Starting phenix.real_space_refine on Sat Mar 7 14:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ut7_20868/03_2026/6ut7_20868.map" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 12 5.21 5 S 54 5.16 5 C 29266 2.51 5 N 7730 2.21 5 O 7968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45062 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3193 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3218 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3178 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3227 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 374} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3186 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3183 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 16, 'TRANS': 375} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 17, 'TRANS': 396} Chain breaks: 4 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 21, 'ASP:plan': 12, 'ASN:plan1': 8, 'ARG:plan': 7, 'TYR:plan': 6, 'PHE:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 253 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: H, I, J, K, L, M, N Time building chain proxies: 13.42, per 1000 atoms: 0.30 Number of scatterers: 45062 At special positions: 0 Unit cell: (183.75, 213.75, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 32 15.00 Mg 12 11.99 O 7968 8.00 N 7730 7.00 C 29266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10388 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 60 sheets defined 47.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 197 through 208 removed outlier: 3.689A pdb=" N ASP A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.505A pdb=" N PHE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.775A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.798A pdb=" N THR A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 299 " --> pdb=" O ASP A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.626A pdb=" N GLU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.859A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.898A pdb=" N ILE A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.828A pdb=" N LEU A 419 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 removed outlier: 3.984A pdb=" N PHE A 438 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.625A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.541A pdb=" N LYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.720A pdb=" N LEU A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.596A pdb=" N HIS A 497 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 498 " --> pdb=" O ARG A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.144A pdb=" N ASN A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.615A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.554A pdb=" N ASN B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.934A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.972A pdb=" N ARG B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.568A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.559A pdb=" N ILE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.512A pdb=" N LEU B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.854A pdb=" N PHE B 438 " --> pdb=" O ARG B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 removed outlier: 4.314A pdb=" N LYS B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 4.129A pdb=" N ARG B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.373A pdb=" N ARG B 488 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.120A pdb=" N ASN B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 507 " --> pdb=" O PHE B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.714A pdb=" N LYS B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.666A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.517A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.790A pdb=" N VAL C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.202A pdb=" N ARG C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 318 through 337 removed outlier: 3.758A pdb=" N GLU C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 362 through 367 removed outlier: 3.682A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.578A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 427 removed outlier: 3.939A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 427' Processing helix chain 'C' and resid 435 through 439 removed outlier: 3.711A pdb=" N PHE C 438 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.578A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 471 removed outlier: 4.137A pdb=" N LYS C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 4.542A pdb=" N ARG C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.663A pdb=" N ILE C 536 " --> pdb=" O ASP C 532 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 540 " --> pdb=" O ILE C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.961A pdb=" N ASN D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 234 Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.759A pdb=" N ARG D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.535A pdb=" N ARG D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 336 removed outlier: 4.555A pdb=" N GLU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 removed outlier: 4.321A pdb=" N ASN D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.678A pdb=" N THR D 372 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 439 removed outlier: 3.905A pdb=" N PHE D 438 " --> pdb=" O ARG D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 476 through 491 removed outlier: 3.755A pdb=" N THR D 480 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.983A pdb=" N ASN D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 507 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 507' Processing helix chain 'D' and resid 509 through 518 Processing helix chain 'D' and resid 521 through 529 removed outlier: 3.760A pdb=" N PHE D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.522A pdb=" N ILE D 536 " --> pdb=" O ASP D 532 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 540 " --> pdb=" O ILE D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 4.049A pdb=" N ILE D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.521A pdb=" N MET E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.502A pdb=" N VAL E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 291 removed outlier: 3.959A pdb=" N ARG E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 Processing helix chain 'E' and resid 318 through 336 removed outlier: 4.160A pdb=" N GLU E 323 " --> pdb=" O PRO E 319 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 334 " --> pdb=" O ARG E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.560A pdb=" N GLY E 361 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.982A pdb=" N ILE E 371 " --> pdb=" O GLY E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.623A pdb=" N ARG E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 3.690A pdb=" N PHE E 438 " --> pdb=" O ARG E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.729A pdb=" N LYS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 471 Processing helix chain 'E' and resid 476 through 491 removed outlier: 4.164A pdb=" N ARG E 488 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.894A pdb=" N ASN E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL E 507 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 509 through 519 removed outlier: 3.502A pdb=" N TYR E 519 " --> pdb=" O HIS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 529 Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.553A pdb=" N TRP E 538 " --> pdb=" O GLU E 534 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 540 " --> pdb=" O ILE E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 581 removed outlier: 3.715A pdb=" N ILE E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.630A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 204 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.685A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.645A pdb=" N PHE F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.941A pdb=" N ARG F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE F 292 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 294 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 318 through 337 removed outlier: 4.026A pdb=" N GLU F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.537A pdb=" N LYS F 343 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU F 344 " --> pdb=" O LYS F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.530A pdb=" N ARG F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 426' Processing helix chain 'F' and resid 435 through 439 removed outlier: 3.872A pdb=" N PHE F 438 " --> pdb=" O ARG F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 451 removed outlier: 3.507A pdb=" N LYS F 450 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 451 " --> pdb=" O ILE F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 471 removed outlier: 3.569A pdb=" N ARG F 457 " --> pdb=" O LYS F 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 493 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.901A pdb=" N ASN F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 509 through 518 Processing helix chain 'F' and resid 521 through 529 Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.712A pdb=" N VAL F 539 " --> pdb=" O THR F 535 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 535 through 540' Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.639A pdb=" N ILE G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.624A pdb=" N SER G 61 " --> pdb=" O ILE G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.709A pdb=" N LEU G 114 " --> pdb=" O TRP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 134 removed outlier: 3.667A pdb=" N LEU G 133 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 162 Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.036A pdb=" N ARG G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 196 removed outlier: 4.002A pdb=" N LEU G 196 " --> pdb=" O PRO G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 225 removed outlier: 3.626A pdb=" N ARG G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'G' and resid 254 through 259 removed outlier: 3.909A pdb=" N VAL G 259 " --> pdb=" O HIS G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 267 No H-bonds generated for 'chain 'G' and resid 265 through 267' Processing helix chain 'G' and resid 268 through 279 removed outlier: 3.546A pdb=" N PHE G 272 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 274 " --> pdb=" O ARG G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 314 removed outlier: 3.629A pdb=" N GLU G 307 " --> pdb=" O GLU G 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL G 309 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 311 " --> pdb=" O GLU G 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 312 " --> pdb=" O ARG G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 364 removed outlier: 3.903A pdb=" N ARG G 363 " --> pdb=" O LEU G 360 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 364 " --> pdb=" O LYS G 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 360 through 364' Processing helix chain 'G' and resid 366 through 379 removed outlier: 3.694A pdb=" N GLN G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 375 " --> pdb=" O ARG G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 453 removed outlier: 3.701A pdb=" N ASN G 444 " --> pdb=" O LYS G 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 208 removed outlier: 3.690A pdb=" N ASP H 202 " --> pdb=" O TYR H 198 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 207 " --> pdb=" O MET H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 234 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.505A pdb=" N PHE H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 291 removed outlier: 3.775A pdb=" N ARG H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 removed outlier: 3.798A pdb=" N THR H 298 " --> pdb=" O GLU H 295 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE H 299 " --> pdb=" O ASP H 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 295 through 299' Processing helix chain 'H' and resid 300 through 313 Processing helix chain 'H' and resid 318 through 337 removed outlier: 3.626A pdb=" N GLU H 324 " --> pdb=" O THR H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 367 removed outlier: 3.860A pdb=" N PHE H 367 " --> pdb=" O ILE H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 374 removed outlier: 3.898A pdb=" N ILE H 371 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR H 372 " --> pdb=" O GLU H 369 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU H 374 " --> pdb=" O ILE H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 419 removed outlier: 3.828A pdb=" N LEU H 419 " --> pdb=" O ILE H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 3.983A pdb=" N PHE H 438 " --> pdb=" O ARG H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 449 removed outlier: 3.625A pdb=" N LYS H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 471 removed outlier: 3.541A pdb=" N LYS H 458 " --> pdb=" O THR H 454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS H 470 " --> pdb=" O GLU H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 490 removed outlier: 3.720A pdb=" N LEU H 482 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG H 488 " --> pdb=" O LYS H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 498 removed outlier: 3.596A pdb=" N HIS H 497 " --> pdb=" O ASP H 494 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG H 498 " --> pdb=" O ARG H 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 494 through 498' Processing helix chain 'H' and resid 503 through 507 removed outlier: 4.144A pdb=" N ASN H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL H 507 " --> pdb=" O PHE H 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 503 through 507' Processing helix chain 'H' and resid 509 through 520 Processing helix chain 'H' and resid 521 through 529 Processing helix chain 'H' and resid 533 through 540 Processing helix chain 'H' and resid 573 through 581 removed outlier: 3.616A pdb=" N ILE H 577 " --> pdb=" O GLY H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 584 No H-bonds generated for 'chain 'H' and resid 582 through 584' Processing helix chain 'I' and resid 194 through 207 removed outlier: 3.554A pdb=" N ASN I 206 " --> pdb=" O ASP I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 234 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 278 through 293 removed outlier: 3.934A pdb=" N GLU I 293 " --> pdb=" O LYS I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.972A pdb=" N ARG I 306 " --> pdb=" O ASP I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 337 removed outlier: 3.568A pdb=" N GLU I 334 " --> pdb=" O ARG I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 367 removed outlier: 3.559A pdb=" N ILE I 366 " --> pdb=" O ASN I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 379 removed outlier: 3.512A pdb=" N LEU I 374 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 375 " --> pdb=" O THR I 372 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS I 376 " --> pdb=" O LEU I 373 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP I 377 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG I 379 " --> pdb=" O LYS I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 439 removed outlier: 3.853A pdb=" N PHE I 438 " --> pdb=" O ARG I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 452 removed outlier: 4.314A pdb=" N LYS I 451 " --> pdb=" O ILE I 447 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 452 " --> pdb=" O ARG I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 removed outlier: 4.129A pdb=" N ARG I 459 " --> pdb=" O GLU I 455 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU I 466 " --> pdb=" O GLU I 462 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 491 removed outlier: 4.373A pdb=" N ARG I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 507 removed outlier: 4.119A pdb=" N ASN I 506 " --> pdb=" O TYR I 503 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 507 " --> pdb=" O PHE I 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 503 through 507' Processing helix chain 'I' and resid 509 through 520 Processing helix chain 'I' and resid 521 through 526 Processing helix chain 'I' and resid 532 through 540 removed outlier: 3.715A pdb=" N LYS I 537 " --> pdb=" O TRP I 533 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP I 538 " --> pdb=" O GLU I 534 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU I 540 " --> pdb=" O ILE I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 582 removed outlier: 3.667A pdb=" N ILE I 577 " --> pdb=" O GLY I 573 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG I 582 " --> pdb=" O GLY I 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 206 removed outlier: 3.515A pdb=" N VAL J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 234 removed outlier: 3.789A pdb=" N VAL J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 292 removed outlier: 4.202A pdb=" N ARG J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 310 Processing helix chain 'J' and resid 318 through 337 removed outlier: 3.758A pdb=" N GLU J 323 " --> pdb=" O PRO J 319 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU J 324 " --> pdb=" O THR J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 345 Processing helix chain 'J' and resid 362 through 367 removed outlier: 3.681A pdb=" N PHE J 367 " --> pdb=" O ILE J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 379 removed outlier: 3.579A pdb=" N ARG J 379 " --> pdb=" O LYS J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 427 removed outlier: 3.939A pdb=" N ARG J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE J 427 " --> pdb=" O LEU J 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 422 through 427' Processing helix chain 'J' and resid 435 through 439 removed outlier: 3.711A pdb=" N PHE J 438 " --> pdb=" O ARG J 435 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 451 removed outlier: 3.578A pdb=" N LEU J 444 " --> pdb=" O GLU J 440 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS J 450 " --> pdb=" O LYS J 446 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS J 451 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 471 removed outlier: 4.137A pdb=" N LYS J 458 " --> pdb=" O THR J 454 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG J 459 " --> pdb=" O GLU J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 493 removed outlier: 4.543A pdb=" N ARG J 488 " --> pdb=" O LYS J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 520 Processing helix chain 'J' and resid 521 through 529 Processing helix chain 'J' and resid 532 through 540 removed outlier: 3.663A pdb=" N ILE J 536 " --> pdb=" O ASP J 532 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP J 538 " --> pdb=" O GLU J 534 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU J 540 " --> pdb=" O ILE J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 579 Processing helix chain 'K' and resid 195 through 208 removed outlier: 3.961A pdb=" N ASN K 206 " --> pdb=" O ASP K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 234 Processing helix chain 'K' and resid 279 through 291 removed outlier: 3.759A pdb=" N ARG K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 310 removed outlier: 3.535A pdb=" N ARG K 306 " --> pdb=" O ASP K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 336 removed outlier: 4.556A pdb=" N GLU K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 346 removed outlier: 4.320A pdb=" N ASN K 346 " --> pdb=" O ASP K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 367 Processing helix chain 'K' and resid 368 through 372 removed outlier: 3.678A pdb=" N THR K 372 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 439 removed outlier: 3.905A pdb=" N PHE K 438 " --> pdb=" O ARG K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 449 Processing helix chain 'K' and resid 456 through 469 Processing helix chain 'K' and resid 476 through 491 removed outlier: 3.754A pdb=" N THR K 480 " --> pdb=" O TYR K 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 488 " --> pdb=" O LYS K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 507 removed outlier: 3.982A pdb=" N ASN K 506 " --> pdb=" O TYR K 503 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL K 507 " --> pdb=" O PHE K 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 503 through 507' Processing helix chain 'K' and resid 509 through 518 Processing helix chain 'K' and resid 521 through 529 removed outlier: 3.760A pdb=" N PHE K 529 " --> pdb=" O LEU K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 540 removed outlier: 3.522A pdb=" N ILE K 536 " --> pdb=" O ASP K 532 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP K 538 " --> pdb=" O GLU K 534 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU K 540 " --> pdb=" O ILE K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 581 removed outlier: 4.050A pdb=" N ILE K 577 " --> pdb=" O GLY K 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 209 removed outlier: 3.521A pdb=" N MET L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU L 204 " --> pdb=" O ARG L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 234 removed outlier: 3.501A pdb=" N VAL L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 291 removed outlier: 3.959A pdb=" N ARG L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 313 Processing helix chain 'L' and resid 318 through 336 removed outlier: 4.159A pdb=" N GLU L 323 " --> pdb=" O PRO L 319 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU L 324 " --> pdb=" O THR L 320 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 334 " --> pdb=" O ARG L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 361 removed outlier: 3.560A pdb=" N GLY L 361 " --> pdb=" O ILE L 358 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 367 Processing helix chain 'L' and resid 368 through 372 removed outlier: 3.983A pdb=" N ILE L 371 " --> pdb=" O GLY L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 425 removed outlier: 3.623A pdb=" N ARG L 425 " --> pdb=" O VAL L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 439 removed outlier: 3.690A pdb=" N PHE L 438 " --> pdb=" O ARG L 435 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 452 removed outlier: 3.728A pdb=" N LYS L 450 " --> pdb=" O LYS L 446 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS L 451 " --> pdb=" O ILE L 447 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 452 " --> pdb=" O ARG L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 471 Processing helix chain 'L' and resid 476 through 491 removed outlier: 4.164A pdb=" N ARG L 488 " --> pdb=" O LYS L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 507 removed outlier: 3.895A pdb=" N ASN L 506 " --> pdb=" O TYR L 503 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL L 507 " --> pdb=" O PHE L 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 503 through 507' Processing helix chain 'L' and resid 509 through 519 removed outlier: 3.502A pdb=" N TYR L 519 " --> pdb=" O HIS L 515 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 540 removed outlier: 3.553A pdb=" N TRP L 538 " --> pdb=" O GLU L 534 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU L 540 " --> pdb=" O ILE L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 573 through 581 removed outlier: 3.715A pdb=" N ILE L 577 " --> pdb=" O GLY L 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 206 removed outlier: 3.631A pdb=" N VAL M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN M 206 " --> pdb=" O ASP M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 233 removed outlier: 3.685A pdb=" N GLU M 231 " --> pdb=" O LYS M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 257 removed outlier: 3.643A pdb=" N PHE M 256 " --> pdb=" O SER M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 294 removed outlier: 3.941A pdb=" N ARG M 285 " --> pdb=" O LYS M 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE M 292 " --> pdb=" O VAL M 288 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU M 293 " --> pdb=" O LYS M 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU M 294 " --> pdb=" O GLY M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 312 Processing helix chain 'M' and resid 318 through 337 removed outlier: 4.026A pdb=" N GLU M 323 " --> pdb=" O PRO M 319 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU M 324 " --> pdb=" O THR M 320 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY M 337 " --> pdb=" O TRP M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 344 removed outlier: 3.536A pdb=" N LYS M 343 " --> pdb=" O PRO M 340 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 344 " --> pdb=" O LYS M 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 340 through 344' Processing helix chain 'M' and resid 362 through 367 Processing helix chain 'M' and resid 421 through 426 removed outlier: 3.530A pdb=" N ARG M 425 " --> pdb=" O VAL M 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 426 " --> pdb=" O ALA M 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 421 through 426' Processing helix chain 'M' and resid 435 through 439 removed outlier: 3.872A pdb=" N PHE M 438 " --> pdb=" O ARG M 435 " (cutoff:3.500A) Processing helix chain 'M' and resid 440 through 451 removed outlier: 3.508A pdb=" N LYS M 450 " --> pdb=" O LYS M 446 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS M 451 " --> pdb=" O ILE M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 471 removed outlier: 3.569A pdb=" N ARG M 457 " --> pdb=" O LYS M 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS M 458 " --> pdb=" O THR M 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG M 459 " --> pdb=" O GLU M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 476 through 493 Processing helix chain 'M' and resid 503 through 507 removed outlier: 3.901A pdb=" N ASN M 506 " --> pdb=" O TYR M 503 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 507 " --> pdb=" O PHE M 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 503 through 507' Processing helix chain 'M' and resid 509 through 518 Processing helix chain 'M' and resid 521 through 529 Processing helix chain 'M' and resid 535 through 540 removed outlier: 3.712A pdb=" N VAL M 539 " --> pdb=" O THR M 535 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 540 " --> pdb=" O ILE M 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 535 through 540' Processing helix chain 'M' and resid 573 through 581 Processing helix chain 'N' and resid 23 through 41 removed outlier: 3.638A pdb=" N ILE N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE N 32 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS N 33 " --> pdb=" O ASP N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 61 removed outlier: 3.624A pdb=" N SER N 61 " --> pdb=" O ILE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 3.709A pdb=" N LEU N 114 " --> pdb=" O TRP N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 134 removed outlier: 3.668A pdb=" N LEU N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 162 Processing helix chain 'N' and resid 185 through 190 removed outlier: 4.036A pdb=" N ARG N 190 " --> pdb=" O SER N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 196 removed outlier: 4.002A pdb=" N LEU N 196 " --> pdb=" O PRO N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 225 removed outlier: 3.627A pdb=" N ARG N 225 " --> pdb=" O ARG N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 231 through 243 Processing helix chain 'N' and resid 254 through 259 removed outlier: 3.909A pdb=" N VAL N 259 " --> pdb=" O HIS N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 267 No H-bonds generated for 'chain 'N' and resid 265 through 267' Processing helix chain 'N' and resid 268 through 279 removed outlier: 3.546A pdb=" N PHE N 272 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU N 274 " --> pdb=" O ARG N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 314 removed outlier: 3.629A pdb=" N GLU N 307 " --> pdb=" O GLU N 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL N 309 " --> pdb=" O PHE N 305 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL N 311 " --> pdb=" O GLU N 307 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 312 " --> pdb=" O ARG N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 364 removed outlier: 3.904A pdb=" N ARG N 363 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 364 " --> pdb=" O LYS N 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 360 through 364' Processing helix chain 'N' and resid 366 through 379 removed outlier: 3.694A pdb=" N GLN N 372 " --> pdb=" O ASP N 368 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL N 375 " --> pdb=" O ARG N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 440 through 453 removed outlier: 3.702A pdb=" N ASN N 444 " --> pdb=" O LYS N 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 246 removed outlier: 6.419A pdb=" N GLU A 243 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP A 356 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 245 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 211 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET A 409 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 213 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 430 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 212 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 263 Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AA5, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.497A pdb=" N GLU B 243 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 356 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 245 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 353 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 408 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 355 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASN B 410 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 211 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET B 409 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 213 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AA9, first strand: chain 'C' and resid 242 through 246 removed outlier: 6.350A pdb=" N GLU C 243 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP C 356 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE C 245 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN C 210 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE C 430 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 212 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 258 through 263 removed outlier: 3.562A pdb=" N ARG C 263 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 271 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AB4, first strand: chain 'D' and resid 242 through 244 removed outlier: 7.804A pdb=" N THR D 408 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE D 355 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN D 410 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 211 " --> pdb=" O GLY D 407 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET D 409 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 213 " --> pdb=" O MET D 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 258 through 262 removed outlier: 3.757A pdb=" N VAL D 273 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AB7, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB8, first strand: chain 'E' and resid 210 through 212 Processing sheet with id=AB9, first strand: chain 'E' and resid 258 through 263 removed outlier: 3.552A pdb=" N VAL E 273 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 271 " --> pdb=" O ARG E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AC2, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AC3, first strand: chain 'F' and resid 211 through 214 removed outlier: 5.944A pdb=" N ILE F 212 " --> pdb=" O ILE F 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 245 through 246 removed outlier: 6.710A pdb=" N ILE F 245 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 258 through 260 Processing sheet with id=AC6, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=AC7, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AC8, first strand: chain 'F' and resid 552 through 554 Processing sheet with id=AC9, first strand: chain 'G' and resid 6 through 10 removed outlier: 3.587A pdb=" N VAL G 83 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE G 294 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 14 through 16 Processing sheet with id=AD2, first strand: chain 'G' and resid 168 through 176 removed outlier: 3.841A pdb=" N LYS G 182 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 318 through 321 removed outlier: 3.622A pdb=" N TYR G 318 " --> pdb=" O ARG G 344 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL G 352 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE G 415 " --> pdb=" O ALA G 427 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 242 through 246 removed outlier: 6.419A pdb=" N GLU H 243 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASP H 356 " --> pdb=" O GLU H 243 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 245 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL H 211 " --> pdb=" O GLY H 407 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET H 409 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU H 213 " --> pdb=" O MET H 409 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE H 430 " --> pdb=" O GLN H 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE H 212 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 258 through 263 Processing sheet with id=AD6, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AD7, first strand: chain 'H' and resid 552 through 553 Processing sheet with id=AD8, first strand: chain 'I' and resid 242 through 246 removed outlier: 6.497A pdb=" N GLU I 243 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASP I 356 " --> pdb=" O GLU I 243 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE I 245 " --> pdb=" O ASP I 356 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU I 353 " --> pdb=" O ILE I 406 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR I 408 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE I 355 " --> pdb=" O THR I 408 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASN I 410 " --> pdb=" O ILE I 355 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL I 211 " --> pdb=" O GLY I 407 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET I 409 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU I 213 " --> pdb=" O MET I 409 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 258 through 262 Processing sheet with id=AE1, first strand: chain 'I' and resid 388 through 389 Processing sheet with id=AE2, first strand: chain 'I' and resid 552 through 554 Processing sheet with id=AE3, first strand: chain 'J' and resid 242 through 246 removed outlier: 6.350A pdb=" N GLU J 243 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP J 356 " --> pdb=" O GLU J 243 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE J 245 " --> pdb=" O ASP J 356 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN J 210 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE J 430 " --> pdb=" O GLN J 210 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 212 " --> pdb=" O ILE J 430 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 258 through 263 removed outlier: 3.562A pdb=" N ARG J 263 " --> pdb=" O ARG J 271 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 271 " --> pdb=" O ARG J 263 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'J' and resid 552 through 554 Processing sheet with id=AE7, first strand: chain 'K' and resid 242 through 244 removed outlier: 7.805A pdb=" N THR K 408 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE K 355 " --> pdb=" O THR K 408 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN K 410 " --> pdb=" O ILE K 355 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL K 211 " --> pdb=" O GLY K 407 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET K 409 " --> pdb=" O VAL K 211 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU K 213 " --> pdb=" O MET K 409 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 258 through 262 removed outlier: 3.757A pdb=" N VAL K 273 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 388 through 389 Processing sheet with id=AF1, first strand: chain 'K' and resid 552 through 554 Processing sheet with id=AF2, first strand: chain 'L' and resid 210 through 212 Processing sheet with id=AF3, first strand: chain 'L' and resid 258 through 263 removed outlier: 3.552A pdb=" N VAL L 273 " --> pdb=" O ARG L 261 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG L 271 " --> pdb=" O ARG L 263 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 388 through 389 Processing sheet with id=AF5, first strand: chain 'L' and resid 552 through 554 Processing sheet with id=AF6, first strand: chain 'M' and resid 211 through 214 removed outlier: 5.944A pdb=" N ILE M 212 " --> pdb=" O ILE M 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'M' and resid 245 through 246 removed outlier: 6.708A pdb=" N ILE M 245 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 258 through 260 Processing sheet with id=AF9, first strand: chain 'M' and resid 263 through 264 Processing sheet with id=AG1, first strand: chain 'M' and resid 388 through 389 Processing sheet with id=AG2, first strand: chain 'M' and resid 552 through 554 Processing sheet with id=AG3, first strand: chain 'N' and resid 6 through 10 removed outlier: 3.588A pdb=" N VAL N 83 " --> pdb=" O VAL N 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE N 294 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 14 through 16 Processing sheet with id=AG5, first strand: chain 'N' and resid 168 through 176 removed outlier: 3.841A pdb=" N LYS N 182 " --> pdb=" O GLU N 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 318 through 321 removed outlier: 3.622A pdb=" N TYR N 318 " --> pdb=" O ARG N 344 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL N 352 " --> pdb=" O VAL N 397 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE N 415 " --> pdb=" O ALA N 427 " (cutoff:3.500A) 1596 hydrogen bonds defined for protein. 4602 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: 10.46 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7415 1.32 - 1.44: 12146 1.44 - 1.57: 26381 1.57 - 1.69: 52 1.69 - 1.81: 100 Bond restraints: 46094 Sorted by residual: bond pdb=" CA ALA D 417 " pdb=" CB ALA D 417 " ideal model delta sigma weight residual 1.535 1.469 0.066 1.93e-02 2.68e+03 1.16e+01 bond pdb=" CA ALA K 417 " pdb=" CB ALA K 417 " ideal model delta sigma weight residual 1.535 1.470 0.065 1.93e-02 2.68e+03 1.13e+01 bond pdb=" CA ALA K 422 " pdb=" CB ALA K 422 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.74e-02 3.30e+03 1.02e+01 bond pdb=" CA ALA D 422 " pdb=" CB ALA D 422 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.74e-02 3.30e+03 9.94e+00 bond pdb=" C LEU K 423 " pdb=" O LEU K 423 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.39e-02 5.18e+03 7.59e+00 ... (remaining 46089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 60253 2.08 - 4.16: 1809 4.16 - 6.25: 236 6.25 - 8.33: 66 8.33 - 10.41: 6 Bond angle restraints: 62370 Sorted by residual: angle pdb=" N ILE C 485 " pdb=" CA ILE C 485 " pdb=" C ILE C 485 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" N ILE J 485 " pdb=" CA ILE J 485 " pdb=" C ILE J 485 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" N LEU D 423 " pdb=" CA LEU D 423 " pdb=" C LEU D 423 " ideal model delta sigma weight residual 112.94 105.11 7.83 1.41e+00 5.03e-01 3.08e+01 angle pdb=" N LEU K 423 " pdb=" CA LEU K 423 " pdb=" C LEU K 423 " ideal model delta sigma weight residual 112.94 105.14 7.80 1.41e+00 5.03e-01 3.06e+01 angle pdb=" CA ALA K 417 " pdb=" C ALA K 417 " pdb=" O ALA K 417 " ideal model delta sigma weight residual 121.46 115.61 5.85 1.17e+00 7.31e-01 2.50e+01 ... (remaining 62365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 27110 35.75 - 71.51: 482 71.51 - 107.26: 48 107.26 - 143.02: 0 143.02 - 178.77: 2 Dihedral angle restraints: 27642 sinusoidal: 11486 harmonic: 16156 Sorted by residual: dihedral pdb=" O2B GDP F 701 " pdb=" O3A GDP F 701 " pdb=" PB GDP F 701 " pdb=" PA GDP F 701 " ideal model delta sinusoidal sigma weight residual 180.00 1.23 178.77 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2B GDP M 701 " pdb=" O3A GDP M 701 " pdb=" PB GDP M 701 " pdb=" PA GDP M 701 " ideal model delta sinusoidal sigma weight residual 180.00 1.28 178.72 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GSP E 701 " pdb=" O3A GSP E 701 " pdb=" PB GSP E 701 " pdb=" PA GSP E 701 " ideal model delta sinusoidal sigma weight residual 93.55 170.01 -76.46 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 27639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 6072 0.080 - 0.160: 680 0.160 - 0.240: 67 0.240 - 0.320: 23 0.320 - 0.400: 4 Chirality restraints: 6846 Sorted by residual: chirality pdb=" CA ILE K 416 " pdb=" N ILE K 416 " pdb=" C ILE K 416 " pdb=" CB ILE K 416 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA ILE D 416 " pdb=" N ILE D 416 " pdb=" C ILE D 416 " pdb=" CB ILE D 416 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ASP D 420 " pdb=" N ASP D 420 " pdb=" C ASP D 420 " pdb=" CB ASP D 420 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 6843 not shown) Planarity restraints: 7814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 522 " -0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO H 523 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 523 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 523 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 522 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO A 523 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 237 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO C 238 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.034 5.00e-02 4.00e+02 ... (remaining 7811 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 811 2.67 - 3.23: 39510 3.23 - 3.79: 69275 3.79 - 4.34: 96067 4.34 - 4.90: 157280 Nonbonded interactions: 362943 Sorted by model distance: nonbonded pdb=" OG1 THR L 222 " pdb="MG MG L 702 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR E 222 " pdb="MG MG E 702 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR C 222 " pdb="MG MG C 702 " model vdw 2.131 2.170 nonbonded pdb=" OG1 THR J 222 " pdb="MG MG J 702 " model vdw 2.131 2.170 nonbonded pdb=" OG1 THR D 222 " pdb="MG MG D 702 " model vdw 2.143 2.170 ... (remaining 362938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' } 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 group one per residue 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: 1.200 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: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 42.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 46094 Z= 0.208 Angle : 0.842 10.412 62370 Z= 0.465 Chirality : 0.055 0.400 6846 Planarity : 0.006 0.075 7814 Dihedral : 14.740 178.770 17254 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.44 % Allowed : 6.46 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.08), residues: 5478 helix: -4.58 (0.04), residues: 2284 sheet: -2.80 (0.20), residues: 510 loop : -2.45 (0.10), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 459 TYR 0.018 0.002 TYR B 251 PHE 0.019 0.002 PHE G 294 TRP 0.015 0.002 TRP L 538 HIS 0.007 0.001 HIS M 515 Details of bonding type rmsd covalent geometry : bond 0.00451 (46094) covalent geometry : angle 0.84161 (62370) hydrogen bonds : bond 0.27941 ( 1596) hydrogen bonds : angle 9.70570 ( 4602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 1442 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 ASN cc_start: 0.8968 (t0) cc_final: 0.8615 (t0) REVERT: B 421 VAL cc_start: 0.8102 (t) cc_final: 0.7450 (t) REVERT: C 250 SER cc_start: 0.8221 (p) cc_final: 0.7907 (t) REVERT: C 439 LEU cc_start: 0.4985 (mt) cc_final: 0.4761 (mt) REVERT: C 513 LEU cc_start: 0.9148 (tp) cc_final: 0.8807 (tt) REVERT: C 574 ASP cc_start: 0.5577 (t70) cc_final: 0.5191 (t70) REVERT: D 359 ASN cc_start: 0.8964 (p0) cc_final: 0.8346 (p0) REVERT: D 364 SER cc_start: 0.8545 (m) cc_final: 0.7648 (t) REVERT: D 371 ILE cc_start: 0.7942 (tp) cc_final: 0.7531 (tp) REVERT: D 486 ASN cc_start: 0.7536 (m-40) cc_final: 0.7245 (m-40) REVERT: D 494 ASP cc_start: 0.7036 (p0) cc_final: 0.6729 (p0) REVERT: D 497 HIS cc_start: 0.6553 (m170) cc_final: 0.6197 (m170) REVERT: D 522 LEU cc_start: 0.8150 (tp) cc_final: 0.7933 (tp) REVERT: E 248 HIS cc_start: 0.9040 (p-80) cc_final: 0.8739 (p90) REVERT: E 363 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8217 (mm) REVERT: E 364 SER cc_start: 0.8493 (m) cc_final: 0.8177 (p) REVERT: E 370 LEU cc_start: 0.8907 (mp) cc_final: 0.8634 (mm) REVERT: G 65 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7688 (t) REVERT: G 196 LEU cc_start: 0.8384 (tp) cc_final: 0.7252 (tp) REVERT: G 197 ASN cc_start: 0.8317 (p0) cc_final: 0.7835 (p0) REVERT: G 205 GLU cc_start: 0.7550 (pt0) cc_final: 0.7334 (pt0) REVERT: G 207 ILE cc_start: 0.9168 (pt) cc_final: 0.8877 (pt) REVERT: G 208 GLU cc_start: 0.7283 (mp0) cc_final: 0.7006 (mp0) REVERT: I 410 ASN cc_start: 0.8979 (t0) cc_final: 0.8591 (t0) REVERT: I 421 VAL cc_start: 0.8117 (t) cc_final: 0.7465 (t) REVERT: J 250 SER cc_start: 0.8229 (p) cc_final: 0.7897 (t) REVERT: J 513 LEU cc_start: 0.9176 (tp) cc_final: 0.8839 (tt) REVERT: J 574 ASP cc_start: 0.5579 (t70) cc_final: 0.5171 (t70) REVERT: K 359 ASN cc_start: 0.8967 (p0) cc_final: 0.8348 (p0) REVERT: K 364 SER cc_start: 0.8589 (m) cc_final: 0.7596 (t) REVERT: K 371 ILE cc_start: 0.7907 (tp) cc_final: 0.7700 (tp) REVERT: K 486 ASN cc_start: 0.7548 (m-40) cc_final: 0.7282 (m-40) REVERT: K 494 ASP cc_start: 0.6991 (p0) cc_final: 0.6737 (p0) REVERT: K 497 HIS cc_start: 0.6552 (m170) cc_final: 0.6186 (m170) REVERT: K 522 LEU cc_start: 0.8169 (tp) cc_final: 0.7965 (tp) REVERT: K 530 TYR cc_start: 0.7332 (t80) cc_final: 0.7056 (t80) REVERT: L 248 HIS cc_start: 0.9049 (p-80) cc_final: 0.8722 (p90) REVERT: L 363 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8189 (mm) REVERT: L 364 SER cc_start: 0.8471 (m) cc_final: 0.8170 (p) REVERT: L 370 LEU cc_start: 0.8899 (mp) cc_final: 0.8608 (mm) REVERT: L 374 LEU cc_start: 0.8134 (mt) cc_final: 0.7923 (mt) REVERT: N 65 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (t) REVERT: N 196 LEU cc_start: 0.8383 (tp) cc_final: 0.7245 (tp) REVERT: N 197 ASN cc_start: 0.8310 (p0) cc_final: 0.7837 (p0) REVERT: N 199 PHE cc_start: 0.8572 (m-80) cc_final: 0.8291 (m-10) REVERT: N 205 GLU cc_start: 0.7534 (pt0) cc_final: 0.7301 (pt0) REVERT: N 207 ILE cc_start: 0.9166 (pt) cc_final: 0.8879 (pt) REVERT: N 208 GLU cc_start: 0.7278 (mp0) cc_final: 0.6971 (mp0) outliers start: 20 outliers final: 0 residues processed: 1454 average time/residue: 0.2908 time to fit residues: 683.2683 Evaluate side-chains 640 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 636 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 541 ASN A 549 ASN B 248 HIS B 515 HIS B 541 ASN C 248 HIS C 385 GLN C 465 ASN C 475 ASN D 248 HIS D 266 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 248 HIS E 249 GLN E 266 ASN E 346 ASN E 385 GLN E 443 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS F 266 ASN F 461 ASN F 465 ASN F 541 ASN F 549 ASN G 137 GLN G 162 GLN H 248 HIS H 541 ASN H 549 ASN I 248 HIS I 443 ASN I 515 HIS I 541 ASN J 248 HIS J 385 GLN J 465 ASN J 475 ASN J 497 HIS K 248 HIS K 266 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN L 248 HIS L 249 GLN L 266 ASN L 346 ASN L 385 GLN L 443 ASN ** L 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 HIS M 266 ASN M 461 ASN M 465 ASN ** M 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 541 ASN M 549 ASN M 567 GLN N 137 GLN N 162 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076326 restraints weight = 146761.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078567 restraints weight = 85146.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080104 restraints weight = 58728.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081095 restraints weight = 45604.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081638 restraints weight = 38666.927| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 46094 Z= 0.222 Angle : 0.700 9.749 62370 Z= 0.362 Chirality : 0.046 0.209 6846 Planarity : 0.005 0.061 7814 Dihedral : 6.932 169.412 6270 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.10), residues: 5478 helix: -2.11 (0.09), residues: 2328 sheet: -2.29 (0.19), residues: 650 loop : -1.95 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 424 TYR 0.027 0.002 TYR E 530 PHE 0.025 0.002 PHE M 429 TRP 0.024 0.002 TRP F 533 HIS 0.008 0.002 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00486 (46094) covalent geometry : angle 0.69995 (62370) hydrogen bonds : bond 0.04135 ( 1596) hydrogen bonds : angle 4.93287 ( 4602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 744 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 ILE cc_start: 0.8597 (tt) cc_final: 0.8387 (tt) REVERT: B 364 SER cc_start: 0.8149 (p) cc_final: 0.7846 (m) REVERT: C 291 LEU cc_start: 0.8922 (mp) cc_final: 0.8499 (tt) REVERT: C 374 LEU cc_start: 0.8897 (tp) cc_final: 0.8598 (tp) REVERT: C 377 ASP cc_start: 0.8430 (m-30) cc_final: 0.7787 (m-30) REVERT: C 513 LEU cc_start: 0.8976 (tp) cc_final: 0.8549 (tt) REVERT: D 359 ASN cc_start: 0.9371 (p0) cc_final: 0.9140 (p0) REVERT: D 364 SER cc_start: 0.9360 (m) cc_final: 0.8856 (t) REVERT: D 385 GLN cc_start: 0.6965 (pp30) cc_final: 0.6230 (pp30) REVERT: D 409 MET cc_start: 0.9050 (ppp) cc_final: 0.8637 (ppp) REVERT: D 423 LEU cc_start: 0.9801 (mt) cc_final: 0.9578 (mm) REVERT: D 497 HIS cc_start: 0.8606 (m170) cc_final: 0.8396 (m90) REVERT: E 203 MET cc_start: 0.8009 (tmm) cc_final: 0.7734 (tmm) REVERT: E 364 SER cc_start: 0.9370 (m) cc_final: 0.8980 (p) REVERT: E 413 ASP cc_start: 0.8412 (t0) cc_final: 0.7799 (m-30) REVERT: E 527 GLU cc_start: 0.8608 (tt0) cc_final: 0.8278 (tm-30) REVERT: F 210 GLN cc_start: 0.8354 (pm20) cc_final: 0.7909 (pm20) REVERT: F 567 GLN cc_start: 0.8735 (tt0) cc_final: 0.7936 (tt0) REVERT: G 80 PHE cc_start: 0.8707 (p90) cc_final: 0.8319 (p90) REVERT: G 152 LEU cc_start: 0.9720 (mt) cc_final: 0.9516 (mt) REVERT: G 196 LEU cc_start: 0.9226 (tp) cc_final: 0.8911 (tp) REVERT: G 206 LEU cc_start: 0.8959 (pt) cc_final: 0.8716 (pt) REVERT: G 222 GLU cc_start: 0.8543 (tt0) cc_final: 0.8202 (tt0) REVERT: G 266 GLU cc_start: 0.7686 (tp30) cc_final: 0.7439 (tp30) REVERT: H 203 MET cc_start: 0.8242 (ptm) cc_final: 0.8026 (ppp) REVERT: I 282 ILE cc_start: 0.8614 (tt) cc_final: 0.8408 (tt) REVERT: I 364 SER cc_start: 0.8132 (p) cc_final: 0.7875 (m) REVERT: I 409 MET cc_start: 0.8395 (tmm) cc_final: 0.8172 (tmm) REVERT: J 291 LEU cc_start: 0.8916 (mp) cc_final: 0.8505 (tt) REVERT: J 377 ASP cc_start: 0.8397 (m-30) cc_final: 0.7832 (m-30) REVERT: J 513 LEU cc_start: 0.9012 (tp) cc_final: 0.8596 (tt) REVERT: K 359 ASN cc_start: 0.9383 (p0) cc_final: 0.9147 (p0) REVERT: K 364 SER cc_start: 0.9349 (m) cc_final: 0.8855 (t) REVERT: K 385 GLN cc_start: 0.6529 (pp30) cc_final: 0.5970 (pp30) REVERT: K 409 MET cc_start: 0.9073 (ppp) cc_final: 0.8800 (ppp) REVERT: K 423 LEU cc_start: 0.9796 (mt) cc_final: 0.9583 (mm) REVERT: K 486 ASN cc_start: 0.8961 (m-40) cc_final: 0.8666 (m-40) REVERT: L 203 MET cc_start: 0.8058 (tmm) cc_final: 0.7704 (tmm) REVERT: L 364 SER cc_start: 0.9384 (m) cc_final: 0.9018 (p) REVERT: L 374 LEU cc_start: 0.9052 (mt) cc_final: 0.8836 (mt) REVERT: L 413 ASP cc_start: 0.8392 (t0) cc_final: 0.7780 (m-30) REVERT: L 527 GLU cc_start: 0.8660 (tt0) cc_final: 0.8294 (tm-30) REVERT: M 210 GLN cc_start: 0.8346 (pm20) cc_final: 0.7940 (pm20) REVERT: M 221 LYS cc_start: 0.8361 (mtmm) cc_final: 0.7794 (mtmm) REVERT: M 410 ASN cc_start: 0.8747 (m-40) cc_final: 0.8052 (t0) REVERT: M 567 GLN cc_start: 0.8697 (tt0) cc_final: 0.8202 (tt0) REVERT: N 122 MET cc_start: 0.7577 (mtm) cc_final: 0.7337 (mtt) REVERT: N 146 TYR cc_start: 0.7740 (t80) cc_final: 0.7389 (t80) REVERT: N 152 LEU cc_start: 0.9722 (mt) cc_final: 0.9507 (mt) REVERT: N 157 LEU cc_start: 0.9482 (tp) cc_final: 0.9256 (tp) REVERT: N 196 LEU cc_start: 0.9258 (tp) cc_final: 0.8968 (tp) REVERT: N 199 PHE cc_start: 0.8889 (m-80) cc_final: 0.8294 (m-10) REVERT: N 266 GLU cc_start: 0.7680 (tp30) cc_final: 0.7460 (tp30) outliers start: 8 outliers final: 0 residues processed: 750 average time/residue: 0.2604 time to fit residues: 329.5077 Evaluate side-chains 427 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 143 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 358 optimal weight: 0.9980 chunk 522 optimal weight: 0.5980 chunk 463 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 531 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 chunk 480 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 443 ASN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 206 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN E 486 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS H 210 GLN H 402 ASN ** J 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 515 HIS K 206 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 410 ASN L 486 ASN ** M 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN N 255 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078395 restraints weight = 145073.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080684 restraints weight = 83956.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082212 restraints weight = 57566.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083166 restraints weight = 44586.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083888 restraints weight = 37848.576| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 46094 Z= 0.118 Angle : 0.590 6.880 62370 Z= 0.298 Chirality : 0.043 0.212 6846 Planarity : 0.004 0.047 7814 Dihedral : 6.450 168.957 6270 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.11), residues: 5478 helix: -1.13 (0.10), residues: 2356 sheet: -1.99 (0.20), residues: 568 loop : -1.64 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 459 TYR 0.024 0.001 TYR L 530 PHE 0.027 0.001 PHE K 429 TRP 0.015 0.001 TRP B 223 HIS 0.007 0.001 HIS H 514 Details of bonding type rmsd covalent geometry : bond 0.00268 (46094) covalent geometry : angle 0.58968 (62370) hydrogen bonds : bond 0.03316 ( 1596) hydrogen bonds : angle 4.46199 ( 4602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 695 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8066 (ppp) cc_final: 0.7596 (ppp) REVERT: A 250 SER cc_start: 0.9273 (t) cc_final: 0.9067 (t) REVERT: A 387 ILE cc_start: 0.8828 (mm) cc_final: 0.8481 (pt) REVERT: A 530 TYR cc_start: 0.6517 (p90) cc_final: 0.6214 (t80) REVERT: A 532 ASP cc_start: 0.6953 (p0) cc_final: 0.5617 (t0) REVERT: B 364 SER cc_start: 0.8290 (p) cc_final: 0.8051 (m) REVERT: C 254 GLU cc_start: 0.8393 (mp0) cc_final: 0.8159 (mt-10) REVERT: C 257 ILE cc_start: 0.8528 (tt) cc_final: 0.8053 (tp) REVERT: C 291 LEU cc_start: 0.8869 (mp) cc_final: 0.8420 (tt) REVERT: C 366 ILE cc_start: 0.8338 (mm) cc_final: 0.8111 (mm) REVERT: C 513 LEU cc_start: 0.8922 (tp) cc_final: 0.8568 (tt) REVERT: C 561 ASN cc_start: 0.8088 (p0) cc_final: 0.7817 (t0) REVERT: D 347 LEU cc_start: 0.8093 (mp) cc_final: 0.7836 (mp) REVERT: D 385 GLN cc_start: 0.7010 (pp30) cc_final: 0.6407 (pp30) REVERT: D 486 ASN cc_start: 0.8709 (m110) cc_final: 0.8439 (m110) REVERT: D 497 HIS cc_start: 0.8696 (m170) cc_final: 0.8157 (m170) REVERT: E 527 GLU cc_start: 0.8553 (tt0) cc_final: 0.8241 (tm-30) REVERT: F 210 GLN cc_start: 0.8344 (pm20) cc_final: 0.7858 (pm20) REVERT: F 252 SER cc_start: 0.9034 (t) cc_final: 0.8029 (t) REVERT: F 524 LEU cc_start: 0.8386 (tp) cc_final: 0.8179 (tp) REVERT: G 80 PHE cc_start: 0.8699 (p90) cc_final: 0.8265 (p90) REVERT: G 137 GLN cc_start: 0.8865 (mt0) cc_final: 0.8592 (mt0) REVERT: G 157 LEU cc_start: 0.9354 (tp) cc_final: 0.9112 (tp) REVERT: G 196 LEU cc_start: 0.9326 (tp) cc_final: 0.8900 (tp) REVERT: G 197 ASN cc_start: 0.9006 (p0) cc_final: 0.8776 (p0) REVERT: G 199 PHE cc_start: 0.8627 (m-10) cc_final: 0.7878 (m-10) REVERT: G 206 LEU cc_start: 0.8897 (pt) cc_final: 0.8663 (pt) REVERT: G 240 MET cc_start: 0.9130 (tpp) cc_final: 0.8480 (mmm) REVERT: G 257 GLU cc_start: 0.8123 (tp30) cc_final: 0.7904 (tp30) REVERT: G 266 GLU cc_start: 0.7588 (tp30) cc_final: 0.7342 (tp30) REVERT: H 210 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: H 250 SER cc_start: 0.9298 (t) cc_final: 0.9082 (t) REVERT: H 363 ILE cc_start: 0.9351 (tp) cc_final: 0.9107 (tp) REVERT: H 377 ASP cc_start: 0.7788 (t0) cc_final: 0.7511 (t0) REVERT: H 387 ILE cc_start: 0.8845 (mm) cc_final: 0.8547 (pt) REVERT: H 532 ASP cc_start: 0.6981 (p0) cc_final: 0.5671 (t0) REVERT: H 552 PHE cc_start: 0.8331 (m-10) cc_final: 0.8083 (m-80) REVERT: I 364 SER cc_start: 0.8260 (p) cc_final: 0.8017 (m) REVERT: J 254 GLU cc_start: 0.8410 (mp0) cc_final: 0.8151 (mt-10) REVERT: J 291 LEU cc_start: 0.8877 (mp) cc_final: 0.8459 (tt) REVERT: J 366 ILE cc_start: 0.8354 (mm) cc_final: 0.8074 (mm) REVERT: J 513 LEU cc_start: 0.8939 (tp) cc_final: 0.8590 (tt) REVERT: J 561 ASN cc_start: 0.8093 (p0) cc_final: 0.7838 (t0) REVERT: J 567 GLN cc_start: 0.6127 (tm-30) cc_final: 0.5771 (tm-30) REVERT: K 347 LEU cc_start: 0.8000 (mp) cc_final: 0.7766 (mp) REVERT: K 385 GLN cc_start: 0.6709 (pp30) cc_final: 0.6068 (pp30) REVERT: L 203 MET cc_start: 0.7998 (tmm) cc_final: 0.7790 (tmm) REVERT: L 364 SER cc_start: 0.9128 (m) cc_final: 0.8927 (p) REVERT: L 374 LEU cc_start: 0.8975 (mt) cc_final: 0.8773 (mt) REVERT: L 512 ASP cc_start: 0.8490 (t0) cc_final: 0.7857 (t70) REVERT: L 527 GLU cc_start: 0.8601 (tt0) cc_final: 0.8205 (tm-30) REVERT: M 210 GLN cc_start: 0.8333 (pm20) cc_final: 0.7872 (pm20) REVERT: M 252 SER cc_start: 0.9021 (t) cc_final: 0.8066 (t) REVERT: M 410 ASN cc_start: 0.8561 (m-40) cc_final: 0.8314 (t0) REVERT: M 524 LEU cc_start: 0.8401 (tp) cc_final: 0.8174 (tp) REVERT: N 80 PHE cc_start: 0.8810 (p90) cc_final: 0.8225 (p90) REVERT: N 196 LEU cc_start: 0.9277 (tp) cc_final: 0.8890 (tp) REVERT: N 205 GLU cc_start: 0.7584 (pt0) cc_final: 0.7298 (pt0) REVERT: N 206 LEU cc_start: 0.8883 (pt) cc_final: 0.8673 (pt) REVERT: N 257 GLU cc_start: 0.8111 (tp30) cc_final: 0.7879 (tp30) REVERT: N 266 GLU cc_start: 0.7584 (tp30) cc_final: 0.7355 (tp30) outliers start: 3 outliers final: 0 residues processed: 696 average time/residue: 0.2455 time to fit residues: 293.7632 Evaluate side-chains 427 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 376 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 247 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN B 531 ASN D 443 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 188 GLN I 461 ASN I 531 ASN K 384 ASN K 443 ASN K 497 HIS ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 GLN ** M 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 188 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073325 restraints weight = 149621.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075451 restraints weight = 88102.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076862 restraints weight = 61240.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077715 restraints weight = 48076.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078376 restraints weight = 41355.125| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 46094 Z= 0.205 Angle : 0.660 9.787 62370 Z= 0.335 Chirality : 0.045 0.258 6846 Planarity : 0.004 0.049 7814 Dihedral : 6.445 171.421 6270 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.11), residues: 5478 helix: -0.52 (0.11), residues: 2378 sheet: -2.00 (0.18), residues: 700 loop : -1.35 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 285 TYR 0.024 0.002 TYR E 530 PHE 0.020 0.002 PHE L 247 TRP 0.030 0.002 TRP J 538 HIS 0.006 0.001 HIS J 248 Details of bonding type rmsd covalent geometry : bond 0.00457 (46094) covalent geometry : angle 0.65999 (62370) hydrogen bonds : bond 0.03327 ( 1596) hydrogen bonds : angle 4.37315 ( 4602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 564 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8680 (mp) cc_final: 0.8473 (mp) REVERT: A 552 PHE cc_start: 0.8268 (m-10) cc_final: 0.8053 (m-80) REVERT: A 576 PHE cc_start: 0.6508 (t80) cc_final: 0.6286 (t80) REVERT: B 378 LYS cc_start: 0.8950 (mptt) cc_final: 0.8725 (mmtt) REVERT: C 254 GLU cc_start: 0.8450 (mp0) cc_final: 0.8189 (mt-10) REVERT: C 257 ILE cc_start: 0.8381 (tt) cc_final: 0.8046 (tp) REVERT: C 291 LEU cc_start: 0.8844 (mp) cc_final: 0.8389 (tt) REVERT: C 513 LEU cc_start: 0.8923 (tp) cc_final: 0.8597 (tt) REVERT: D 385 GLN cc_start: 0.7132 (pp30) cc_final: 0.6574 (pp30) REVERT: E 249 GLN cc_start: 0.8435 (tp40) cc_final: 0.8057 (tp40) REVERT: E 413 ASP cc_start: 0.8405 (t0) cc_final: 0.7590 (m-30) REVERT: E 527 GLU cc_start: 0.8647 (tt0) cc_final: 0.8121 (tm-30) REVERT: F 210 GLN cc_start: 0.8259 (pm20) cc_final: 0.7926 (pm20) REVERT: F 252 SER cc_start: 0.8947 (t) cc_final: 0.8315 (t) REVERT: G 157 LEU cc_start: 0.9393 (tp) cc_final: 0.9182 (tp) REVERT: G 186 SER cc_start: 0.9264 (p) cc_final: 0.8833 (t) REVERT: G 195 GLN cc_start: 0.9069 (pt0) cc_final: 0.8869 (pt0) REVERT: G 196 LEU cc_start: 0.9430 (tp) cc_final: 0.8951 (tp) REVERT: G 199 PHE cc_start: 0.9051 (m-10) cc_final: 0.8295 (m-10) REVERT: G 222 GLU cc_start: 0.8683 (tt0) cc_final: 0.8457 (tt0) REVERT: G 266 GLU cc_start: 0.7906 (tp30) cc_final: 0.7521 (tp30) REVERT: G 376 TYR cc_start: 0.7327 (m-10) cc_final: 0.7088 (m-80) REVERT: H 250 SER cc_start: 0.9393 (t) cc_final: 0.9152 (t) REVERT: H 552 PHE cc_start: 0.8282 (m-10) cc_final: 0.8073 (m-80) REVERT: J 254 GLU cc_start: 0.8479 (mp0) cc_final: 0.8221 (mt-10) REVERT: J 291 LEU cc_start: 0.8829 (mp) cc_final: 0.8391 (tt) REVERT: J 385 GLN cc_start: 0.8459 (tt0) cc_final: 0.8191 (tt0) REVERT: J 513 LEU cc_start: 0.8894 (tp) cc_final: 0.8571 (tt) REVERT: J 532 ASP cc_start: 0.8324 (t70) cc_final: 0.8109 (t70) REVERT: J 561 ASN cc_start: 0.8257 (p0) cc_final: 0.8019 (t0) REVERT: K 385 GLN cc_start: 0.6830 (pp30) cc_final: 0.6319 (pp30) REVERT: L 249 GLN cc_start: 0.8390 (tp40) cc_final: 0.8023 (tp40) REVERT: L 413 ASP cc_start: 0.8320 (t70) cc_final: 0.7396 (m-30) REVERT: L 527 GLU cc_start: 0.8582 (tt0) cc_final: 0.8075 (tm-30) REVERT: M 210 GLN cc_start: 0.8212 (pm20) cc_final: 0.7766 (pm20) REVERT: N 137 GLN cc_start: 0.8920 (mt0) cc_final: 0.8693 (mt0) REVERT: N 186 SER cc_start: 0.9263 (p) cc_final: 0.8845 (t) REVERT: N 196 LEU cc_start: 0.9407 (tp) cc_final: 0.8992 (tp) REVERT: N 266 GLU cc_start: 0.7913 (tp30) cc_final: 0.7546 (tp30) outliers start: 1 outliers final: 0 residues processed: 564 average time/residue: 0.2453 time to fit residues: 239.9365 Evaluate side-chains 357 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 239 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 457 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 467 optimal weight: 0.9980 chunk 361 optimal weight: 1.9990 chunk 534 optimal weight: 0.6980 chunk 471 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS D 384 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 GLN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 475 ASN ** M 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075523 restraints weight = 147289.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077628 restraints weight = 86693.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079056 restraints weight = 60382.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080005 restraints weight = 47167.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080486 restraints weight = 40043.366| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46094 Z= 0.131 Angle : 0.583 8.113 62370 Z= 0.293 Chirality : 0.043 0.303 6846 Planarity : 0.004 0.049 7814 Dihedral : 6.257 178.455 6270 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.11), residues: 5478 helix: -0.22 (0.11), residues: 2390 sheet: -1.73 (0.20), residues: 582 loop : -1.23 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 285 TYR 0.021 0.001 TYR L 530 PHE 0.015 0.001 PHE H 576 TRP 0.025 0.001 TRP C 538 HIS 0.009 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00301 (46094) covalent geometry : angle 0.58340 (62370) hydrogen bonds : bond 0.02893 ( 1596) hydrogen bonds : angle 4.19742 ( 4602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 SER cc_start: 0.9365 (t) cc_final: 0.9086 (t) REVERT: A 552 PHE cc_start: 0.8180 (m-10) cc_final: 0.7961 (m-80) REVERT: A 576 PHE cc_start: 0.6598 (t80) cc_final: 0.6334 (t80) REVERT: B 251 TYR cc_start: 0.9241 (t80) cc_final: 0.9029 (t80) REVERT: C 291 LEU cc_start: 0.8847 (mp) cc_final: 0.8385 (tt) REVERT: C 513 LEU cc_start: 0.8857 (tp) cc_final: 0.8512 (tt) REVERT: C 526 MET cc_start: 0.8885 (mtp) cc_final: 0.8454 (mmm) REVERT: D 385 GLN cc_start: 0.7146 (pp30) cc_final: 0.6817 (pp30) REVERT: D 486 ASN cc_start: 0.8731 (m110) cc_final: 0.8431 (m110) REVERT: E 403 LEU cc_start: 0.8856 (tp) cc_final: 0.8655 (tt) REVERT: E 423 LEU cc_start: 0.9377 (tp) cc_final: 0.9162 (tp) REVERT: E 512 ASP cc_start: 0.8305 (t0) cc_final: 0.7741 (t70) REVERT: E 527 GLU cc_start: 0.8635 (tt0) cc_final: 0.8034 (tm-30) REVERT: F 210 GLN cc_start: 0.8227 (pm20) cc_final: 0.7870 (pm20) REVERT: G 157 LEU cc_start: 0.9366 (tp) cc_final: 0.9052 (tp) REVERT: G 177 LYS cc_start: 0.9144 (ptmt) cc_final: 0.8847 (ptpp) REVERT: G 186 SER cc_start: 0.9290 (p) cc_final: 0.8887 (t) REVERT: G 196 LEU cc_start: 0.9431 (tp) cc_final: 0.8889 (tp) REVERT: G 206 LEU cc_start: 0.8689 (pt) cc_final: 0.7823 (pt) REVERT: G 240 MET cc_start: 0.9219 (tpp) cc_final: 0.8995 (tpp) REVERT: G 266 GLU cc_start: 0.7785 (tp30) cc_final: 0.7488 (tp30) REVERT: G 376 TYR cc_start: 0.7542 (m-10) cc_final: 0.7293 (m-80) REVERT: H 250 SER cc_start: 0.9362 (t) cc_final: 0.9046 (t) REVERT: H 258 GLU cc_start: 0.8889 (pt0) cc_final: 0.8582 (pt0) REVERT: H 392 TYR cc_start: 0.8405 (m-80) cc_final: 0.8189 (m-80) REVERT: H 552 PHE cc_start: 0.8337 (m-10) cc_final: 0.8000 (m-80) REVERT: J 254 GLU cc_start: 0.8492 (mp0) cc_final: 0.8282 (mt-10) REVERT: J 291 LEU cc_start: 0.8870 (mp) cc_final: 0.8411 (tt) REVERT: J 385 GLN cc_start: 0.8397 (tt0) cc_final: 0.8171 (tt0) REVERT: J 513 LEU cc_start: 0.8885 (tp) cc_final: 0.8539 (tt) REVERT: J 526 MET cc_start: 0.8855 (mtp) cc_final: 0.8448 (mmm) REVERT: K 385 GLN cc_start: 0.6900 (pp30) cc_final: 0.6669 (pp30) REVERT: L 423 LEU cc_start: 0.9365 (tp) cc_final: 0.9162 (tp) REVERT: L 527 GLU cc_start: 0.8625 (tt0) cc_final: 0.7948 (tm-30) REVERT: M 210 GLN cc_start: 0.8336 (pm20) cc_final: 0.7921 (pm20) REVERT: N 152 LEU cc_start: 0.9650 (mt) cc_final: 0.9438 (mt) REVERT: N 177 LYS cc_start: 0.9173 (ptmt) cc_final: 0.8767 (ptpp) REVERT: N 186 SER cc_start: 0.9287 (p) cc_final: 0.8881 (t) REVERT: N 196 LEU cc_start: 0.9398 (tp) cc_final: 0.8857 (tp) REVERT: N 199 PHE cc_start: 0.8804 (m-10) cc_final: 0.8158 (m-10) REVERT: N 206 LEU cc_start: 0.8643 (pt) cc_final: 0.7829 (pt) REVERT: N 240 MET cc_start: 0.9277 (tpp) cc_final: 0.9045 (tpp) REVERT: N 266 GLU cc_start: 0.7797 (tp30) cc_final: 0.7472 (tp30) outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.2448 time to fit residues: 242.3799 Evaluate side-chains 380 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 250 optimal weight: 6.9990 chunk 384 optimal weight: 0.0970 chunk 182 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 492 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 541 ASN B 384 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN G 204 HIS H 541 ASN ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 561 ASN ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071787 restraints weight = 151014.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073727 restraints weight = 90010.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075066 restraints weight = 63597.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075839 restraints weight = 50289.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076440 restraints weight = 43562.793| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 46094 Z= 0.234 Angle : 0.669 8.739 62370 Z= 0.339 Chirality : 0.045 0.319 6846 Planarity : 0.004 0.050 7814 Dihedral : 6.383 171.326 6270 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.11), residues: 5478 helix: 0.01 (0.11), residues: 2406 sheet: -1.89 (0.19), residues: 668 loop : -1.08 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 424 TYR 0.026 0.002 TYR C 566 PHE 0.017 0.002 PHE H 576 TRP 0.038 0.002 TRP J 538 HIS 0.006 0.001 HIS N 255 Details of bonding type rmsd covalent geometry : bond 0.00522 (46094) covalent geometry : angle 0.66923 (62370) hydrogen bonds : bond 0.03203 ( 1596) hydrogen bonds : angle 4.36657 ( 4602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 SER cc_start: 0.9408 (t) cc_final: 0.9151 (t) REVERT: A 551 PHE cc_start: 0.6138 (m-80) cc_final: 0.5652 (m-80) REVERT: A 552 PHE cc_start: 0.8329 (m-10) cc_final: 0.8005 (m-80) REVERT: B 364 SER cc_start: 0.8603 (m) cc_final: 0.8213 (m) REVERT: C 291 LEU cc_start: 0.8891 (mp) cc_final: 0.8412 (tt) REVERT: C 385 GLN cc_start: 0.8437 (tt0) cc_final: 0.8118 (tt0) REVERT: C 513 LEU cc_start: 0.8876 (tp) cc_final: 0.8543 (tt) REVERT: D 385 GLN cc_start: 0.7339 (pp30) cc_final: 0.6706 (pp30) REVERT: D 486 ASN cc_start: 0.8847 (m110) cc_final: 0.8614 (m110) REVERT: E 249 GLN cc_start: 0.8665 (mt0) cc_final: 0.8455 (tt0) REVERT: E 403 LEU cc_start: 0.8919 (tp) cc_final: 0.8613 (tt) REVERT: E 527 GLU cc_start: 0.8743 (tt0) cc_final: 0.8116 (tm-30) REVERT: E 583 ILE cc_start: 0.9124 (mp) cc_final: 0.8908 (mp) REVERT: F 210 GLN cc_start: 0.8323 (pm20) cc_final: 0.7945 (pm20) REVERT: G 146 TYR cc_start: 0.8228 (t80) cc_final: 0.7853 (t80) REVERT: G 186 SER cc_start: 0.9253 (p) cc_final: 0.8972 (p) REVERT: G 196 LEU cc_start: 0.9455 (tp) cc_final: 0.8917 (tp) REVERT: G 266 GLU cc_start: 0.7959 (tp30) cc_final: 0.7627 (tp30) REVERT: G 376 TYR cc_start: 0.7804 (m-10) cc_final: 0.7572 (m-80) REVERT: H 250 SER cc_start: 0.9415 (t) cc_final: 0.9129 (t) REVERT: H 258 GLU cc_start: 0.8764 (pt0) cc_final: 0.8453 (pt0) REVERT: H 392 TYR cc_start: 0.8398 (m-80) cc_final: 0.8044 (m-10) REVERT: H 551 PHE cc_start: 0.6127 (m-80) cc_final: 0.5729 (m-80) REVERT: H 552 PHE cc_start: 0.8373 (m-10) cc_final: 0.8052 (m-80) REVERT: J 254 GLU cc_start: 0.8554 (mp0) cc_final: 0.8244 (mt-10) REVERT: J 291 LEU cc_start: 0.8909 (mp) cc_final: 0.8445 (tt) REVERT: J 385 GLN cc_start: 0.8425 (tt0) cc_final: 0.8218 (tt0) REVERT: J 513 LEU cc_start: 0.8900 (tp) cc_final: 0.8575 (tt) REVERT: J 526 MET cc_start: 0.8869 (mtp) cc_final: 0.8574 (mmm) REVERT: K 385 GLN cc_start: 0.7100 (pp30) cc_final: 0.6570 (pp30) REVERT: L 527 GLU cc_start: 0.8790 (tt0) cc_final: 0.8133 (tm-30) REVERT: L 583 ILE cc_start: 0.9124 (mp) cc_final: 0.8918 (mp) REVERT: M 210 GLN cc_start: 0.8317 (pm20) cc_final: 0.7911 (pm20) REVERT: N 146 TYR cc_start: 0.8178 (t80) cc_final: 0.7796 (t80) REVERT: N 186 SER cc_start: 0.9307 (p) cc_final: 0.8863 (t) REVERT: N 196 LEU cc_start: 0.9451 (tp) cc_final: 0.8959 (tp) REVERT: N 206 LEU cc_start: 0.8506 (pt) cc_final: 0.8209 (pt) REVERT: N 266 GLU cc_start: 0.7969 (tp30) cc_final: 0.7637 (tp30) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.2318 time to fit residues: 203.0624 Evaluate side-chains 340 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 86 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 508 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 271 optimal weight: 0.0020 chunk 349 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 548 optimal weight: 8.9990 chunk 377 optimal weight: 8.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 HIS D 549 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN G 255 HIS I 384 ASN ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN N 255 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073604 restraints weight = 149472.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075647 restraints weight = 88800.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076983 restraints weight = 62294.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077854 restraints weight = 49305.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078327 restraints weight = 42466.341| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 46094 Z= 0.144 Angle : 0.596 8.579 62370 Z= 0.300 Chirality : 0.044 0.315 6846 Planarity : 0.004 0.049 7814 Dihedral : 6.224 168.417 6270 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.11), residues: 5478 helix: 0.19 (0.11), residues: 2394 sheet: -1.77 (0.20), residues: 614 loop : -0.99 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 226 TYR 0.026 0.001 TYR D 528 PHE 0.019 0.001 PHE H 576 TRP 0.031 0.001 TRP C 538 HIS 0.007 0.001 HIS K 514 Details of bonding type rmsd covalent geometry : bond 0.00331 (46094) covalent geometry : angle 0.59593 (62370) hydrogen bonds : bond 0.02899 ( 1596) hydrogen bonds : angle 4.22457 ( 4602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8534 (mp) cc_final: 0.7925 (mp) REVERT: A 250 SER cc_start: 0.9363 (t) cc_final: 0.9076 (t) REVERT: A 258 GLU cc_start: 0.8871 (pt0) cc_final: 0.8456 (pt0) REVERT: A 551 PHE cc_start: 0.6110 (m-80) cc_final: 0.5810 (m-80) REVERT: A 552 PHE cc_start: 0.8333 (m-10) cc_final: 0.8003 (m-80) REVERT: C 291 LEU cc_start: 0.8868 (mp) cc_final: 0.8411 (tt) REVERT: C 385 GLN cc_start: 0.8360 (tt0) cc_final: 0.8128 (tt0) REVERT: C 513 LEU cc_start: 0.8866 (tp) cc_final: 0.8495 (tt) REVERT: C 526 MET cc_start: 0.8800 (mtp) cc_final: 0.8508 (mmm) REVERT: D 385 GLN cc_start: 0.7353 (pp30) cc_final: 0.6770 (pp30) REVERT: E 527 GLU cc_start: 0.8782 (tt0) cc_final: 0.8136 (tm-30) REVERT: F 210 GLN cc_start: 0.8031 (pm20) cc_final: 0.7670 (pm20) REVERT: F 252 SER cc_start: 0.9381 (p) cc_final: 0.9089 (t) REVERT: F 561 ASN cc_start: 0.7605 (p0) cc_final: 0.7342 (p0) REVERT: G 146 TYR cc_start: 0.7983 (t80) cc_final: 0.7665 (t80) REVERT: G 196 LEU cc_start: 0.9447 (tp) cc_final: 0.8882 (tp) REVERT: G 263 ARG cc_start: 0.8984 (ppt170) cc_final: 0.8599 (ttp80) REVERT: G 266 GLU cc_start: 0.7902 (tp30) cc_final: 0.7515 (tp30) REVERT: G 376 TYR cc_start: 0.7769 (m-10) cc_final: 0.7549 (m-80) REVERT: H 250 SER cc_start: 0.9399 (t) cc_final: 0.9083 (t) REVERT: H 258 GLU cc_start: 0.8801 (pt0) cc_final: 0.8383 (pt0) REVERT: H 392 TYR cc_start: 0.8418 (m-80) cc_final: 0.8058 (m-80) REVERT: H 551 PHE cc_start: 0.6195 (m-80) cc_final: 0.5781 (m-80) REVERT: H 552 PHE cc_start: 0.8380 (m-10) cc_final: 0.8015 (m-80) REVERT: I 250 SER cc_start: 0.9234 (t) cc_final: 0.9023 (t) REVERT: J 254 GLU cc_start: 0.8539 (mp0) cc_final: 0.8337 (mt-10) REVERT: J 291 LEU cc_start: 0.8834 (mp) cc_final: 0.8406 (tt) REVERT: J 513 LEU cc_start: 0.8864 (tp) cc_final: 0.8499 (tt) REVERT: J 526 MET cc_start: 0.8799 (mtp) cc_final: 0.8427 (mmm) REVERT: K 385 GLN cc_start: 0.7380 (pp30) cc_final: 0.6916 (pp30) REVERT: L 527 GLU cc_start: 0.8725 (tt0) cc_final: 0.8074 (tm-30) REVERT: M 210 GLN cc_start: 0.8104 (pm20) cc_final: 0.7776 (pm20) REVERT: N 146 TYR cc_start: 0.7936 (t80) cc_final: 0.7611 (t80) REVERT: N 186 SER cc_start: 0.9297 (p) cc_final: 0.8887 (t) REVERT: N 196 LEU cc_start: 0.9449 (tp) cc_final: 0.8895 (tp) REVERT: N 257 GLU cc_start: 0.8043 (tp30) cc_final: 0.7799 (tp30) REVERT: N 263 ARG cc_start: 0.9013 (ppt170) cc_final: 0.8595 (ttp80) REVERT: N 266 GLU cc_start: 0.7895 (tp30) cc_final: 0.7543 (tp30) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.2404 time to fit residues: 220.0263 Evaluate side-chains 359 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 374 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 342 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 452 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 GLN ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 385 GLN K 549 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN N 204 HIS N 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072438 restraints weight = 152310.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074430 restraints weight = 90478.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075743 restraints weight = 63592.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.076601 restraints weight = 50552.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.077142 restraints weight = 43554.671| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 46094 Z= 0.174 Angle : 0.624 9.968 62370 Z= 0.314 Chirality : 0.045 0.338 6846 Planarity : 0.004 0.044 7814 Dihedral : 6.216 173.600 6270 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.11), residues: 5478 helix: 0.30 (0.11), residues: 2388 sheet: -1.78 (0.18), residues: 720 loop : -0.88 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 424 TYR 0.028 0.002 TYR I 214 PHE 0.022 0.002 PHE N 38 TRP 0.032 0.001 TRP C 538 HIS 0.019 0.001 HIS J 515 Details of bonding type rmsd covalent geometry : bond 0.00394 (46094) covalent geometry : angle 0.62432 (62370) hydrogen bonds : bond 0.02907 ( 1596) hydrogen bonds : angle 4.23852 ( 4602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8686 (mp) cc_final: 0.8477 (mp) REVERT: A 250 SER cc_start: 0.9356 (t) cc_final: 0.9107 (t) REVERT: A 258 GLU cc_start: 0.8777 (pt0) cc_final: 0.8428 (pt0) REVERT: A 551 PHE cc_start: 0.6133 (m-80) cc_final: 0.5796 (m-80) REVERT: A 552 PHE cc_start: 0.8436 (m-10) cc_final: 0.8094 (m-80) REVERT: C 291 LEU cc_start: 0.8833 (mp) cc_final: 0.8383 (tt) REVERT: C 385 GLN cc_start: 0.8384 (tt0) cc_final: 0.8116 (tt0) REVERT: C 513 LEU cc_start: 0.8842 (tp) cc_final: 0.8436 (tt) REVERT: C 526 MET cc_start: 0.8771 (mtp) cc_final: 0.8309 (mmm) REVERT: D 385 GLN cc_start: 0.7400 (pp30) cc_final: 0.6750 (pp30) REVERT: E 527 GLU cc_start: 0.8810 (tt0) cc_final: 0.8147 (tm-30) REVERT: E 583 ILE cc_start: 0.9099 (mp) cc_final: 0.8810 (mp) REVERT: F 203 MET cc_start: 0.7868 (tmm) cc_final: 0.7572 (tmm) REVERT: F 210 GLN cc_start: 0.8097 (pm20) cc_final: 0.7725 (pm20) REVERT: F 561 ASN cc_start: 0.7708 (p0) cc_final: 0.7425 (p0) REVERT: G 146 TYR cc_start: 0.8040 (t80) cc_final: 0.7736 (t80) REVERT: G 196 LEU cc_start: 0.9465 (tp) cc_final: 0.8876 (tp) REVERT: G 207 ILE cc_start: 0.9198 (pt) cc_final: 0.8955 (pt) REVERT: G 240 MET cc_start: 0.9223 (tpp) cc_final: 0.8988 (tpp) REVERT: G 263 ARG cc_start: 0.8994 (ppt170) cc_final: 0.8560 (ttp80) REVERT: G 266 GLU cc_start: 0.7931 (tp30) cc_final: 0.7564 (tp30) REVERT: H 250 SER cc_start: 0.9389 (t) cc_final: 0.9120 (t) REVERT: H 258 GLU cc_start: 0.8796 (pt0) cc_final: 0.8303 (pt0) REVERT: H 392 TYR cc_start: 0.8414 (m-80) cc_final: 0.8050 (m-80) REVERT: H 551 PHE cc_start: 0.5856 (m-80) cc_final: 0.5632 (m-80) REVERT: H 552 PHE cc_start: 0.8439 (m-10) cc_final: 0.8089 (m-80) REVERT: I 533 TRP cc_start: 0.8402 (m100) cc_final: 0.7584 (m100) REVERT: J 291 LEU cc_start: 0.8848 (mp) cc_final: 0.8434 (tt) REVERT: J 526 MET cc_start: 0.8802 (mtp) cc_final: 0.8414 (mmm) REVERT: K 385 GLN cc_start: 0.7308 (pp30) cc_final: 0.6819 (pp30) REVERT: L 527 GLU cc_start: 0.8787 (tt0) cc_final: 0.8114 (tm-30) REVERT: L 583 ILE cc_start: 0.9113 (mp) cc_final: 0.8827 (mp) REVERT: M 203 MET cc_start: 0.7835 (tmm) cc_final: 0.7591 (tmm) REVERT: M 210 GLN cc_start: 0.8127 (pm20) cc_final: 0.7663 (pm20) REVERT: M 561 ASN cc_start: 0.7712 (p0) cc_final: 0.7490 (p0) REVERT: N 146 TYR cc_start: 0.8000 (t80) cc_final: 0.7704 (t80) REVERT: N 186 SER cc_start: 0.9294 (p) cc_final: 0.9031 (p) REVERT: N 196 LEU cc_start: 0.9451 (tp) cc_final: 0.8872 (tp) REVERT: N 257 GLU cc_start: 0.8035 (tp30) cc_final: 0.7772 (tp30) REVERT: N 263 ARG cc_start: 0.8995 (ppt170) cc_final: 0.8580 (ttp80) REVERT: N 266 GLU cc_start: 0.7935 (tp30) cc_final: 0.7554 (tp30) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.2336 time to fit residues: 201.7073 Evaluate side-chains 353 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 422 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 438 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 402 optimal weight: 0.0170 chunk 330 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 2.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 ASN ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072662 restraints weight = 151509.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074725 restraints weight = 89545.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076093 restraints weight = 62393.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076986 restraints weight = 49148.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077451 restraints weight = 42189.664| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 46094 Z= 0.164 Angle : 0.621 11.877 62370 Z= 0.311 Chirality : 0.044 0.290 6846 Planarity : 0.004 0.043 7814 Dihedral : 6.191 178.215 6270 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.02 % Allowed : 0.74 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5478 helix: 0.40 (0.11), residues: 2360 sheet: -1.77 (0.19), residues: 674 loop : -0.85 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 424 TYR 0.040 0.002 TYR N 376 PHE 0.027 0.002 PHE N 38 TRP 0.035 0.002 TRP H 242 HIS 0.018 0.001 HIS E 515 Details of bonding type rmsd covalent geometry : bond 0.00373 (46094) covalent geometry : angle 0.62122 (62370) hydrogen bonds : bond 0.02921 ( 1596) hydrogen bonds : angle 4.23644 ( 4602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7530 (m-10) cc_final: 0.7294 (m-80) REVERT: A 250 SER cc_start: 0.9354 (t) cc_final: 0.9110 (t) REVERT: A 258 GLU cc_start: 0.8804 (pt0) cc_final: 0.8456 (pt0) REVERT: A 551 PHE cc_start: 0.6144 (m-80) cc_final: 0.5777 (m-80) REVERT: A 552 PHE cc_start: 0.8421 (m-10) cc_final: 0.8046 (m-80) REVERT: B 533 TRP cc_start: 0.8399 (m100) cc_final: 0.7520 (m100) REVERT: C 291 LEU cc_start: 0.8845 (mp) cc_final: 0.8387 (tt) REVERT: C 385 GLN cc_start: 0.8394 (tt0) cc_final: 0.8118 (tt0) REVERT: C 513 LEU cc_start: 0.8926 (tp) cc_final: 0.8698 (tt) REVERT: C 526 MET cc_start: 0.8777 (mtp) cc_final: 0.8349 (mmm) REVERT: D 360 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: D 385 GLN cc_start: 0.7397 (pp30) cc_final: 0.6804 (pp30) REVERT: E 527 GLU cc_start: 0.8651 (tt0) cc_final: 0.8067 (tm-30) REVERT: E 583 ILE cc_start: 0.9104 (mp) cc_final: 0.8816 (mp) REVERT: F 210 GLN cc_start: 0.8099 (pm20) cc_final: 0.7730 (pm20) REVERT: F 561 ASN cc_start: 0.7706 (p0) cc_final: 0.7450 (p0) REVERT: G 146 TYR cc_start: 0.7832 (t80) cc_final: 0.7602 (t80) REVERT: G 196 LEU cc_start: 0.9477 (tp) cc_final: 0.8883 (tp) REVERT: G 240 MET cc_start: 0.9259 (tpp) cc_final: 0.9038 (tpp) REVERT: G 263 ARG cc_start: 0.9037 (ppt170) cc_final: 0.8581 (ttp80) REVERT: G 266 GLU cc_start: 0.7942 (tp30) cc_final: 0.7555 (tp30) REVERT: H 250 SER cc_start: 0.9398 (t) cc_final: 0.9126 (t) REVERT: H 258 GLU cc_start: 0.8758 (pt0) cc_final: 0.8367 (pt0) REVERT: H 551 PHE cc_start: 0.5878 (m-80) cc_final: 0.5518 (m-80) REVERT: H 552 PHE cc_start: 0.8438 (m-10) cc_final: 0.8101 (m-80) REVERT: I 533 TRP cc_start: 0.8375 (m100) cc_final: 0.7584 (m100) REVERT: J 291 LEU cc_start: 0.8860 (mp) cc_final: 0.8427 (tt) REVERT: J 385 GLN cc_start: 0.8408 (tt0) cc_final: 0.8173 (tt0) REVERT: J 526 MET cc_start: 0.8849 (mtp) cc_final: 0.8381 (mmm) REVERT: J 533 TRP cc_start: 0.9025 (m100) cc_final: 0.8678 (m100) REVERT: K 385 GLN cc_start: 0.7449 (pp30) cc_final: 0.6991 (pp30) REVERT: K 413 ASP cc_start: 0.8377 (t70) cc_final: 0.8172 (t70) REVERT: K 416 ILE cc_start: 0.9213 (pt) cc_final: 0.8936 (pt) REVERT: K 524 LEU cc_start: 0.9165 (tt) cc_final: 0.8783 (tt) REVERT: L 249 GLN cc_start: 0.8595 (tt0) cc_final: 0.7778 (tt0) REVERT: L 527 GLU cc_start: 0.8864 (tt0) cc_final: 0.8145 (tm-30) REVERT: L 583 ILE cc_start: 0.9111 (mp) cc_final: 0.8829 (mp) REVERT: M 210 GLN cc_start: 0.8030 (pm20) cc_final: 0.7425 (pm20) REVERT: N 146 TYR cc_start: 0.8004 (t80) cc_final: 0.7724 (t80) REVERT: N 196 LEU cc_start: 0.9466 (tp) cc_final: 0.8884 (tp) REVERT: N 206 LEU cc_start: 0.8678 (pt) cc_final: 0.7933 (pt) REVERT: N 263 ARG cc_start: 0.8993 (ppt170) cc_final: 0.8634 (ttp80) REVERT: N 266 GLU cc_start: 0.7967 (tp30) cc_final: 0.7550 (tp30) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.2356 time to fit residues: 203.6647 Evaluate side-chains 350 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 545 optimal weight: 0.6980 chunk 152 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 58 optimal weight: 0.0170 chunk 451 optimal weight: 4.9990 chunk 348 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN D 531 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 372 GLN H 514 HIS H 515 HIS ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 531 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 195 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.074292 restraints weight = 151106.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.076423 restraints weight = 87739.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077853 restraints weight = 60721.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078760 restraints weight = 47423.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079199 restraints weight = 40588.732| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 46094 Z= 0.112 Angle : 0.592 9.583 62370 Z= 0.295 Chirality : 0.044 0.281 6846 Planarity : 0.004 0.048 7814 Dihedral : 5.997 171.871 6270 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.04 % Allowed : 0.24 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 5478 helix: 0.43 (0.11), residues: 2366 sheet: -1.58 (0.20), residues: 656 loop : -0.81 (0.13), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 226 TYR 0.030 0.001 TYR N 376 PHE 0.021 0.001 PHE N 38 TRP 0.037 0.001 TRP A 242 HIS 0.018 0.001 HIS J 515 Details of bonding type rmsd covalent geometry : bond 0.00258 (46094) covalent geometry : angle 0.59209 (62370) hydrogen bonds : bond 0.02709 ( 1596) hydrogen bonds : angle 4.12284 ( 4602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10956 Ramachandran restraints generated. 5478 Oldfield, 0 Emsley, 5478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7543 (m-10) cc_final: 0.7223 (m-80) REVERT: A 250 SER cc_start: 0.9321 (t) cc_final: 0.9031 (t) REVERT: A 258 GLU cc_start: 0.8733 (pt0) cc_final: 0.8318 (pt0) REVERT: A 551 PHE cc_start: 0.5870 (m-80) cc_final: 0.5476 (m-80) REVERT: A 552 PHE cc_start: 0.8376 (m-10) cc_final: 0.8001 (m-80) REVERT: B 456 ASP cc_start: 0.7824 (t0) cc_final: 0.7596 (p0) REVERT: B 533 TRP cc_start: 0.8344 (m100) cc_final: 0.7414 (m100) REVERT: C 291 LEU cc_start: 0.8840 (mp) cc_final: 0.8405 (tt) REVERT: C 385 GLN cc_start: 0.8320 (tt0) cc_final: 0.8024 (tt0) REVERT: C 494 ASP cc_start: 0.8729 (p0) cc_final: 0.8517 (p0) REVERT: C 513 LEU cc_start: 0.8859 (tp) cc_final: 0.8497 (tt) REVERT: D 385 GLN cc_start: 0.7308 (pp30) cc_final: 0.6655 (pp30) REVERT: E 249 GLN cc_start: 0.8257 (tt0) cc_final: 0.7360 (tt0) REVERT: E 374 LEU cc_start: 0.8969 (mt) cc_final: 0.8768 (mt) REVERT: E 527 GLU cc_start: 0.8446 (tt0) cc_final: 0.7989 (tm-30) REVERT: E 528 TYR cc_start: 0.8405 (m-80) cc_final: 0.7855 (m-80) REVERT: E 583 ILE cc_start: 0.9093 (mp) cc_final: 0.8818 (mp) REVERT: F 210 GLN cc_start: 0.8098 (pm20) cc_final: 0.7638 (pm20) REVERT: F 561 ASN cc_start: 0.7667 (p0) cc_final: 0.7444 (p0) REVERT: G 196 LEU cc_start: 0.9468 (tp) cc_final: 0.8862 (tp) REVERT: G 206 LEU cc_start: 0.8336 (pt) cc_final: 0.7557 (pt) REVERT: G 240 MET cc_start: 0.9246 (tpp) cc_final: 0.8995 (tpp) REVERT: G 263 ARG cc_start: 0.9045 (ppt170) cc_final: 0.8603 (ttp80) REVERT: G 266 GLU cc_start: 0.7860 (tp30) cc_final: 0.7487 (tp30) REVERT: H 203 MET cc_start: 0.8656 (ppp) cc_final: 0.8404 (ppp) REVERT: H 250 SER cc_start: 0.9370 (t) cc_final: 0.9037 (t) REVERT: H 258 GLU cc_start: 0.8644 (pt0) cc_final: 0.8252 (pt0) REVERT: H 392 TYR cc_start: 0.8420 (m-80) cc_final: 0.7666 (m-80) REVERT: H 551 PHE cc_start: 0.5824 (m-80) cc_final: 0.5443 (m-80) REVERT: H 552 PHE cc_start: 0.8421 (m-10) cc_final: 0.8039 (m-80) REVERT: I 533 TRP cc_start: 0.8378 (m100) cc_final: 0.7453 (m100) REVERT: J 291 LEU cc_start: 0.8792 (mp) cc_final: 0.8350 (tt) REVERT: J 385 GLN cc_start: 0.8310 (tt0) cc_final: 0.8028 (tt0) REVERT: J 526 MET cc_start: 0.8821 (mtp) cc_final: 0.8424 (mmm) REVERT: J 533 TRP cc_start: 0.8964 (m100) cc_final: 0.8631 (m100) REVERT: K 385 GLN cc_start: 0.7410 (pp30) cc_final: 0.6870 (pp30) REVERT: K 413 ASP cc_start: 0.8369 (t70) cc_final: 0.8148 (t70) REVERT: K 416 ILE cc_start: 0.9198 (pt) cc_final: 0.8896 (pt) REVERT: L 214 TYR cc_start: 0.8755 (p90) cc_final: 0.8470 (p90) REVERT: L 249 GLN cc_start: 0.8392 (tt0) cc_final: 0.7607 (tt0) REVERT: L 527 GLU cc_start: 0.8782 (tt0) cc_final: 0.8110 (tm-30) REVERT: L 528 TYR cc_start: 0.8777 (m-80) cc_final: 0.7919 (m-80) REVERT: L 583 ILE cc_start: 0.9097 (mp) cc_final: 0.8828 (mp) REVERT: M 210 GLN cc_start: 0.7942 (pm20) cc_final: 0.7672 (pm20) REVERT: N 196 LEU cc_start: 0.9469 (tp) cc_final: 0.8868 (tp) REVERT: N 206 LEU cc_start: 0.8581 (pt) cc_final: 0.7825 (pt) REVERT: N 263 ARG cc_start: 0.9025 (ppt170) cc_final: 0.8597 (ttp80) REVERT: N 266 GLU cc_start: 0.7848 (tp30) cc_final: 0.7464 (tp30) outliers start: 2 outliers final: 0 residues processed: 517 average time/residue: 0.2425 time to fit residues: 217.5646 Evaluate side-chains 374 residues out of total 5010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 550 random chunks: chunk 396 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 397 optimal weight: 0.4980 chunk 490 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 416 optimal weight: 5.9990 chunk 463 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS D 531 ASN ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 GLN ** I 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 515 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN N 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072908 restraints weight = 151851.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074901 restraints weight = 91070.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076211 restraints weight = 64386.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077069 restraints weight = 51245.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.077534 restraints weight = 44238.242| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46094 Z= 0.153 Angle : 0.610 9.360 62370 Z= 0.306 Chirality : 0.044 0.274 6846 Planarity : 0.004 0.045 7814 Dihedral : 5.988 163.966 6270 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.12), residues: 5478 helix: 0.49 (0.11), residues: 2374 sheet: -1.66 (0.20), residues: 670 loop : -0.75 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.026 0.002 TYR C 392 PHE 0.021 0.001 PHE G 38 TRP 0.043 0.002 TRP F 538 HIS 0.014 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00350 (46094) covalent geometry : angle 0.61008 (62370) hydrogen bonds : bond 0.02805 ( 1596) hydrogen bonds : angle 4.15693 ( 4602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7434.26 seconds wall clock time: 130 minutes 23.02 seconds (7823.02 seconds total)