TYR A 128 ARG 0.011 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 327 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5505 (tt0) cc_final: 0.5277 (tm-30) REVERT: J 156 ASP cc_start: 0.5740 (m-30) cc_final: 0.5463 (m-30) REVERT: I 116 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.4291 (tp30) REVERT: D 33 GLU cc_start: 0.5373 (tt0) cc_final: 0.5173 (mm-30) outliers start: 121 outliers final: 49 residues processed: 409 average time/residue: 1.3015 time to fit residues: 613.9433 Evaluate side-chains 335 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 285 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 0.0570 chunk 260 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 274 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 422 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1415 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24744 Z= 0.284 Angle : 0.643 13.945 33631 Z= 0.320 Chirality : 0.047 0.265 4007 Planarity : 0.005 0.066 4297 Dihedral : 6.665 167.718 3481 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.04 % Allowed : 18.32 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.39 (0.15), residues: 3152 helix: 0.88 (0.15), residues: 1224 sheet: -1.40 (0.22), residues: 489 loop : -0.76 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 HIS 0.006 0.001 HIS B 288 PHE 0.022 0.002 PHE D 177 TYR 0.023 0.002 TYR B 128 ARG 0.011 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 312 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5656 (tt0) cc_final: 0.5433 (tm-30) outliers start: 128 outliers final: 68 residues processed: 401 average time/residue: 1.4117 time to fit residues: 650.7809 Evaluate side-chains 356 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 288 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 253 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1410 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24744 Z= 0.244 Angle : 0.613 12.717 33631 Z= 0.305 Chirality : 0.045 0.267 4007 Planarity : 0.005 0.061 4297 Dihedral : 6.530 165.725 3481 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.49 % Allowed : 18.95 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.26 (0.15), residues: 3152 helix: 0.98 (0.15), residues: 1246 sheet: -1.43 (0.23), residues: 445 loop : -0.69 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 366 HIS 0.006 0.001 HIS B 352 PHE 0.019 0.002 PHE D 177 TYR 0.021 0.001 TYR A 128 ARG 0.008 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 298 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5610 (tt0) cc_final: 0.5392 (tm-30) outliers start: 114 outliers final: 70 residues processed: 383 average time/residue: 1.3532 time to fit residues: 598.4028 Evaluate side-chains 349 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 279 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 304 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1385 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 24744 Z= 0.445 Angle : 0.747 12.400 33631 Z= 0.376 Chirality : 0.051 0.297 4007 Planarity : 0.006 0.064 4297 Dihedral : 7.191 172.717 3481 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.24 % Allowed : 18.52 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.60 (0.15), residues: 3152 helix: 0.62 (0.15), residues: 1234 sheet: -1.50 (0.21), residues: 483 loop : -0.80 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 366 HIS 0.008 0.002 HIS A 352 PHE 0.028 0.003 PHE D 177 TYR 0.028 0.003 TYR A 128 ARG 0.009 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 299 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6557 (mtt180) cc_final: 0.6174 (ttm110) REVERT: B 104 GLU cc_start: 0.5640 (tt0) cc_final: 0.5430 (tm-30) REVERT: H 103 ARG cc_start: 0.4497 (mmm-85) cc_final: 0.4138 (tpt170) REVERT: G 103 ARG cc_start: 0.4919 (mmm-85) cc_final: 0.4312 (tpt170) outliers start: 133 outliers final: 82 residues processed: 400 average time/residue: 1.3790 time to fit residues: 633.2359 Evaluate side-chains 367 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 285 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 371 HIS E 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1398 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24744 Z= 0.226 Angle : 0.618 11.466 33631 Z= 0.311 Chirality : 0.046 0.268 4007 Planarity : 0.005 0.060 4297 Dihedral : 6.639 165.724 3481 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 20.53 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.24 (0.15), residues: 3152 helix: 0.99 (0.15), residues: 1248 sheet: -1.36 (0.23), residues: 437 loop : -0.71 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 366 HIS 0.006 0.001 HIS A 352 PHE 0.019 0.002 PHE C 177 TYR 0.020 0.001 TYR B 128 ARG 0.008 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 290 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6551 (mtt180) cc_final: 0.6140 (ttm110) REVERT: B 104 GLU cc_start: 0.5682 (tt0) cc_final: 0.5458 (tm-30) REVERT: H 103 ARG cc_start: 0.4369 (mmm-85) cc_final: 0.3992 (tpt170) REVERT: C 212 ILE cc_start: -0.0729 (OUTLIER) cc_final: -0.0946 (mt) REVERT: G 103 ARG cc_start: 0.4844 (mmm-85) cc_final: 0.4236 (tpt170) REVERT: D 212 ILE cc_start: -0.0573 (OUTLIER) cc_final: -0.0789 (mt) outliers start: 93 outliers final: 61 residues processed: 361 average time/residue: 1.4463 time to fit residues: 595.0612 Evaluate side-chains 339 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 256 optimal weight: 0.7980 chunk 268 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 HIS H 109 ASN C 252 HIS F 254 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1400 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24744 Z= 0.245 Angle : 0.626 11.373 33631 Z= 0.313 Chirality : 0.046 0.247 4007 Planarity : 0.005 0.057 4297 Dihedral : 6.589 165.228 3481 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.70 % Allowed : 20.41 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.10 (0.15), residues: 3152 helix: 1.16 (0.15), residues: 1236 sheet: -1.28 (0.23), residues: 457 loop : -0.66 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 97 HIS 0.007 0.001 HIS B 352 PHE 0.020 0.002 PHE C 177 TYR 0.022 0.002 TYR I 210 ARG 0.006 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 287 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5683 (tt0) cc_final: 0.5461 (tm-30) REVERT: H 103 ARG cc_start: 0.4387 (mmm-85) cc_final: 0.4006 (tpt170) REVERT: C 212 ILE cc_start: -0.0649 (OUTLIER) cc_final: -0.0876 (mt) REVERT: G 103 ARG cc_start: 0.4856 (mmm-85) cc_final: 0.4234 (tpt170) REVERT: D 212 ILE cc_start: -0.0488 (OUTLIER) cc_final: -0.0713 (mt) outliers start: 94 outliers final: 67 residues processed: 357 average time/residue: 1.4460 time to fit residues: 593.4942 Evaluate side-chains 341 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 208 optimal weight: 0.0670 chunk 314 optimal weight: 0.4980 chunk 289 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1403 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24744 Z= 0.231 Angle : 0.620 11.299 33631 Z= 0.310 Chirality : 0.046 0.234 4007 Planarity : 0.005 0.057 4297 Dihedral : 6.514 163.965 3481 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.11 % Allowed : 21.28 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3152 helix: 1.17 (0.15), residues: 1248 sheet: -1.23 (0.23), residues: 457 loop : -0.63 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.007 0.001 HIS B 352 PHE 0.019 0.002 PHE C 177 TYR 0.020 0.001 TYR A 128 ARG 0.006 0.000 ARG B 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 286 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5656 (tt0) cc_final: 0.5439 (tm-30) REVERT: J 217 GLU cc_start: 0.4031 (mm-30) cc_final: 0.3547 (mt-10) REVERT: H 103 ARG cc_start: 0.4337 (mmm-85) cc_final: 0.3950 (tpt170) REVERT: C 212 ILE cc_start: -0.0657 (OUTLIER) cc_final: -0.0882 (mt) REVERT: I 217 GLU cc_start: 0.3837 (mm-30) cc_final: 0.3445 (mt-10) REVERT: G 20 MET cc_start: 0.1380 (ttt) cc_final: 0.1031 (tpt) REVERT: G 103 ARG cc_start: 0.4854 (mmm-85) cc_final: 0.4224 (tpt170) REVERT: D 212 ILE cc_start: -0.0503 (OUTLIER) cc_final: -0.0731 (mt) outliers start: 79 outliers final: 62 residues processed: 346 average time/residue: 1.4219 time to fit residues: 563.0658 Evaluate side-chains 340 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 276 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 0.0870 chunk 69 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 422 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.172035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146959 restraints weight = 33702.500| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.51 r_work: 0.3614 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24744 Z= 0.199 Angle : 0.596 11.252 33631 Z= 0.298 Chirality : 0.045 0.231 4007 Planarity : 0.004 0.057 4297 Dihedral : 6.339 161.217 3481 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.72 % Allowed : 21.79 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.09 (0.16), residues: 3152 helix: 1.30 (0.15), residues: 1242 sheet: -1.17 (0.24), residues: 447 loop : -0.55 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 97 HIS 0.007 0.001 HIS A 352 PHE 0.017 0.001 PHE C 177 TYR 0.024 0.001 TYR J 210 ARG 0.005 0.000 ARG B 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11589.04 seconds wall clock time: 202 minutes 10.38 seconds (12130.38 seconds total)