Starting phenix.real_space_refine on Sat Sep 28 11:57:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ut4_20865/09_2024/6ut4_20865.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 18 5.49 5 Mg 6 5.21 5 S 24 5.16 5 C 12412 2.51 5 N 3224 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19126 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3164 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 370} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3152 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3144 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3109 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3164 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3183 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 373} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "A" 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: "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: 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: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.46, per 1000 atoms: 0.65 Number of scatterers: 19126 At special positions: 0 Unit cell: (136.25, 123.75, 88.75, 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 24 16.00 P 18 15.00 Mg 6 11.99 O 3442 8.00 N 3224 7.00 C 12412 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: 5.50 Conformation dependent library (CDL) restraints added in 2.5 seconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4330 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 51.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.915A pdb=" N MET A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.625A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.609A pdb=" N GLY A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 336 removed outlier: 4.140A pdb=" N GLU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.559A pdb=" N ARG A 424 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.613A pdb=" N LYS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.842A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.750A pdb=" N VAL A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 4.052A pdb=" N HIS A 497 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.707A 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 500 through 504 removed outlier: 3.990A pdb=" N TYR A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.581A pdb=" N LEU A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.821A pdb=" N LEU A 540 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.530A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 208 removed outlier: 3.507A pdb=" N LYS B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 277 through 294 removed outlier: 4.083A pdb=" N LEU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 318 through 336 removed outlier: 4.609A pdb=" N GLU B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.808A pdb=" N THR B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.670A pdb=" N ARG B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.697A pdb=" N GLU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 Processing helix chain 'B' and resid 500 through 504 removed outlier: 4.057A pdb=" N TYR B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 521 removed outlier: 3.693A pdb=" N VAL B 521 " --> pdb=" O TRP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.527A pdb=" N ILE B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 removed outlier: 3.607A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 209 removed outlier: 3.590A pdb=" N ASN C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 277 through 294 removed outlier: 3.744A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 318 through 336 removed outlier: 3.936A pdb=" N GLU C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 removed outlier: 4.223A pdb=" N ASN C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.701A pdb=" N GLY C 361 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 454 through 460 Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.511A pdb=" N SER C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 491 removed outlier: 3.612A pdb=" N VAL C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 521 through 529 Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.788A pdb=" N ILE C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 removed outlier: 3.677A pdb=" N ASN D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 234 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 277 through 294 removed outlier: 4.136A pdb=" N GLU D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 318 through 336 removed outlier: 3.852A pdb=" N GLU D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.815A pdb=" N GLY D 361 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.586A pdb=" N LEU D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.654A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 3.597A pdb=" N GLU D 440 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 449 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.665A pdb=" N LYS D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 Processing helix chain 'D' and resid 494 through 498 removed outlier: 3.577A pdb=" N HIS D 497 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 498 " --> pdb=" O ARG D 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 494 through 498' Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.779A pdb=" N ILE D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'E' and resid 220 through 233 Processing helix chain 'E' and resid 277 through 291 removed outlier: 3.616A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.652A pdb=" N ARG E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.589A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.633A 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 369 through 374 removed outlier: 3.562A pdb=" N LEU E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 426 removed outlier: 3.597A pdb=" N ARG E 425 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.804A pdb=" N LYS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS E 451 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU E 452 " --> pdb=" O ARG E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 472 removed outlier: 4.463A pdb=" N GLU E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 493 removed outlier: 4.415A pdb=" N ARG E 488 " --> pdb=" O LYS E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 504 removed outlier: 3.651A pdb=" N TYR E 503 " --> pdb=" O GLY E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 521 through 529 Processing helix chain 'E' and resid 532 through 540 removed outlier: 3.725A pdb=" N TRP E 538 " --> pdb=" O GLU E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 584 removed outlier: 4.089A pdb=" N ILE E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 583 " --> pdb=" O ALA E 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 209 Processing helix chain 'F' and resid 220 through 233 Processing helix chain 'F' and resid 277 through 293 removed outlier: 4.026A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.838A pdb=" N ARG F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 336 removed outlier: 3.827A pdb=" N GLU F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.664A pdb=" N LEU F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 3.883A pdb=" N GLY F 361 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 420 through 427 removed outlier: 3.652A pdb=" N ARG F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE F 427 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 Processing helix chain 'F' and resid 440 through 450 Processing helix chain 'F' and resid 455 through 469 removed outlier: 4.074A pdb=" N ARG F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 493 removed outlier: 3.937A pdb=" N VAL F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 498 removed outlier: 3.515A pdb=" N HIS F 497 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG F 498 " --> pdb=" O ARG F 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 494 through 498' Processing helix chain 'F' and resid 500 through 504 removed outlier: 4.015A pdb=" N TYR F 503 " --> pdb=" O GLY F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 521 removed outlier: 3.777A pdb=" N VAL F 521 " --> pdb=" O TRP F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 529 Processing helix chain 'F' and resid 532 through 540 removed outlier: 3.539A pdb=" N LEU F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 582 removed outlier: 3.624A pdb=" N ILE F 577 " --> pdb=" O GLY F 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 242 through 246 removed outlier: 6.348A pdb=" N GLU A 243 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 356 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 245 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN A 210 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 430 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 6.322A 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 264 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 554 Processing sheet with id=AA5, first strand: chain 'B' and resid 242 through 246 removed outlier: 6.173A pdb=" N GLU B 243 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP B 356 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 245 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 351 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 406 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 353 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 408 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 355 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 211 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 212 " --> pdb=" O ILE B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 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: 6.483A pdb=" N PHE C 351 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE C 406 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 353 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 408 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 355 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASN C 410 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 215 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN C 210 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE C 430 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 6.198A 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 262 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 246 removed outlier: 6.397A pdb=" N PHE D 351 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 406 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 353 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR D 408 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 355 " --> pdb=" O THR D 408 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ASN D 410 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 211 " --> pdb=" O GLY D 407 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N MET D 409 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.459A 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 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 242 through 246 removed outlier: 6.719A pdb=" N GLU E 243 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP E 356 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE E 245 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 351 " --> pdb=" O TYR E 404 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE E 406 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 353 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N THR E 408 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE E 355 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN E 410 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL E 211 " --> pdb=" O GLY E 407 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET E 409 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 213 " --> pdb=" O MET E 409 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN E 210 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE E 430 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 212 " --> pdb=" O ILE E 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 258 through 263 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 242 through 246 removed outlier: 6.508A pdb=" N GLU F 243 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP F 356 " --> pdb=" O GLU F 243 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE F 245 " --> pdb=" O ASP F 356 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE F 351 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE F 406 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 353 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR F 408 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 355 " --> pdb=" O THR F 408 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN F 410 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN F 210 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE F 430 " --> pdb=" O GLN F 210 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE F 212 " --> pdb=" O ILE F 430 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 258 through 265 removed outlier: 3.773A pdb=" N LYS F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'F' and resid 552 through 554 741 hydrogen bonds defined for protein. 2115 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: 6.78 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5906 1.34 - 1.46: 3854 1.46 - 1.58: 9724 1.58 - 1.70: 34 1.70 - 1.82: 38 Bond restraints: 19556 Sorted by residual: bond pdb=" C THR C 348 " pdb=" N PRO C 349 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.52e+00 bond pdb=" C THR F 348 " pdb=" N PRO F 349 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR D 348 " pdb=" N PRO D 349 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 bond pdb=" C THR E 348 " pdb=" N PRO E 349 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" C THR B 237 " pdb=" N PRO B 238 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.42e+00 ... (remaining 19551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 25978 2.31 - 4.62: 432 4.62 - 6.94: 50 6.94 - 9.25: 13 9.25 - 11.56: 1 Bond angle restraints: 26474 Sorted by residual: angle pdb=" C LEU D 540 " pdb=" N ASN D 541 " pdb=" CA ASN D 541 " ideal model delta sigma weight residual 122.46 128.54 -6.08 1.41e+00 5.03e-01 1.86e+01 angle pdb=" C LEU A 540 " pdb=" N ASN A 541 " pdb=" CA ASN A 541 " ideal model delta sigma weight residual 121.54 129.61 -8.07 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LEU B 540 " pdb=" N ASN B 541 " pdb=" CA ASN B 541 " ideal model delta sigma weight residual 122.46 128.31 -5.85 1.41e+00 5.03e-01 1.72e+01 angle pdb=" C LEU C 540 " pdb=" N ASN C 541 " pdb=" CA ASN C 541 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C LEU E 540 " pdb=" N ASN E 541 " pdb=" CA ASN E 541 " ideal model delta sigma weight residual 122.46 128.13 -5.67 1.41e+00 5.03e-01 1.62e+01 ... (remaining 26469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10467 17.90 - 35.79: 1016 35.79 - 53.69: 161 53.69 - 71.59: 31 71.59 - 89.48: 16 Dihedral angle restraints: 11691 sinusoidal: 4938 harmonic: 6753 Sorted by residual: dihedral pdb=" CA PHE C 427 " pdb=" C PHE C 427 " pdb=" N ALA C 428 " pdb=" CA ALA C 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE E 427 " pdb=" C PHE E 427 " pdb=" N ALA E 428 " pdb=" CA ALA E 428 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CA GLU A 268 " pdb=" CB GLU A 268 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2609 0.081 - 0.162: 261 0.162 - 0.243: 18 0.243 - 0.324: 1 0.324 - 0.404: 2 Chirality restraints: 2891 Sorted by residual: chirality pdb=" CA GLU A 268 " pdb=" N GLU A 268 " pdb=" C GLU A 268 " pdb=" CB GLU A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB ILE F 416 " pdb=" CA ILE F 416 " pdb=" CG1 ILE F 416 " pdb=" CG2 ILE F 416 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE B 354 " pdb=" CA ILE B 354 " pdb=" CG1 ILE B 354 " pdb=" CG2 ILE B 354 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2888 not shown) Planarity restraints: 3311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 251 " 0.012 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR E 251 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 251 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 251 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 251 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 251 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 251 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 395 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO F 396 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 395 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO B 396 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " -0.032 5.00e-02 4.00e+02 ... (remaining 3308 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 344 2.67 - 3.23: 16826 3.23 - 3.78: 31148 3.78 - 4.34: 44581 4.34 - 4.90: 71895 Nonbonded interactions: 164794 Sorted by model distance: nonbonded pdb="MG MG C 702 " pdb=" O HOH C 801 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR F 222 " pdb="MG MG F 702 " model vdw 2.112 2.170 nonbonded pdb="MG MG B 702 " pdb=" O HOH C 802 " model vdw 2.115 2.170 nonbonded pdb=" O2B GSP D 701 " pdb="MG MG D 702 " model vdw 2.122 2.170 nonbonded pdb=" O2G GSP F 701 " pdb="MG MG F 702 " model vdw 2.122 2.170 ... (remaining 164789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 295 or (resid 296 through 298 and (name N or name CA or name C or name O or nam \ e CB )) or resid 299 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 394 or (resid 395 and (name N or name CA or name C or name O or nam \ e CB )) or resid 396 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 439 or (resid 440 through 441 and ( \ name N or name CA or name C or name O or name CB )) or resid 442 through 444 or \ (resid 445 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 or (resid 448 through 459 and (name N or name CA or name C or name \ O or name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or \ name C or name O or name CB )) or resid 495 through 544 or (resid 545 through 5 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 548 or (res \ id 549 and (name N or name CA or name C or name O or name CB )) or resid 550 thr \ ough 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) \ or resid 554 through 555 or (resid 556 and (name N or name CA or name C or name \ O or name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or \ name C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name \ N or name CA or name C or name O or name CB )) or resid 573 through 584 or resi \ d 701 through 702)) selection = (chain 'B' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 230 or (resid 231 and (name N or name CA or \ name C or name O or name CB )) or resid 232 through 242 or (resid 243 and (name \ N or name CA or name C or name O or name CB )) or resid 244 through 263 or resi \ d 270 through 292 or (resid 293 and (name N or name CA or name C or name O or na \ me CB )) or resid 294 through 300 or (resid 301 through 302 and (name N or name \ CA or name C or name O or name CB )) or resid 303 through 368 or (resid 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 through 394 or \ (resid 395 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 6 through 404 or (resid 405 and (name N or name CA or name C or name O or name C \ B )) or resid 406 through 417 or (resid 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 439 or (resid 440 through 441 and (nam \ e N or name CA or name C or name O or name CB )) or resid 442 through 444 or (re \ sid 445 through 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 or (resid 448 through 459 and (name N or name CA or name C or name O o \ r name CB )) or resid 460 through 493 or (resid 494 and (name N or name CA or na \ me C or name O or name CB )) or resid 495 through 545 or (resid 546 through 547 \ and (name N or name CA or name C or name O or name CB )) or resid 548 or (resid \ 549 and (name N or name CA or name C or name O or name CB )) or resid 550 throug \ h 552 or (resid 553 and (name N or name CA or name C or name O or name CB )) or \ resid 554 through 555 or (resid 556 and (name N or name CA or name C or name O o \ r name CB )) or resid 557 through 560 or (resid 561 and (name N or name CA or na \ me C or name O or name CB )) or resid 562 through 571 or (resid 572 and (name N \ or name CA or name C or name O or name CB )) or resid 573 through 584 or resid 7 \ 01 through 702)) selection = (chain 'C' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 292 or (resid 293 and (name \ N or name CA or name C or name O or name CB )) or resid 294 through 295 or (res \ id 296 through 298 and (name N or name CA or name C or name O or name CB )) or r \ esid 299 through 300 or (resid 301 through 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 314 or (resid 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 or (resid 3 \ 20 through 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 394 or (resid 395 and (name N or name CA or name C \ or name O or name CB )) or resid 396 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 439 \ or (resid 440 through 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 444 or (resid 445 through 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 544 or (resid 545 through 547 and (name N or name CA or name C or name O or \ name CB )) or resid 548 or (resid 549 and (name N or name CA or name C or name \ O or name CB )) or resid 550 through 555 or (resid 556 and (name N or name CA or \ name C or name O or name CB )) or resid 557 through 560 or (resid 561 and (name \ N or name CA or name C or name O or name CB )) or resid 562 through 571 or (res \ id 572 and (name N or name CA or name C or name O or name CB )) or resid 573 thr \ ough 584 or resid 701 through 702)) selection = (chain 'D' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 270 or (resid 271 and (name \ N or name CA or name C or name O or name CB )) or resid 272 through 292 or (res \ id 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thr \ ough 295 or (resid 296 through 298 and (name N or name CA or name C or name O or \ name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or na \ me CA or name C or name O or name CB )) or resid 303 through 314 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 through 317 \ or (resid 318 and (name N or name CA or name C or name O or name CB )) or resid \ 319 or (resid 320 through 321 and (name N or name CA or name C or name O or nam \ e CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name C \ or name O or name CB )) or resid 370 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 417 or (resid 418 a \ nd (name N or name CA or name C or name O or name CB )) or resid 419 through 452 \ or (resid 453 through 459 and (name N or name CA or name C or name O or name CB \ )) or resid 460 through 555 or (resid 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 584 or resid 701 through 702)) selection = (chain 'E' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 263 or (resid 270 through 2 \ 71 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or r \ esid 294 through 295 or (resid 296 through 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 300 or (resid 301 through 302 and ( \ name N or name CA or name C or name O or name CB )) or resid 303 through 314 or \ (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ through 317 or (resid 318 and (name N or name CA or name C or name O or name CB \ )) or resid 319 or (resid 320 through 321 and (name N or name CA or name C or n \ ame O or name CB )) or resid 322 through 368 or (resid 369 and (name N or name C \ A or name C or name O or name CB )) or resid 370 through 394 or (resid 395 and ( \ name N or name CA or name C or name O or name CB )) or resid 396 through 417 or \ (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 419 \ through 439 or (resid 440 through 441 and (name N or name CA or name C or name \ O or name CB )) or resid 442 through 445 or (resid 446 and (name N or name CA or \ name C or name O or name CB )) or resid 447 or (resid 448 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 493 or (res \ id 494 and (name N or name CA or name C or name O or name CB )) or resid 495 thr \ ough 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) \ or resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 550 through 552 or (resid 553 and (name N or name CA or name C or n \ ame O or name CB )) or resid 554 through 560 or (resid 561 and (name N or name C \ A or name C or name O or name CB )) or resid 562 through 584 or resid 701 throug \ h 702)) selection = (chain 'F' and ((resid 198 through 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 262 or (resid 263 and (name \ N or name CA or name C or name O or name CB )) or (resid 270 through 271 and (n \ ame N or name CA or name C or name O or name CB )) or resid 272 through 292 or ( \ resid 293 and (name N or name CA or name C or name O or name CB )) or resid 294 \ through 295 or (resid 296 through 298 and (name N or name CA or name C or name O \ or name CB )) or resid 299 through 300 or (resid 301 through 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 through 314 or (resid 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or re \ sid 319 or (resid 320 through 321 and (name N or name CA or name C or name O or \ name CB )) or resid 322 through 368 or (resid 369 and (name N or name CA or name \ C or name O or name CB )) or resid 370 through 394 or (resid 395 and (name N or \ name CA or name C or name O or name CB )) or resid 396 through 404 or (resid 40 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 406 through \ 417 or (resid 418 and (name N or name CA or name C or name O or name CB )) or re \ sid 419 through 439 or (resid 440 through 441 and (name N or name CA or name C o \ r name O or name CB )) or resid 442 through 444 or (resid 445 through 446 and (n \ ame N or name CA or name C or name O or name CB )) or resid 447 through 452 or ( \ resid 453 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 493 or (resid 494 and (name N or name CA or name C or name O \ or name CB )) or resid 495 through 544 or (resid 545 through 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 or (resid 549 and (name \ N or name CA or name C or name O or name CB )) or resid 550 through 552 or (resi \ d 553 and (name N or name CA or name C or name O or name CB )) or resid 554 thro \ ugh 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) o \ r resid 557 through 584 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.000 Extract box with map and model: 1.330 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 45.810 Find NCS groups from input model: 1.330 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.004 0.050 19556 Z= 0.279 Angle : 0.751 11.562 26474 Z= 0.411 Chirality : 0.050 0.404 2891 Planarity : 0.006 0.059 3311 Dihedral : 14.347 89.483 7361 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.15 % Allowed : 5.52 % Favored : 94.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.14), residues: 2295 helix: -3.30 (0.10), residues: 1025 sheet: -2.40 (0.26), residues: 284 loop : -1.24 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 242 HIS 0.009 0.001 HIS E 248 PHE 0.018 0.002 PHE B 247 TYR 0.041 0.002 TYR E 251 ARG 0.005 0.000 ARG B 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 TYR cc_start: 0.8319 (m-80) cc_final: 0.7991 (m-10) REVERT: B 409 MET cc_start: 0.8136 (ttt) cc_final: 0.7845 (tmm) REVERT: B 435 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7454 (mtt180) REVERT: B 515 HIS cc_start: 0.8465 (m170) cc_final: 0.8057 (m90) REVERT: B 542 GLU cc_start: 0.8256 (pt0) cc_final: 0.7943 (pt0) REVERT: C 261 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7377 (mmm160) REVERT: C 305 HIS cc_start: 0.7562 (t70) cc_final: 0.7342 (t-90) REVERT: C 415 SER cc_start: 0.9072 (p) cc_final: 0.8816 (p) REVERT: C 446 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8235 (ttmt) REVERT: C 577 ILE cc_start: 0.9153 (mm) cc_final: 0.8898 (mm) REVERT: D 253 TYR cc_start: 0.8738 (t80) cc_final: 0.8401 (t80) REVERT: D 255 GLU cc_start: 0.8060 (mp0) cc_final: 0.7328 (mp0) REVERT: F 518 TYR cc_start: 0.8538 (m-80) cc_final: 0.8297 (m-80) outliers start: 3 outliers final: 2 residues processed: 310 average time/residue: 0.4149 time to fit residues: 181.7638 Evaluate side-chains 196 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 346 ASN A 461 ASN A 506 ASN A 515 HIS A 541 ASN B 248 HIS B 384 ASN B 465 ASN B 473 ASN B 501 HIS B 515 HIS B 561 ASN C 248 HIS C 249 GLN C 384 ASN C 497 HIS C 501 HIS C 531 ASN C 541 ASN D 248 HIS D 305 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS F 385 GLN F 461 ASN F 541 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19556 Z= 0.218 Angle : 0.544 8.157 26474 Z= 0.276 Chirality : 0.041 0.159 2891 Planarity : 0.004 0.050 3311 Dihedral : 6.079 58.871 2647 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.27 % Allowed : 10.43 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2295 helix: -1.53 (0.14), residues: 1068 sheet: -2.28 (0.26), residues: 290 loop : -0.57 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 333 HIS 0.004 0.001 HIS E 515 PHE 0.018 0.001 PHE A 477 TYR 0.018 0.001 TYR E 251 ARG 0.007 0.000 ARG F 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 409 MET cc_start: 0.8427 (ttp) cc_final: 0.8182 (ttp) REVERT: B 409 MET cc_start: 0.8036 (ttt) cc_final: 0.7703 (tmm) REVERT: B 542 GLU cc_start: 0.8372 (pt0) cc_final: 0.8056 (pt0) REVERT: C 261 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7366 (mmm160) REVERT: C 305 HIS cc_start: 0.7627 (t70) cc_final: 0.7386 (t-90) REVERT: C 488 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7934 (mtp85) REVERT: C 549 ASN cc_start: 0.8361 (m-40) cc_final: 0.8033 (p0) REVERT: D 253 TYR cc_start: 0.8710 (t80) cc_final: 0.8471 (t80) REVERT: D 255 GLU cc_start: 0.7911 (mp0) cc_final: 0.7418 (mp0) REVERT: D 458 LYS cc_start: 0.7987 (tptt) cc_final: 0.7674 (pttp) REVERT: F 210 GLN cc_start: 0.9049 (pm20) cc_final: 0.8722 (pm20) outliers start: 25 outliers final: 14 residues processed: 230 average time/residue: 0.3676 time to fit residues: 125.6625 Evaluate side-chains 199 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 292 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19556 Z= 0.301 Angle : 0.564 8.322 26474 Z= 0.285 Chirality : 0.043 0.168 2891 Planarity : 0.004 0.050 3311 Dihedral : 5.970 55.349 2646 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.52 % Allowed : 12.04 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2295 helix: -0.83 (0.15), residues: 1084 sheet: -2.19 (0.26), residues: 298 loop : -0.14 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 333 HIS 0.020 0.001 HIS D 305 PHE 0.017 0.001 PHE D 279 TYR 0.022 0.002 TYR E 251 ARG 0.008 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 2.272 Fit side-chains REVERT: A 227 LYS cc_start: 0.7926 (tttm) cc_final: 0.7633 (tttm) REVERT: A 520 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7277 (mt-10) REVERT: B 542 GLU cc_start: 0.8414 (pt0) cc_final: 0.8123 (pt0) REVERT: C 261 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7200 (mmm160) REVERT: C 526 MET cc_start: 0.8653 (mtp) cc_final: 0.8418 (mtp) REVERT: D 255 GLU cc_start: 0.7905 (mp0) cc_final: 0.7349 (mp0) REVERT: E 323 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: E 470 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8536 (mmmm) REVERT: F 445 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8133 (ttmt) outliers start: 30 outliers final: 20 residues processed: 216 average time/residue: 0.3496 time to fit residues: 113.1771 Evaluate side-chains 200 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 470 LYS Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 494 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 221 optimal weight: 0.0270 chunk 109 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN C 206 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19556 Z= 0.151 Angle : 0.497 7.431 26474 Z= 0.249 Chirality : 0.040 0.163 2891 Planarity : 0.003 0.039 3311 Dihedral : 5.571 55.319 2646 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.42 % Allowed : 13.06 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2295 helix: -0.23 (0.16), residues: 1071 sheet: -2.13 (0.28), residues: 274 loop : -0.03 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.004 0.001 HIS A 515 PHE 0.016 0.001 PHE D 279 TYR 0.015 0.001 TYR E 322 ARG 0.005 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 2.549 Fit side-chains revert: symmetry clash REVERT: A 204 LEU cc_start: 0.8972 (mt) cc_final: 0.8667 (mt) REVERT: A 249 GLN cc_start: 0.7645 (mp10) cc_final: 0.7421 (mp10) REVERT: A 520 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 249 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8182 (mm110) REVERT: B 348 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6973 (m) REVERT: B 542 GLU cc_start: 0.8293 (pt0) cc_final: 0.7983 (pt0) REVERT: C 261 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7188 (mmm160) REVERT: C 488 ARG cc_start: 0.8217 (mtt-85) cc_final: 0.7909 (mtp85) REVERT: C 526 MET cc_start: 0.8575 (mtp) cc_final: 0.8319 (mtp) REVERT: C 532 ASP cc_start: 0.8320 (t0) cc_final: 0.8097 (t0) REVERT: D 255 GLU cc_start: 0.7923 (mp0) cc_final: 0.7443 (mp0) REVERT: D 460 LEU cc_start: 0.8550 (tp) cc_final: 0.8200 (tt) REVERT: F 445 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (ttmt) outliers start: 28 outliers final: 18 residues processed: 241 average time/residue: 0.3475 time to fit residues: 125.1023 Evaluate side-chains 206 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 515 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19556 Z= 0.197 Angle : 0.506 6.873 26474 Z= 0.254 Chirality : 0.041 0.163 2891 Planarity : 0.003 0.037 3311 Dihedral : 5.396 57.393 2646 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.87 % Allowed : 14.07 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2295 helix: 0.03 (0.16), residues: 1078 sheet: -1.94 (0.27), residues: 296 loop : 0.13 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 242 HIS 0.005 0.001 HIS D 305 PHE 0.015 0.001 PHE D 279 TYR 0.017 0.001 TYR E 322 ARG 0.005 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 2.526 Fit side-chains REVERT: A 409 MET cc_start: 0.8387 (ttp) cc_final: 0.8106 (mtp) REVERT: A 520 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7185 (mt-10) REVERT: B 348 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.6978 (m) REVERT: B 409 MET cc_start: 0.7967 (ttt) cc_final: 0.7692 (tmm) REVERT: B 542 GLU cc_start: 0.8312 (pt0) cc_final: 0.8015 (pt0) REVERT: C 258 GLU cc_start: 0.8171 (pt0) cc_final: 0.7817 (pt0) REVERT: C 435 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: C 488 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.8014 (mtp85) REVERT: C 532 ASP cc_start: 0.8340 (t0) cc_final: 0.8095 (t0) REVERT: D 255 GLU cc_start: 0.7917 (mp0) cc_final: 0.7416 (mp0) REVERT: D 530 TYR cc_start: 0.7654 (t80) cc_final: 0.7447 (t80) REVERT: E 323 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6672 (pm20) REVERT: E 470 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8512 (mmmm) REVERT: F 292 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: F 445 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (ttmt) outliers start: 37 outliers final: 22 residues processed: 235 average time/residue: 0.3519 time to fit residues: 124.7175 Evaluate side-chains 212 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 470 LYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 221 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN D 531 ASN E 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19556 Z= 0.226 Angle : 0.519 6.670 26474 Z= 0.261 Chirality : 0.042 0.163 2891 Planarity : 0.003 0.037 3311 Dihedral : 5.325 58.760 2646 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.97 % Allowed : 14.47 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2295 helix: 0.13 (0.16), residues: 1084 sheet: -1.84 (0.28), residues: 298 loop : 0.24 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 242 HIS 0.006 0.001 HIS D 305 PHE 0.015 0.001 PHE D 279 TYR 0.018 0.001 TYR E 322 ARG 0.006 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 2.608 Fit side-chains REVERT: A 409 MET cc_start: 0.8367 (ttp) cc_final: 0.8135 (mtp) REVERT: B 348 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6964 (m) REVERT: B 542 GLU cc_start: 0.8326 (pt0) cc_final: 0.8011 (pt0) REVERT: C 258 GLU cc_start: 0.8193 (pt0) cc_final: 0.7840 (pt0) REVERT: C 488 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.8034 (mtp85) REVERT: C 526 MET cc_start: 0.8577 (mtp) cc_final: 0.8349 (mtp) REVERT: C 532 ASP cc_start: 0.8289 (t0) cc_final: 0.8056 (t0) REVERT: C 566 TYR cc_start: 0.9043 (m-80) cc_final: 0.8812 (m-80) REVERT: D 255 GLU cc_start: 0.7958 (mp0) cc_final: 0.7401 (mp0) REVERT: D 460 LEU cc_start: 0.8428 (tp) cc_final: 0.8108 (tt) REVERT: D 530 TYR cc_start: 0.7787 (t80) cc_final: 0.7575 (t80) REVERT: E 294 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8686 (mp) REVERT: E 323 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: F 292 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: F 445 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8357 (ttmt) outliers start: 39 outliers final: 26 residues processed: 222 average time/residue: 0.3432 time to fit residues: 115.1963 Evaluate side-chains 216 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19556 Z= 0.248 Angle : 0.529 6.964 26474 Z= 0.266 Chirality : 0.042 0.166 2891 Planarity : 0.004 0.037 3311 Dihedral : 5.306 58.902 2646 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.97 % Allowed : 14.83 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2295 helix: 0.18 (0.16), residues: 1082 sheet: -1.80 (0.28), residues: 298 loop : 0.26 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 242 HIS 0.005 0.001 HIS D 305 PHE 0.015 0.001 PHE D 279 TYR 0.018 0.001 TYR E 322 ARG 0.005 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 2.249 Fit side-chains REVERT: A 409 MET cc_start: 0.8342 (ttp) cc_final: 0.8134 (mtp) REVERT: B 348 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6986 (m) REVERT: B 542 GLU cc_start: 0.8340 (pt0) cc_final: 0.8042 (pt0) REVERT: C 258 GLU cc_start: 0.8197 (pt0) cc_final: 0.7849 (pt0) REVERT: C 526 MET cc_start: 0.8624 (mtp) cc_final: 0.8340 (mtp) REVERT: C 532 ASP cc_start: 0.8341 (t0) cc_final: 0.8096 (t0) REVERT: C 566 TYR cc_start: 0.9011 (m-80) cc_final: 0.8771 (m-80) REVERT: D 255 GLU cc_start: 0.7951 (mp0) cc_final: 0.7379 (mp0) REVERT: D 530 TYR cc_start: 0.7818 (t80) cc_final: 0.7616 (t80) REVERT: E 294 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8668 (mp) REVERT: E 323 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: E 470 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (mmmm) REVERT: F 292 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6839 (m-10) REVERT: F 445 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8317 (ttmt) REVERT: F 503 TYR cc_start: 0.8486 (m-80) cc_final: 0.7744 (m-80) outliers start: 39 outliers final: 27 residues processed: 213 average time/residue: 0.3392 time to fit residues: 110.6142 Evaluate side-chains 215 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 470 LYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19556 Z= 0.185 Angle : 0.506 7.647 26474 Z= 0.254 Chirality : 0.041 0.162 2891 Planarity : 0.003 0.035 3311 Dihedral : 5.114 57.991 2646 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.67 % Allowed : 15.59 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2295 helix: 0.32 (0.16), residues: 1081 sheet: -1.79 (0.28), residues: 294 loop : 0.32 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.006 0.001 HIS D 305 PHE 0.014 0.001 PHE D 279 TYR 0.019 0.001 TYR E 322 ARG 0.005 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 2.510 Fit side-chains REVERT: A 204 LEU cc_start: 0.9006 (mt) cc_final: 0.8717 (mt) REVERT: A 532 ASP cc_start: 0.7887 (t0) cc_final: 0.7614 (t0) REVERT: B 249 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8253 (mm110) REVERT: B 348 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6933 (m) REVERT: B 370 LEU cc_start: 0.8816 (mm) cc_final: 0.8572 (mt) REVERT: B 542 GLU cc_start: 0.8311 (pt0) cc_final: 0.8018 (pt0) REVERT: C 258 GLU cc_start: 0.8202 (pt0) cc_final: 0.7856 (pt0) REVERT: C 261 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7139 (mmm160) REVERT: C 488 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7980 (mtp85) REVERT: C 526 MET cc_start: 0.8606 (mtp) cc_final: 0.8372 (mtp) REVERT: C 532 ASP cc_start: 0.8239 (t0) cc_final: 0.8010 (t0) REVERT: C 566 TYR cc_start: 0.9018 (m-80) cc_final: 0.8750 (m-80) REVERT: D 255 GLU cc_start: 0.7948 (mp0) cc_final: 0.7392 (mp0) REVERT: D 460 LEU cc_start: 0.8530 (tp) cc_final: 0.8312 (tt) REVERT: E 323 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: E 470 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8423 (mttt) REVERT: F 292 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: F 445 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8311 (ttmt) REVERT: F 503 TYR cc_start: 0.8426 (m-80) cc_final: 0.7700 (m-80) outliers start: 33 outliers final: 23 residues processed: 221 average time/residue: 0.3383 time to fit residues: 114.0037 Evaluate side-chains 214 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 470 LYS Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19556 Z= 0.214 Angle : 0.519 8.269 26474 Z= 0.261 Chirality : 0.042 0.163 2891 Planarity : 0.004 0.035 3311 Dihedral : 5.141 58.039 2646 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.77 % Allowed : 15.54 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2295 helix: 0.36 (0.16), residues: 1085 sheet: -1.75 (0.28), residues: 295 loop : 0.34 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 333 HIS 0.006 0.001 HIS D 305 PHE 0.015 0.001 PHE D 279 TYR 0.020 0.001 TYR E 322 ARG 0.005 0.000 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 2.420 Fit side-chains REVERT: B 348 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6952 (m) REVERT: B 370 LEU cc_start: 0.8804 (mm) cc_final: 0.8564 (mt) REVERT: B 542 GLU cc_start: 0.8338 (pt0) cc_final: 0.8033 (pt0) REVERT: C 258 GLU cc_start: 0.8208 (pt0) cc_final: 0.7856 (pt0) REVERT: C 261 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7145 (mmm160) REVERT: C 488 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.8058 (mtp85) REVERT: C 526 MET cc_start: 0.8595 (mtp) cc_final: 0.8328 (mtp) REVERT: C 532 ASP cc_start: 0.8317 (t0) cc_final: 0.8073 (t0) REVERT: C 566 TYR cc_start: 0.9029 (m-80) cc_final: 0.8759 (m-80) REVERT: D 255 GLU cc_start: 0.7938 (mp0) cc_final: 0.7385 (mp0) REVERT: E 323 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: F 292 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6773 (m-10) REVERT: F 445 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8295 (ttmt) REVERT: F 457 ARG cc_start: 0.8262 (mtm180) cc_final: 0.8038 (mmm-85) REVERT: F 503 TYR cc_start: 0.8459 (m-80) cc_final: 0.7719 (m-80) outliers start: 35 outliers final: 29 residues processed: 213 average time/residue: 0.3232 time to fit residues: 105.2117 Evaluate side-chains 214 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19556 Z= 0.248 Angle : 0.538 8.993 26474 Z= 0.271 Chirality : 0.042 0.165 2891 Planarity : 0.004 0.036 3311 Dihedral : 5.226 58.410 2646 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.87 % Allowed : 15.69 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2295 helix: 0.37 (0.16), residues: 1076 sheet: -1.75 (0.29), residues: 296 loop : 0.32 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 333 HIS 0.007 0.001 HIS D 305 PHE 0.024 0.001 PHE A 477 TYR 0.021 0.001 TYR E 322 ARG 0.006 0.000 ARG B 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 2.271 Fit side-chains REVERT: B 348 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6910 (m) REVERT: B 370 LEU cc_start: 0.8824 (mm) cc_final: 0.8595 (mt) REVERT: B 542 GLU cc_start: 0.8360 (pt0) cc_final: 0.8055 (pt0) REVERT: C 258 GLU cc_start: 0.8215 (pt0) cc_final: 0.7876 (pt0) REVERT: C 526 MET cc_start: 0.8615 (mtp) cc_final: 0.8385 (mtp) REVERT: C 532 ASP cc_start: 0.8350 (t0) cc_final: 0.8099 (t0) REVERT: C 566 TYR cc_start: 0.9036 (m-80) cc_final: 0.8761 (m-80) REVERT: D 255 GLU cc_start: 0.7958 (mp0) cc_final: 0.7387 (mp0) REVERT: D 460 LEU cc_start: 0.8509 (tp) cc_final: 0.8215 (tt) REVERT: E 323 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: F 292 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: F 445 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (ttmt) REVERT: F 457 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8033 (mmm-85) REVERT: F 503 TYR cc_start: 0.8503 (m-80) cc_final: 0.7706 (m-80) outliers start: 37 outliers final: 28 residues processed: 210 average time/residue: 0.3572 time to fit residues: 114.6686 Evaluate side-chains 215 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 292 PHE Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 445 LYS Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102197 restraints weight = 26551.547| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.75 r_work: 0.2998 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19556 Z= 0.156 Angle : 0.501 9.011 26474 Z= 0.251 Chirality : 0.041 0.161 2891 Planarity : 0.003 0.034 3311 Dihedral : 4.972 56.672 2646 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.62 % Allowed : 15.99 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2295 helix: 0.52 (0.16), residues: 1077 sheet: -1.64 (0.30), residues: 272 loop : 0.37 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 333 HIS 0.005 0.001 HIS D 305 PHE 0.018 0.001 PHE C 279 TYR 0.020 0.001 TYR E 322 ARG 0.006 0.000 ARG B 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4030.18 seconds wall clock time: 75 minutes 56.83 seconds (4556.83 seconds total)