Starting phenix.real_space_refine on Mon Mar 18 15:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ej1_31148/03_2024/7ej1_31148_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.002 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 P 12 5.49 5 S 104 5.16 5 C 13696 2.51 5 N 3572 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21236 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2707 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 161 Chain: "C" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2707 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 161 Chain: "E" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "F" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2707 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 161 Chain: "G" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2554 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "H" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2707 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.81, per 1000 atoms: 0.56 Number of scatterers: 21236 At special positions: 0 Unit cell: (128.778, 128.778, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 12 15.00 O 3852 8.00 N 3572 7.00 C 13696 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 3.8 seconds 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 16 sheets defined 52.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.785A pdb=" N ILE A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.696A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.539A pdb=" N MET A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.571A pdb=" N VAL A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.742A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.500A pdb=" N LYS A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.673A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.867A pdb=" N CYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.557A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.556A pdb=" N TYR B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 4.092A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.558A pdb=" N PHE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.977A pdb=" N LEU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 254 removed outlier: 3.621A pdb=" N VAL B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 314 removed outlier: 3.798A pdb=" N VAL B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.774A pdb=" N THR B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 380 removed outlier: 3.624A pdb=" N ARG B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.567A pdb=" N ILE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 420 removed outlier: 3.626A pdb=" N GLY B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 407 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 removed outlier: 4.806A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 470 removed outlier: 4.107A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 3.523A pdb=" N VAL B 480 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 481 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 482 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 485 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS B 488 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 489 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 490 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 491 " --> pdb=" O HIS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.786A pdb=" N ILE C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.696A pdb=" N ILE C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 179 Processing helix chain 'C' and resid 192 through 204 removed outlier: 3.539A pdb=" N MET C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.570A pdb=" N VAL C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 227' Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.741A pdb=" N HIS C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.500A pdb=" N LYS C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.673A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.868A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.557A pdb=" N GLN D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.556A pdb=" N TYR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 4.093A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.559A pdb=" N PHE D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D 198 " --> pdb=" O MET D 194 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.979A pdb=" N LEU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 254 removed outlier: 3.620A pdb=" N VAL D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 314 removed outlier: 3.798A pdb=" N VAL D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 327 through 330 No H-bonds generated for 'chain 'D' and resid 327 through 330' Processing helix chain 'D' and resid 332 through 335 Processing helix chain 'D' and resid 337 through 346 removed outlier: 3.773A pdb=" N THR D 342 " --> pdb=" O PRO D 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 380 removed outlier: 3.624A pdb=" N ARG D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU D 377 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG D 379 " --> pdb=" O PHE D 375 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.569A pdb=" N ILE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 420 removed outlier: 3.626A pdb=" N GLY D 399 " --> pdb=" O MET D 395 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 407 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 4.806A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 470 removed outlier: 4.107A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 491 removed outlier: 3.523A pdb=" N VAL D 480 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER D 481 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D 482 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 484 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 485 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS D 488 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 489 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 490 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR D 491 " --> pdb=" O HIS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 77 Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.786A pdb=" N ILE E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.697A pdb=" N ILE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.538A pdb=" N MET E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 227 removed outlier: 3.570A pdb=" N VAL E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 223 through 227' Processing helix chain 'E' and resid 229 through 235 removed outlier: 3.742A pdb=" N HIS E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.500A pdb=" N LYS E 276 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 298 removed outlier: 3.672A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 297 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.868A pdb=" N CYS E 311 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 345 through 355 Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.557A pdb=" N GLN F 124 " --> pdb=" O LYS F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 156 through 165 removed outlier: 3.555A pdb=" N TYR F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 187 removed outlier: 4.092A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.558A pdb=" N PHE F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG F 198 " --> pdb=" O MET F 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.979A pdb=" N LEU F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 254 removed outlier: 3.622A pdb=" N VAL F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU F 242 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE F 244 " --> pdb=" O SER F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 314 removed outlier: 3.798A pdb=" N VAL F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS F 302 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 304 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 310 " --> pdb=" O PHE F 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'F' and resid 327 through 330 No H-bonds generated for 'chain 'F' and resid 327 through 330' Processing helix chain 'F' and resid 332 through 335 Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.775A pdb=" N THR F 342 " --> pdb=" O PRO F 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 380 removed outlier: 3.624A pdb=" N ARG F 364 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG F 370 " --> pdb=" O ILE F 366 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG F 379 " --> pdb=" O PHE F 375 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.567A pdb=" N ILE F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 420 removed outlier: 3.629A pdb=" N GLY F 399 " --> pdb=" O MET F 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE F 407 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER F 413 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 442 removed outlier: 4.805A pdb=" N TRP F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 470 removed outlier: 4.107A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 491 removed outlier: 3.522A pdb=" N VAL F 480 " --> pdb=" O PRO F 477 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER F 481 " --> pdb=" O VAL F 478 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN F 482 " --> pdb=" O ILE F 479 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR F 485 " --> pdb=" O ASN F 482 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS F 488 " --> pdb=" O TYR F 485 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG F 489 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 490 " --> pdb=" O TYR F 487 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F 491 " --> pdb=" O HIS F 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 77 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.785A pdb=" N ILE G 102 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.696A pdb=" N ILE G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 179 Processing helix chain 'G' and resid 192 through 204 removed outlier: 3.540A pdb=" N MET G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.570A pdb=" N VAL G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 223 through 227' Processing helix chain 'G' and resid 229 through 235 removed outlier: 3.741A pdb=" N HIS G 234 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 277 removed outlier: 3.500A pdb=" N LYS G 276 " --> pdb=" O TRP G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 286 Processing helix chain 'G' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 297 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.866A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 312 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 334 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'H' and resid 119 through 124 removed outlier: 3.558A pdb=" N GLN H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 138 No H-bonds generated for 'chain 'H' and resid 136 through 138' Processing helix chain 'H' and resid 156 through 165 removed outlier: 3.556A pdb=" N TYR H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 187 removed outlier: 4.093A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 201 removed outlier: 3.561A pdb=" N PHE H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG H 198 " --> pdb=" O MET H 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.979A pdb=" N LEU H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE H 224 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 254 removed outlier: 3.621A pdb=" N VAL H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU H 242 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE H 244 " --> pdb=" O SER H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 314 removed outlier: 3.798A pdb=" N VAL H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE H 304 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 310 " --> pdb=" O PHE H 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 312 " --> pdb=" O PHE H 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 324 Processing helix chain 'H' and resid 327 through 330 No H-bonds generated for 'chain 'H' and resid 327 through 330' Processing helix chain 'H' and resid 332 through 335 Processing helix chain 'H' and resid 337 through 346 removed outlier: 3.775A pdb=" N THR H 342 " --> pdb=" O PRO H 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU H 343 " --> pdb=" O TYR H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 380 removed outlier: 3.625A pdb=" N ARG H 364 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL H 365 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG H 370 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL H 371 " --> pdb=" O ARG H 367 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE H 372 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG H 373 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS H 376 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU H 377 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG H 379 " --> pdb=" O PHE H 375 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 392 removed outlier: 3.568A pdb=" N ILE H 386 " --> pdb=" O LYS H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 420 removed outlier: 3.627A pdb=" N GLY H 399 " --> pdb=" O MET H 395 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE H 407 " --> pdb=" O PHE H 403 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER H 413 " --> pdb=" O VAL H 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 442 removed outlier: 4.804A pdb=" N TRP H 436 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 470 removed outlier: 4.108A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 491 removed outlier: 3.523A pdb=" N VAL H 480 " --> pdb=" O PRO H 477 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER H 481 " --> pdb=" O VAL H 478 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN H 482 " --> pdb=" O ILE H 479 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN H 484 " --> pdb=" O SER H 481 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 485 " --> pdb=" O ASN H 482 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS H 488 " --> pdb=" O TYR H 485 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG H 489 " --> pdb=" O PHE H 486 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU H 490 " --> pdb=" O TYR H 487 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR H 491 " --> pdb=" O HIS H 488 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.289A pdb=" N VAL A 320 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 116 through 119 removed outlier: 6.607A pdb=" N VAL A 154 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 156 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 184 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA A 157 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY A 186 " --> pdb=" O ALA A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.469A pdb=" N TYR B 147 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.289A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 116 through 119 removed outlier: 6.607A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 113 through 118 removed outlier: 6.469A pdb=" N TYR D 147 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.290A pdb=" N VAL E 320 " --> pdb=" O GLY E 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.608A pdb=" N VAL E 154 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE E 119 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE E 156 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR E 184 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ALA E 157 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY E 186 " --> pdb=" O ALA E 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 113 through 118 removed outlier: 6.468A pdb=" N TYR F 147 " --> pdb=" O ASN F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 52 through 54 removed outlier: 6.289A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 116 through 119 removed outlier: 6.607A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 113 through 118 removed outlier: 6.468A pdb=" N TYR H 147 " --> pdb=" O ASN H 109 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1911 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: 5.93 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3408 1.31 - 1.43: 5850 1.43 - 1.56: 12274 1.56 - 1.68: 20 1.68 - 1.81: 172 Bond restraints: 21724 Sorted by residual: bond pdb=" C1B NAP A 401 " pdb=" C2B NAP A 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP E 401 " pdb=" C2B NAP E 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP C 401 " pdb=" C2B NAP C 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C4D NAP G 401 " pdb=" O4D NAP G 401 " ideal model delta sigma weight residual 1.447 1.305 0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 21719 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.46: 656 106.46 - 113.41: 11750 113.41 - 120.36: 9007 120.36 - 127.31: 7849 127.31 - 134.26: 262 Bond angle restraints: 29524 Sorted by residual: angle pdb=" N VAL B 476 " pdb=" CA VAL B 476 " pdb=" C VAL B 476 " ideal model delta sigma weight residual 108.88 119.15 -10.27 2.16e+00 2.14e-01 2.26e+01 angle pdb=" N VAL H 476 " pdb=" CA VAL H 476 " pdb=" C VAL H 476 " ideal model delta sigma weight residual 108.88 119.13 -10.25 2.16e+00 2.14e-01 2.25e+01 angle pdb=" N VAL F 476 " pdb=" CA VAL F 476 " pdb=" C VAL F 476 " ideal model delta sigma weight residual 108.88 119.13 -10.25 2.16e+00 2.14e-01 2.25e+01 angle pdb=" N VAL D 476 " pdb=" CA VAL D 476 " pdb=" C VAL D 476 " ideal model delta sigma weight residual 108.88 119.10 -10.22 2.16e+00 2.14e-01 2.24e+01 angle pdb=" N1A NAP A 401 " pdb=" C6A NAP A 401 " pdb=" N6A NAP A 401 " ideal model delta sigma weight residual 119.30 105.71 13.59 3.00e+00 1.11e-01 2.05e+01 ... (remaining 29519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 11312 16.68 - 33.36: 1227 33.36 - 50.03: 326 50.03 - 66.71: 99 66.71 - 83.39: 52 Dihedral angle restraints: 13016 sinusoidal: 5128 harmonic: 7888 Sorted by residual: dihedral pdb=" CA ILE D 366 " pdb=" C ILE D 366 " pdb=" N ARG D 367 " pdb=" CA ARG D 367 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CA ILE B 366 " pdb=" C ILE B 366 " pdb=" N ARG B 367 " pdb=" CA ARG B 367 " ideal model delta harmonic sigma weight residual 180.00 164.42 15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ILE H 366 " pdb=" C ILE H 366 " pdb=" N ARG H 367 " pdb=" CA ARG H 367 " ideal model delta harmonic sigma weight residual 180.00 164.43 15.57 0 5.00e+00 4.00e-02 9.69e+00 ... (remaining 13013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3027 0.090 - 0.179: 291 0.179 - 0.269: 14 0.269 - 0.359: 8 0.359 - 0.449: 4 Chirality restraints: 3344 Sorted by residual: chirality pdb=" C2B NAP A 401 " pdb=" C1B NAP A 401 " pdb=" C3B NAP A 401 " pdb=" O2B NAP A 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C2B NAP G 401 " pdb=" C1B NAP G 401 " pdb=" C3B NAP G 401 " pdb=" O2B NAP G 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C2B NAP E 401 " pdb=" C1B NAP E 401 " pdb=" C3B NAP E 401 " pdb=" O2B NAP E 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.31 -0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 3341 not shown) Planarity restraints: 3728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 431 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO H 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO H 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 432 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 431 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO F 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 432 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 431 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO B 432 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.050 5.00e-02 4.00e+02 ... (remaining 3725 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5560 2.77 - 3.31: 19082 3.31 - 3.84: 34344 3.84 - 4.37: 42181 4.37 - 4.90: 70644 Nonbonded interactions: 171811 Sorted by model distance: nonbonded pdb=" O TYR F 339 " pdb=" OG1 THR F 342 " model vdw 2.243 2.440 nonbonded pdb=" O TYR H 339 " pdb=" OG1 THR H 342 " model vdw 2.243 2.440 nonbonded pdb=" O TYR D 339 " pdb=" OG1 THR D 342 " model vdw 2.243 2.440 nonbonded pdb=" O TYR B 339 " pdb=" OG1 THR B 342 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR B 417 " pdb=" O SER B 429 " model vdw 2.286 2.440 ... (remaining 171806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 6.800 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 55.870 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.011 0.219 21724 Z= 0.693 Angle : 1.032 13.594 29524 Z= 0.525 Chirality : 0.059 0.449 3344 Planarity : 0.007 0.089 3728 Dihedral : 16.482 83.390 7944 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 18.17 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.11), residues: 2708 helix: -4.44 (0.05), residues: 1428 sheet: -3.08 (0.34), residues: 180 loop : -2.84 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 185 HIS 0.007 0.002 HIS A 135 PHE 0.012 0.001 PHE E 60 TYR 0.022 0.002 TYR C 270 ARG 0.003 0.001 ARG E 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8472 (tpp) cc_final: 0.8198 (tpt) REVERT: B 201 GLU cc_start: 0.7855 (tp30) cc_final: 0.7595 (tp30) REVERT: B 221 TRP cc_start: 0.5856 (t-100) cc_final: 0.5301 (t60) REVERT: B 222 LEU cc_start: 0.6578 (mm) cc_final: 0.6227 (mm) REVERT: B 242 LEU cc_start: 0.8358 (mt) cc_final: 0.8136 (mt) REVERT: B 245 LEU cc_start: 0.8383 (tt) cc_final: 0.8013 (pp) REVERT: B 488 HIS cc_start: 0.8362 (m-70) cc_final: 0.7795 (m90) REVERT: C 138 GLU cc_start: 0.7227 (mt-10) cc_final: 0.7025 (mt-10) REVERT: D 194 MET cc_start: 0.8455 (tpp) cc_final: 0.8175 (tpt) REVERT: D 201 GLU cc_start: 0.7917 (tp30) cc_final: 0.7678 (tp30) REVERT: D 221 TRP cc_start: 0.5912 (t-100) cc_final: 0.5342 (t60) REVERT: D 222 LEU cc_start: 0.6514 (mm) cc_final: 0.6170 (mm) REVERT: D 242 LEU cc_start: 0.8283 (mt) cc_final: 0.8039 (mt) REVERT: D 245 LEU cc_start: 0.8392 (tt) cc_final: 0.8008 (pp) REVERT: D 435 PHE cc_start: 0.8407 (m-10) cc_final: 0.7998 (m-80) REVERT: D 488 HIS cc_start: 0.8314 (m-70) cc_final: 0.7753 (m90) REVERT: E 138 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7006 (mt-10) REVERT: F 194 MET cc_start: 0.8463 (tpp) cc_final: 0.8181 (tpt) REVERT: F 201 GLU cc_start: 0.7816 (tp30) cc_final: 0.7572 (tp30) REVERT: F 221 TRP cc_start: 0.5847 (t-100) cc_final: 0.5199 (t60) REVERT: F 222 LEU cc_start: 0.6540 (mm) cc_final: 0.6180 (mm) REVERT: F 242 LEU cc_start: 0.8355 (mt) cc_final: 0.8129 (mt) REVERT: F 245 LEU cc_start: 0.8375 (tt) cc_final: 0.8005 (pp) REVERT: F 488 HIS cc_start: 0.8377 (m-70) cc_final: 0.7812 (m90) REVERT: G 138 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6990 (mt-10) REVERT: H 194 MET cc_start: 0.8464 (tpp) cc_final: 0.8105 (tpt) REVERT: H 201 GLU cc_start: 0.7834 (tp30) cc_final: 0.7565 (tp30) REVERT: H 221 TRP cc_start: 0.5847 (t-100) cc_final: 0.5184 (t60) REVERT: H 222 LEU cc_start: 0.6591 (mm) cc_final: 0.6232 (mm) REVERT: H 242 LEU cc_start: 0.8360 (mt) cc_final: 0.8136 (mt) REVERT: H 245 LEU cc_start: 0.8296 (tt) cc_final: 0.7903 (pp) REVERT: H 488 HIS cc_start: 0.8406 (m-70) cc_final: 0.7899 (m90) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.3740 time to fit residues: 297.4875 Evaluate side-chains 486 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 101 ASN A 135 HIS A 163 ASN A 204 GLN A 333 ASN C 63 GLN C 101 ASN C 135 HIS C 163 ASN C 204 GLN C 333 ASN E 63 GLN E 101 ASN E 135 HIS E 163 ASN E 204 GLN E 333 ASN G 63 GLN G 101 ASN G 135 HIS G 163 ASN G 204 GLN G 333 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21724 Z= 0.202 Angle : 0.590 8.339 29524 Z= 0.294 Chirality : 0.040 0.132 3344 Planarity : 0.005 0.048 3728 Dihedral : 9.675 54.203 3220 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.22 % Favored : 97.64 % Rotamer: Outliers : 1.72 % Allowed : 22.35 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.13), residues: 2708 helix: -2.81 (0.10), residues: 1420 sheet: -2.42 (0.36), residues: 176 loop : -2.13 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.004 0.001 HIS A 135 PHE 0.014 0.001 PHE D 296 TYR 0.016 0.001 TYR A 270 ARG 0.006 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 513 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7709 (mtp85) REVERT: B 192 GLU cc_start: 0.7544 (tp30) cc_final: 0.7137 (tp30) REVERT: B 194 MET cc_start: 0.8437 (tpp) cc_final: 0.8177 (tpt) REVERT: B 195 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: B 221 TRP cc_start: 0.5737 (t-100) cc_final: 0.5188 (t60) REVERT: B 372 PHE cc_start: 0.8385 (m-80) cc_final: 0.8174 (m-80) REVERT: B 488 HIS cc_start: 0.8248 (m-70) cc_final: 0.7877 (m-70) REVERT: C 138 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6845 (mt-10) REVERT: D 192 GLU cc_start: 0.7532 (tp30) cc_final: 0.7133 (tp30) REVERT: D 194 MET cc_start: 0.8400 (tpp) cc_final: 0.8137 (tpt) REVERT: D 195 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: D 221 TRP cc_start: 0.5736 (t-100) cc_final: 0.5201 (t60) REVERT: D 238 ILE cc_start: 0.8042 (tt) cc_final: 0.7619 (mp) REVERT: D 375 PHE cc_start: 0.8147 (m-80) cc_final: 0.7783 (m-80) REVERT: D 488 HIS cc_start: 0.8203 (m-70) cc_final: 0.7831 (m-70) REVERT: F 168 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7726 (mtp85) REVERT: F 192 GLU cc_start: 0.7535 (tp30) cc_final: 0.7158 (tp30) REVERT: F 194 MET cc_start: 0.8428 (tpp) cc_final: 0.8174 (tpt) REVERT: F 195 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: F 221 TRP cc_start: 0.5740 (t-100) cc_final: 0.5154 (t60) REVERT: F 436 TRP cc_start: 0.8006 (t-100) cc_final: 0.7653 (t-100) REVERT: F 488 HIS cc_start: 0.8256 (m-70) cc_final: 0.7943 (m-70) REVERT: G 138 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6773 (mt-10) REVERT: H 168 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7740 (mtp85) REVERT: H 192 GLU cc_start: 0.7642 (tp30) cc_final: 0.7261 (tp30) REVERT: H 194 MET cc_start: 0.8390 (tpp) cc_final: 0.8170 (tpt) REVERT: H 195 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: H 221 TRP cc_start: 0.5746 (t-100) cc_final: 0.5161 (t60) REVERT: H 372 PHE cc_start: 0.8335 (m-80) cc_final: 0.8130 (m-80) REVERT: H 436 TRP cc_start: 0.7968 (t-100) cc_final: 0.7613 (t-100) REVERT: H 484 ASN cc_start: 0.8622 (m-40) cc_final: 0.8074 (m110) REVERT: H 488 HIS cc_start: 0.8280 (m-70) cc_final: 0.7884 (m-70) outliers start: 37 outliers final: 12 residues processed: 540 average time/residue: 0.3612 time to fit residues: 286.7407 Evaluate side-chains 498 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 482 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 195 optimal weight: 0.6980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21724 Z= 0.254 Angle : 0.585 7.986 29524 Z= 0.288 Chirality : 0.041 0.133 3344 Planarity : 0.004 0.041 3728 Dihedral : 9.091 57.985 3220 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.18 % Favored : 96.68 % Rotamer: Outliers : 2.23 % Allowed : 23.65 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2708 helix: -1.72 (0.12), residues: 1456 sheet: -2.24 (0.36), residues: 176 loop : -1.63 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.003 0.001 HIS E 218 PHE 0.010 0.001 PHE D 486 TYR 0.017 0.001 TYR A 270 ARG 0.004 0.000 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 489 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7712 (mtp85) REVERT: B 192 GLU cc_start: 0.7522 (tp30) cc_final: 0.7066 (tp30) REVERT: B 195 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: B 198 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6729 (mtp85) REVERT: B 221 TRP cc_start: 0.5420 (t-100) cc_final: 0.4951 (t60) REVERT: B 372 PHE cc_start: 0.8369 (m-80) cc_final: 0.8099 (m-80) REVERT: B 375 PHE cc_start: 0.8159 (m-80) cc_final: 0.7833 (m-80) REVERT: B 488 HIS cc_start: 0.8347 (m-70) cc_final: 0.8032 (m170) REVERT: C 283 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7753 (mmm160) REVERT: D 192 GLU cc_start: 0.7508 (tp30) cc_final: 0.7077 (tp30) REVERT: D 194 MET cc_start: 0.8373 (tpp) cc_final: 0.8079 (tpt) REVERT: D 195 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: D 198 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6665 (mtp85) REVERT: D 221 TRP cc_start: 0.5387 (t-100) cc_final: 0.4889 (t60) REVERT: D 372 PHE cc_start: 0.8306 (m-80) cc_final: 0.8106 (m-80) REVERT: D 375 PHE cc_start: 0.8194 (m-80) cc_final: 0.7861 (m-80) REVERT: D 488 HIS cc_start: 0.8324 (m-70) cc_final: 0.7974 (m-70) REVERT: F 168 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7716 (mtp85) REVERT: F 192 GLU cc_start: 0.7590 (tp30) cc_final: 0.7138 (tp30) REVERT: F 195 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: F 198 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6672 (mtp85) REVERT: F 221 TRP cc_start: 0.5451 (t-100) cc_final: 0.4944 (t60) REVERT: F 250 ILE cc_start: 0.8867 (pt) cc_final: 0.8610 (mm) REVERT: F 372 PHE cc_start: 0.8314 (m-80) cc_final: 0.8105 (m-80) REVERT: F 375 PHE cc_start: 0.8181 (m-80) cc_final: 0.7842 (m-80) REVERT: F 436 TRP cc_start: 0.7962 (t-100) cc_final: 0.7577 (t-100) REVERT: F 488 HIS cc_start: 0.8350 (m-70) cc_final: 0.7966 (m-70) REVERT: G 138 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6750 (mt-10) REVERT: H 168 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7701 (mtp85) REVERT: H 192 GLU cc_start: 0.7563 (tp30) cc_final: 0.7140 (tp30) REVERT: H 194 MET cc_start: 0.8413 (tpp) cc_final: 0.8120 (tpt) REVERT: H 195 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: H 221 TRP cc_start: 0.5479 (t-100) cc_final: 0.4954 (t60) REVERT: H 250 ILE cc_start: 0.8862 (pt) cc_final: 0.8613 (mm) REVERT: H 372 PHE cc_start: 0.8359 (m-80) cc_final: 0.8096 (m-80) REVERT: H 375 PHE cc_start: 0.8177 (m-80) cc_final: 0.7843 (m-80) REVERT: H 436 TRP cc_start: 0.7967 (t-100) cc_final: 0.7587 (t-100) REVERT: H 484 ASN cc_start: 0.8651 (m-40) cc_final: 0.8084 (m110) REVERT: H 488 HIS cc_start: 0.8320 (m-70) cc_final: 0.7995 (m-70) outliers start: 48 outliers final: 31 residues processed: 516 average time/residue: 0.3957 time to fit residues: 303.9558 Evaluate side-chains 514 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 476 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 478 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 443 THR Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 305 GLN E 305 GLN G 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21724 Z= 0.285 Angle : 0.595 7.025 29524 Z= 0.290 Chirality : 0.043 0.297 3344 Planarity : 0.004 0.052 3728 Dihedral : 8.077 58.167 3220 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.18 % Favored : 96.68 % Rotamer: Outliers : 3.67 % Allowed : 22.91 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2708 helix: -1.18 (0.13), residues: 1480 sheet: -2.19 (0.36), residues: 176 loop : -1.46 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.003 0.001 HIS G 135 PHE 0.011 0.001 PHE H 412 TYR 0.018 0.001 TYR A 270 ARG 0.007 0.001 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 490 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7758 (mtp85) REVERT: B 192 GLU cc_start: 0.7546 (tp30) cc_final: 0.7100 (tp30) REVERT: B 195 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: B 250 ILE cc_start: 0.8988 (pp) cc_final: 0.8767 (mm) REVERT: B 375 PHE cc_start: 0.8139 (m-80) cc_final: 0.7694 (m-80) REVERT: B 403 PHE cc_start: 0.8155 (t80) cc_final: 0.7829 (t80) REVERT: B 436 TRP cc_start: 0.7952 (t-100) cc_final: 0.7556 (t-100) REVERT: B 488 HIS cc_start: 0.8460 (m-70) cc_final: 0.8067 (m-70) REVERT: C 283 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7875 (mmm160) REVERT: D 192 GLU cc_start: 0.7550 (tp30) cc_final: 0.7123 (tp30) REVERT: D 195 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: D 238 ILE cc_start: 0.8029 (tt) cc_final: 0.7684 (mp) REVERT: D 250 ILE cc_start: 0.8869 (pp) cc_final: 0.8631 (mm) REVERT: D 372 PHE cc_start: 0.8326 (m-80) cc_final: 0.8077 (m-80) REVERT: D 375 PHE cc_start: 0.8179 (m-80) cc_final: 0.7834 (m-80) REVERT: D 403 PHE cc_start: 0.8104 (t80) cc_final: 0.7762 (t80) REVERT: D 436 TRP cc_start: 0.7973 (t-100) cc_final: 0.7559 (t-100) REVERT: D 488 HIS cc_start: 0.8447 (m-70) cc_final: 0.8074 (m-70) REVERT: F 168 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7745 (mtp85) REVERT: F 192 GLU cc_start: 0.7559 (tp30) cc_final: 0.7129 (tp30) REVERT: F 195 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: F 372 PHE cc_start: 0.8320 (m-80) cc_final: 0.8085 (m-80) REVERT: F 375 PHE cc_start: 0.8162 (m-80) cc_final: 0.7820 (m-80) REVERT: F 403 PHE cc_start: 0.8114 (t80) cc_final: 0.7771 (t80) REVERT: F 436 TRP cc_start: 0.7951 (t-100) cc_final: 0.7558 (t-100) REVERT: F 488 HIS cc_start: 0.8420 (m-70) cc_final: 0.8075 (m90) REVERT: F 489 ARG cc_start: 0.7222 (mmp-170) cc_final: 0.7016 (mmp-170) REVERT: G 138 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6683 (mt-10) REVERT: H 168 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7739 (mtp85) REVERT: H 192 GLU cc_start: 0.7551 (tp30) cc_final: 0.7114 (tp30) REVERT: H 194 MET cc_start: 0.8406 (tpp) cc_final: 0.8102 (tpt) REVERT: H 195 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: H 375 PHE cc_start: 0.8149 (m-80) cc_final: 0.7725 (m-80) REVERT: H 403 PHE cc_start: 0.8149 (t80) cc_final: 0.7821 (t80) REVERT: H 488 HIS cc_start: 0.8427 (m-70) cc_final: 0.8164 (m90) outliers start: 79 outliers final: 50 residues processed: 538 average time/residue: 0.3546 time to fit residues: 283.0461 Evaluate side-chains 523 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 469 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 443 THR Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 305 GLN H 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21724 Z= 0.260 Angle : 0.582 7.558 29524 Z= 0.283 Chirality : 0.041 0.183 3344 Planarity : 0.004 0.041 3728 Dihedral : 7.553 54.109 3220 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.95 % Allowed : 23.28 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2708 helix: -0.72 (0.13), residues: 1452 sheet: -2.48 (0.36), residues: 172 loop : -1.34 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 221 HIS 0.004 0.001 HIS G 135 PHE 0.010 0.001 PHE H 412 TYR 0.017 0.001 TYR A 270 ARG 0.004 0.000 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 477 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7778 (mtp85) REVERT: B 192 GLU cc_start: 0.7577 (tp30) cc_final: 0.7250 (tp30) REVERT: B 194 MET cc_start: 0.8426 (tpp) cc_final: 0.8129 (tpt) REVERT: B 195 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: B 250 ILE cc_start: 0.8869 (pp) cc_final: 0.8571 (mm) REVERT: B 375 PHE cc_start: 0.8169 (m-80) cc_final: 0.7745 (m-80) REVERT: B 403 PHE cc_start: 0.8144 (t80) cc_final: 0.7797 (t80) REVERT: B 487 TYR cc_start: 0.8793 (t80) cc_final: 0.8550 (t80) REVERT: B 488 HIS cc_start: 0.8418 (m-70) cc_final: 0.8163 (m90) REVERT: D 192 GLU cc_start: 0.7580 (tp30) cc_final: 0.7095 (tp30) REVERT: D 194 MET cc_start: 0.8414 (tpp) cc_final: 0.8138 (tpt) REVERT: D 195 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: D 250 ILE cc_start: 0.8870 (pp) cc_final: 0.8588 (mm) REVERT: D 375 PHE cc_start: 0.8193 (m-80) cc_final: 0.7772 (m-80) REVERT: D 403 PHE cc_start: 0.8120 (t80) cc_final: 0.7758 (t80) REVERT: D 487 TYR cc_start: 0.8787 (t80) cc_final: 0.8536 (t80) REVERT: D 488 HIS cc_start: 0.8394 (m-70) cc_final: 0.8138 (m90) REVERT: F 168 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7770 (mtp85) REVERT: F 192 GLU cc_start: 0.7585 (tp30) cc_final: 0.7259 (tp30) REVERT: F 194 MET cc_start: 0.8398 (tpp) cc_final: 0.8117 (tpt) REVERT: F 195 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: F 375 PHE cc_start: 0.8201 (m-80) cc_final: 0.7783 (m-80) REVERT: F 403 PHE cc_start: 0.8132 (t80) cc_final: 0.7775 (t80) REVERT: F 487 TYR cc_start: 0.8793 (t80) cc_final: 0.8526 (t80) REVERT: F 488 HIS cc_start: 0.8430 (m-70) cc_final: 0.8126 (m90) REVERT: G 138 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6679 (mt-10) REVERT: H 168 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7748 (mtp85) REVERT: H 192 GLU cc_start: 0.7594 (tp30) cc_final: 0.7274 (tp30) REVERT: H 194 MET cc_start: 0.8409 (tpp) cc_final: 0.8083 (tpt) REVERT: H 195 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: H 375 PHE cc_start: 0.8171 (m-80) cc_final: 0.7739 (m-80) REVERT: H 403 PHE cc_start: 0.8142 (t80) cc_final: 0.7787 (t80) REVERT: H 487 TYR cc_start: 0.8793 (t80) cc_final: 0.8541 (t80) REVERT: H 488 HIS cc_start: 0.8386 (m-70) cc_final: 0.8125 (m90) outliers start: 85 outliers final: 53 residues processed: 535 average time/residue: 0.3365 time to fit residues: 268.9502 Evaluate side-chains 522 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 465 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 ASN D 482 ASN E 305 GLN F 482 ASN H 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21724 Z= 0.188 Angle : 0.567 6.928 29524 Z= 0.273 Chirality : 0.040 0.130 3344 Planarity : 0.004 0.054 3728 Dihedral : 6.954 52.884 3220 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.58 % Allowed : 23.93 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2708 helix: -0.43 (0.14), residues: 1468 sheet: -2.42 (0.36), residues: 172 loop : -1.34 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 221 HIS 0.003 0.001 HIS G 135 PHE 0.008 0.001 PHE F 404 TYR 0.014 0.001 TYR A 270 ARG 0.009 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 483 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7760 (mtp85) REVERT: B 192 GLU cc_start: 0.7584 (tp30) cc_final: 0.7248 (tp30) REVERT: B 194 MET cc_start: 0.8382 (tpp) cc_final: 0.8054 (tpt) REVERT: B 195 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: B 250 ILE cc_start: 0.8940 (pp) cc_final: 0.8647 (mm) REVERT: B 251 PHE cc_start: 0.8151 (t80) cc_final: 0.7937 (t80) REVERT: B 375 PHE cc_start: 0.8153 (m-80) cc_final: 0.7730 (m-80) REVERT: B 403 PHE cc_start: 0.8123 (t80) cc_final: 0.7756 (t80) REVERT: B 435 PHE cc_start: 0.8206 (m-10) cc_final: 0.7424 (m-80) REVERT: B 487 TYR cc_start: 0.8774 (t80) cc_final: 0.8428 (t80) REVERT: B 488 HIS cc_start: 0.8351 (m-70) cc_final: 0.8113 (m90) REVERT: D 192 GLU cc_start: 0.7583 (tp30) cc_final: 0.7245 (tp30) REVERT: D 194 MET cc_start: 0.8367 (tpp) cc_final: 0.8084 (tpt) REVERT: D 195 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: D 250 ILE cc_start: 0.8860 (pp) cc_final: 0.8579 (mm) REVERT: D 251 PHE cc_start: 0.8144 (t80) cc_final: 0.7923 (t80) REVERT: D 375 PHE cc_start: 0.8159 (m-80) cc_final: 0.7763 (m-80) REVERT: D 403 PHE cc_start: 0.8068 (t80) cc_final: 0.7677 (t80) REVERT: D 435 PHE cc_start: 0.8179 (m-10) cc_final: 0.7431 (m-80) REVERT: D 487 TYR cc_start: 0.8770 (t80) cc_final: 0.8421 (t80) REVERT: D 488 HIS cc_start: 0.8344 (m-70) cc_final: 0.8102 (m90) REVERT: F 168 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7768 (mtp85) REVERT: F 192 GLU cc_start: 0.7592 (tp30) cc_final: 0.7260 (tp30) REVERT: F 194 MET cc_start: 0.8373 (tpp) cc_final: 0.8025 (tpt) REVERT: F 195 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: F 375 PHE cc_start: 0.8185 (m-80) cc_final: 0.7783 (m-80) REVERT: F 403 PHE cc_start: 0.8101 (t80) cc_final: 0.7715 (t80) REVERT: F 435 PHE cc_start: 0.8170 (m-10) cc_final: 0.7428 (m-80) REVERT: F 487 TYR cc_start: 0.8773 (t80) cc_final: 0.8428 (t80) REVERT: F 488 HIS cc_start: 0.8331 (m-70) cc_final: 0.8090 (m90) REVERT: H 168 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7758 (mtp85) REVERT: H 192 GLU cc_start: 0.7613 (tp30) cc_final: 0.7286 (tp30) REVERT: H 194 MET cc_start: 0.8375 (tpp) cc_final: 0.8018 (tpt) REVERT: H 195 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: H 375 PHE cc_start: 0.8150 (m-80) cc_final: 0.7737 (m-80) REVERT: H 403 PHE cc_start: 0.8136 (t80) cc_final: 0.7764 (t80) REVERT: H 487 TYR cc_start: 0.8765 (t80) cc_final: 0.8405 (t80) REVERT: H 488 HIS cc_start: 0.8332 (m-70) cc_final: 0.8096 (m90) outliers start: 77 outliers final: 65 residues processed: 539 average time/residue: 0.3461 time to fit residues: 277.9937 Evaluate side-chains 537 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 468 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 443 THR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 chunk 218 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 ASN D 482 ASN E 305 GLN F 482 ASN H 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21724 Z= 0.187 Angle : 0.565 8.021 29524 Z= 0.274 Chirality : 0.041 0.203 3344 Planarity : 0.004 0.042 3728 Dihedral : 6.544 50.804 3220 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.28 % Allowed : 23.70 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2708 helix: -0.15 (0.14), residues: 1464 sheet: -2.33 (0.37), residues: 172 loop : -1.29 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 221 HIS 0.003 0.001 HIS G 135 PHE 0.018 0.001 PHE D 404 TYR 0.014 0.001 TYR A 270 ARG 0.005 0.000 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 490 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7744 (mtp85) REVERT: B 192 GLU cc_start: 0.7599 (tp30) cc_final: 0.7275 (tp30) REVERT: B 194 MET cc_start: 0.8383 (tpp) cc_final: 0.8100 (tpt) REVERT: B 195 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: B 250 ILE cc_start: 0.8929 (pp) cc_final: 0.8627 (mm) REVERT: B 251 PHE cc_start: 0.8163 (t80) cc_final: 0.7938 (t80) REVERT: B 375 PHE cc_start: 0.8148 (m-80) cc_final: 0.7725 (m-80) REVERT: B 435 PHE cc_start: 0.8173 (m-10) cc_final: 0.7444 (m-80) REVERT: B 484 ASN cc_start: 0.8597 (m-40) cc_final: 0.7994 (m110) REVERT: B 488 HIS cc_start: 0.8309 (m-70) cc_final: 0.7920 (m90) REVERT: C 256 ASP cc_start: 0.7341 (t70) cc_final: 0.6479 (t70) REVERT: D 192 GLU cc_start: 0.7544 (tp30) cc_final: 0.7183 (tp30) REVERT: D 194 MET cc_start: 0.8366 (tpp) cc_final: 0.8087 (tpt) REVERT: D 195 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: D 221 TRP cc_start: 0.4947 (t-100) cc_final: 0.4739 (t-100) REVERT: D 250 ILE cc_start: 0.8933 (pp) cc_final: 0.8634 (mm) REVERT: D 251 PHE cc_start: 0.8128 (t80) cc_final: 0.7895 (t80) REVERT: D 375 PHE cc_start: 0.8174 (m-80) cc_final: 0.7772 (m-80) REVERT: D 397 GLU cc_start: 0.7873 (mp0) cc_final: 0.7606 (mp0) REVERT: D 435 PHE cc_start: 0.8134 (m-10) cc_final: 0.7417 (m-80) REVERT: D 488 HIS cc_start: 0.8317 (m-70) cc_final: 0.7913 (m90) REVERT: F 192 GLU cc_start: 0.7611 (tp30) cc_final: 0.7271 (tp30) REVERT: F 194 MET cc_start: 0.8379 (tpp) cc_final: 0.8079 (tpt) REVERT: F 195 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: F 375 PHE cc_start: 0.8184 (m-80) cc_final: 0.7789 (m-80) REVERT: F 435 PHE cc_start: 0.8106 (m-10) cc_final: 0.7349 (m-80) REVERT: F 484 ASN cc_start: 0.8602 (m-40) cc_final: 0.8118 (m110) REVERT: H 168 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7741 (mtp85) REVERT: H 192 GLU cc_start: 0.7593 (tp30) cc_final: 0.7266 (tp30) REVERT: H 194 MET cc_start: 0.8379 (tpp) cc_final: 0.8025 (tpt) REVERT: H 195 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: H 375 PHE cc_start: 0.8111 (m-80) cc_final: 0.7694 (m-80) REVERT: H 484 ASN cc_start: 0.8602 (m-40) cc_final: 0.8123 (m110) outliers start: 92 outliers final: 73 residues processed: 558 average time/residue: 0.3379 time to fit residues: 282.6574 Evaluate side-chains 548 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 471 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 443 THR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 164 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 203 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 ASN E 305 GLN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 ASN ** H 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21724 Z= 0.201 Angle : 0.583 8.237 29524 Z= 0.282 Chirality : 0.040 0.144 3344 Planarity : 0.004 0.052 3728 Dihedral : 6.426 50.115 3220 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.23 % Allowed : 23.65 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2708 helix: -0.08 (0.14), residues: 1488 sheet: -2.25 (0.37), residues: 172 loop : -1.27 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 221 HIS 0.003 0.001 HIS C 135 PHE 0.014 0.001 PHE D 404 TYR 0.014 0.001 TYR A 270 ARG 0.012 0.001 ARG F 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5416 Ramachandran restraints generated. 2708 Oldfield, 0 Emsley, 2708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 485 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8202 (pp20) cc_final: 0.7834 (pp20) REVERT: B 168 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7734 (mtp85) REVERT: B 191 GLU cc_start: 0.8092 (pm20) cc_final: 0.7777 (pm20) REVERT: B 192 GLU cc_start: 0.7607 (tp30) cc_final: 0.7144 (tp30) REVERT: B 194 MET cc_start: 0.8390 (tpp) cc_final: 0.8109 (tpt) REVERT: B 195 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: B 250 ILE cc_start: 0.8924 (pp) cc_final: 0.8649 (mm) REVERT: B 375 PHE cc_start: 0.8089 (m-80) cc_final: 0.7681 (m-80) REVERT: B 403 PHE cc_start: 0.8031 (t80) cc_final: 0.7689 (t80) REVERT: B 435 PHE cc_start: 0.8108 (m-10) cc_final: 0.7360 (m-80) REVERT: B 484 ASN cc_start: 0.8599 (m-40) cc_final: 0.7993 (m110) REVERT: B 488 HIS cc_start: 0.8324 (m-70) cc_final: 0.7960 (m90) REVERT: D 192 GLU cc_start: 0.7513 (tp30) cc_final: 0.7190 (tp30) REVERT: D 194 MET cc_start: 0.8375 (tpp) cc_final: 0.8097 (tpt) REVERT: D 250 ILE cc_start: 0.8949 (pp) cc_final: 0.8666 (mm) REVERT: D 375 PHE cc_start: 0.8179 (m-80) cc_final: 0.7782 (m-80) REVERT: D 435 PHE cc_start: 0.8108 (m-10) cc_final: 0.7357 (m-80) REVERT: F 192 GLU cc_start: 0.7590 (tp30) cc_final: 0.7239 (tp30) REVERT: F 194 MET cc_start: 0.8388 (tpp) cc_final: 0.8049 (tpt) REVERT: F 195 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: F 375 PHE cc_start: 0.8201 (m-80) cc_final: 0.7818 (m-80) REVERT: F 435 PHE cc_start: 0.8096 (m-10) cc_final: 0.7350 (m-80) REVERT: F 484 ASN cc_start: 0.8482 (m-40) cc_final: 0.8055 (m110) REVERT: F 488 HIS cc_start: 0.8133 (m90) cc_final: 0.7847 (m90) REVERT: H 168 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7752 (mtp85) REVERT: H 192 GLU cc_start: 0.7613 (tp30) cc_final: 0.7256 (tp30) REVERT: H 194 MET cc_start: 0.8393 (tpp) cc_final: 0.8093 (tpt) REVERT: H 195 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: H 375 PHE cc_start: 0.8066 (m-80) cc_final: 0.7755 (m-80) REVERT: H 403 PHE cc_start: 0.8057 (t80) cc_final: 0.7720 (t80) REVERT: H 435 PHE cc_start: 0.8140 (m-10) cc_final: 0.7383 (m-80) REVERT: H 484 ASN cc_start: 0.8485 (m-40) cc_final: 0.8051 (m110) REVERT: H 488 HIS cc_start: 0.8107 (m90) cc_final: 0.7790 (m90) outliers start: 91 outliers final: 77 residues processed: 555 average time/residue: 0.3356 time to fit residues: 279.7770 Evaluate side-chains 555 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 475 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 295 PHE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 353 SER Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 295 PHE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 200 ASP Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 295 PHE Chi-restraints excluded: chain H residue 334 VAL Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 443 THR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 462 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7047 > 50: distance: 68 - 107: 28.603 distance: 73 - 83: 4.273 distance: 74 - 116: 22.823 distance: 83 - 84: 16.726 distance: 84 - 85: 36.123 distance: 84 - 87: 19.252 distance: 85 - 95: 45.480 distance: 87 - 88: 6.125 distance: 88 - 89: 18.204 distance: 88 - 90: 5.218 distance: 89 - 91: 16.749 distance: 90 - 92: 8.868 distance: 91 - 93: 11.558 distance: 92 - 93: 11.561 distance: 93 - 94: 7.915 distance: 95 - 96: 22.125 distance: 96 - 97: 19.827 distance: 96 - 99: 32.084 distance: 97 - 98: 12.664 distance: 97 - 107: 10.394 distance: 99 - 100: 13.520 distance: 100 - 101: 8.024 distance: 100 - 102: 31.836 distance: 102 - 104: 17.097 distance: 103 - 105: 31.228 distance: 104 - 105: 20.420 distance: 105 - 106: 17.761 distance: 107 - 108: 23.313 distance: 108 - 109: 26.615 distance: 108 - 111: 23.730 distance: 109 - 110: 17.907 distance: 109 - 116: 20.181 distance: 111 - 112: 28.381 distance: 112 - 113: 25.052 distance: 113 - 114: 6.799 distance: 113 - 115: 21.020 distance: 116 - 117: 4.758 distance: 117 - 118: 14.855 distance: 117 - 120: 16.894 distance: 118 - 119: 15.893 distance: 118 - 122: 28.409 distance: 120 - 121: 22.169 distance: 122 - 123: 9.079 distance: 123 - 124: 27.996 distance: 124 - 125: 12.982 distance: 124 - 126: 17.823 distance: 126 - 127: 25.767 distance: 127 - 128: 9.086 distance: 128 - 130: 29.544 distance: 130 - 131: 14.557 distance: 131 - 132: 11.147 distance: 131 - 134: 15.217 distance: 132 - 133: 3.537 distance: 132 - 141: 10.263 distance: 134 - 135: 12.712 distance: 136 - 137: 6.623 distance: 137 - 138: 11.575 distance: 138 - 139: 8.864 distance: 138 - 140: 15.431 distance: 141 - 142: 13.012 distance: 142 - 143: 5.974 distance: 142 - 145: 9.336 distance: 143 - 144: 6.522 distance: 143 - 149: 7.454 distance: 145 - 146: 10.153 distance: 145 - 147: 17.356 distance: 146 - 148: 18.937 distance: 149 - 150: 14.631 distance: 150 - 151: 22.725 distance: 150 - 153: 20.446 distance: 151 - 152: 37.473 distance: 151 - 160: 11.024 distance: 153 - 154: 34.501 distance: 154 - 155: 27.782 distance: 155 - 156: 16.041 distance: 156 - 157: 16.736 distance: 157 - 158: 9.934 distance: 157 - 159: 11.455 distance: 160 - 161: 26.379 distance: 161 - 162: 5.750 distance: 161 - 164: 16.597 distance: 162 - 163: 17.375 distance: 162 - 171: 27.261 distance: 164 - 165: 29.804 distance: 165 - 166: 19.402 distance: 166 - 167: 9.124 distance: 167 - 168: 27.030 distance: 168 - 169: 21.543 distance: 168 - 170: 12.866