Starting phenix.real_space_refine on Sun Jul 21 15:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/07_2024/6qi8_4552.cif" } resolution = 3.75 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 9244 2.51 5 N 2584 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 308": "OD1" <-> "OD2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ASP 353": "OD1" <-> "OD2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E ARG 330": "NH1" <-> "NH2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ASP 385": "OD1" <-> "OD2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E ASP 424": "OD1" <-> "OD2" Residue "E TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 435": "OD1" <-> "OD2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 264": "OD1" <-> "OD2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 274": "OE1" <-> "OE2" Residue "F GLU 282": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 317": "OE1" <-> "OE2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14789 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2423 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2369 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain breaks: 2 Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2401 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 305} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2287 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2585 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2562 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.83, per 1000 atoms: 0.53 Number of scatterers: 14789 At special positions: 0 Unit cell: (135.16, 128.62, 80.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2880 8.00 N 2584 7.00 C 9244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.24 Conformation dependent library (CDL) restraints added in 2.9 seconds 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 49.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.509A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.543A pdb=" N ILE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.575A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.508A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.638A pdb=" N LYS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.601A pdb=" N MET A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.578A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.028A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.958A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.969A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.585A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.554A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.527A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.315A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.849A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.977A pdb=" N ASN B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.774A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.944A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.739A pdb=" N THR B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.760A pdb=" N ILE B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 377 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.568A pdb=" N LEU B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.535A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.510A pdb=" N VAL B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.819A pdb=" N ASN B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.865A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.604A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 4.242A pdb=" N SER C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 19' Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.523A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.754A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.898A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.656A pdb=" N VAL C 245 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 248' Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.984A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.518A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.693A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.618A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.860A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.900A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.794A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.996A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.604A pdb=" N ALA C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.723A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.694A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.553A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.606A pdb=" N ILE D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 287 " --> pdb=" O TRP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.577A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.612A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.702A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.646A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.525A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.840A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 422 through 432 removed outlier: 3.702A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 453 removed outlier: 3.700A pdb=" N THR D 440 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN D 453 " --> pdb=" O ALA D 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 66 removed outlier: 3.989A pdb=" N ALA E 56 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.662A pdb=" N ALA E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 119 through 125 Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.781A pdb=" N ASP E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 270 through 284 removed outlier: 4.188A pdb=" N GLU E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 Processing helix chain 'E' and resid 305 through 313 removed outlier: 3.532A pdb=" N SER E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.739A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.632A pdb=" N LYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU E 377 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 395 removed outlier: 3.593A pdb=" N VAL E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.850A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 427 removed outlier: 3.856A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 438 through 452 removed outlier: 4.131A pdb=" N TYR E 442 " --> pdb=" O ARG E 438 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 444 " --> pdb=" O THR E 440 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.757A pdb=" N GLY F 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F 24 " --> pdb=" O ARG F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.744A pdb=" N ARG F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.935A pdb=" N ALA F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.645A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 244 through 250 removed outlier: 3.633A pdb=" N VAL F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 264 Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.540A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.663A pdb=" N SER F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.878A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.774A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.647A pdb=" N THR F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 392 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 416 removed outlier: 4.250A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 433 removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 452 removed outlier: 3.560A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.637A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 360 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.437A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.277A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.601A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 360 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 97 Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 325 through 328 removed outlier: 6.683A pdb=" N VAL D 73 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR D 328 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 75 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.737A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 104 removed outlier: 5.933A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'F' and resid 332 through 334 435 hydrogen bonds defined for protein. 1248 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: 4.09 Time building geometry restraints manager: 5.79 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: 4978 1.34 - 1.46: 2664 1.46 - 1.58: 7195 1.58 - 1.70: 18 1.70 - 1.81: 120 Bond restraints: 14975 Sorted by residual: bond pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.88e+00 bond pdb=" CA THR C 10 " pdb=" CB THR C 10 " ideal model delta sigma weight residual 1.532 1.564 -0.033 1.36e-02 5.41e+03 5.79e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.72e+00 bond pdb=" N LYS C 7 " pdb=" CA LYS C 7 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.15e-02 7.56e+03 3.59e+00 ... (remaining 14970 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.65: 386 106.65 - 114.27: 9043 114.27 - 121.89: 7697 121.89 - 129.51: 3043 129.51 - 137.12: 63 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 113.53 106.69 6.84 9.80e-01 1.04e+00 4.87e+01 angle pdb=" C VAL A 6 " pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 120.82 130.86 -10.04 1.50e+00 4.44e-01 4.48e+01 angle pdb=" C VAL B 6 " pdb=" N LYS B 7 " pdb=" CA LYS B 7 " ideal model delta sigma weight residual 120.82 130.84 -10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" C ILE E 13 " pdb=" N ARG E 14 " pdb=" CA ARG E 14 " ideal model delta sigma weight residual 121.19 129.37 -8.18 1.59e+00 3.96e-01 2.65e+01 angle pdb=" C GLU D 378 " pdb=" N ASP D 379 " pdb=" CA ASP D 379 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 8927 33.36 - 66.72: 237 66.72 - 100.08: 37 100.08 - 133.44: 3 133.44 - 166.81: 2 Dihedral angle restraints: 9206 sinusoidal: 3737 harmonic: 5469 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 106.81 -166.81 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 81.57 -141.57 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.11 119.10 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1993 0.063 - 0.125: 336 0.125 - 0.188: 52 0.188 - 0.251: 9 0.251 - 0.313: 5 Chirality restraints: 2395 Sorted by residual: chirality pdb=" CB VAL E 10 " pdb=" CA VAL E 10 " pdb=" CG1 VAL E 10 " pdb=" CG2 VAL E 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL F 10 " pdb=" CA VAL F 10 " pdb=" CG1 VAL F 10 " pdb=" CG2 VAL F 10 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL F 16 " pdb=" N VAL F 16 " pdb=" C VAL F 16 " pdb=" CB VAL F 16 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2392 not shown) Planarity restraints: 2578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C VAL A 327 " -0.048 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 328 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO E 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 11 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 10 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO F 11 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 11 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 11 " 0.038 5.00e-02 4.00e+02 ... (remaining 2575 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 113 2.58 - 3.16: 10751 3.16 - 3.74: 21197 3.74 - 4.32: 29446 4.32 - 4.90: 48326 Nonbonded interactions: 109833 Sorted by model distance: nonbonded pdb=" CB ARG F 14 " pdb=" CG1 VAL F 242 " model vdw 1.999 3.860 nonbonded pdb=" O VAL A 6 " pdb=" OD2 ASP A 242 " model vdw 2.037 3.040 nonbonded pdb=" OG SER E 243 " pdb=" OE1 GLU E 246 " model vdw 2.300 2.440 nonbonded pdb=" O SER E 363 " pdb=" OG1 THR E 367 " model vdw 2.304 2.440 nonbonded pdb=" OG SER E 114 " pdb=" OE1 GLU E 117 " model vdw 2.314 2.440 ... (remaining 109828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'B' and (resid 2 through 120 or resid 239 through 248 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 452 or resid 501)) selection = (chain 'C' and (resid 2 through 120 or resid 239 through 248 or resid 274 throug \ h 452 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 23 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 453 or resid 501)) selection = (chain 'E' and (resid 23 through 127 or resid 243 through 249 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 282 or \ (resid 283 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 4 through 451 or (resid 452 through 453 and (name N or name CA or name C or name \ O or name CB )) or resid 501)) selection = (chain 'F' and (resid 23 through 127 or resid 243 through 249 or resid 270 throu \ gh 451 or (resid 452 through 453 and (name N or name CA or name C or name O or n \ ame CB )) or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.060 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0230 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 0.060 14975 Z= 0.271 Angle : 0.910 10.039 20232 Z= 0.529 Chirality : 0.052 0.313 2395 Planarity : 0.006 0.068 2578 Dihedral : 16.348 166.805 5668 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.19 % Allowed : 8.69 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.84 (0.13), residues: 1875 helix: -4.93 (0.05), residues: 871 sheet: -2.18 (0.33), residues: 199 loop : -2.85 (0.16), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS D 245 PHE 0.016 0.001 PHE F 257 TYR 0.009 0.001 TYR B 438 ARG 0.008 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.3534 (mttt) cc_final: 0.3241 (tptp) REVERT: B 61 MET cc_start: 0.0763 (tpp) cc_final: 0.0240 (tpt) REVERT: B 365 LEU cc_start: 0.0754 (mt) cc_final: -0.0956 (tt) REVERT: C 113 MET cc_start: 0.0870 (tpt) cc_final: 0.0538 (ttm) REVERT: D 424 ASP cc_start: 0.1234 (m-30) cc_final: 0.0589 (m-30) REVERT: F 41 GLN cc_start: 0.3192 (tp40) cc_final: 0.2046 (mt0) REVERT: F 320 MET cc_start: -0.0532 (ptt) cc_final: -0.1427 (mtt) outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.2700 time to fit residues: 65.8121 Evaluate side-chains 111 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 429 HIS ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 241 HIS B 316 HIS C 18 HIS C 42 GLN C 85 GLN C 247 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS D 78 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 329 ASN D 344 HIS D 369 GLN E 78 GLN E 251 ASN E 344 HIS ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1510 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 14975 Z= 0.414 Angle : 1.011 11.826 20232 Z= 0.505 Chirality : 0.055 0.698 2395 Planarity : 0.008 0.097 2578 Dihedral : 10.798 177.599 2113 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.75 % Rotamer: Outliers : 2.35 % Allowed : 15.23 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.62 (0.15), residues: 1875 helix: -3.72 (0.11), residues: 883 sheet: -2.12 (0.36), residues: 182 loop : -2.30 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 283 HIS 0.014 0.004 HIS C 305 PHE 0.024 0.004 PHE F 297 TYR 0.028 0.003 TYR B 438 ARG 0.014 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.2548 (tmm) cc_final: 0.1754 (tmm) REVERT: A 450 GLN cc_start: 0.2219 (tp40) cc_final: 0.1813 (tt0) REVERT: B 61 MET cc_start: 0.1271 (tpp) cc_final: 0.0838 (tpt) REVERT: B 359 MET cc_start: 0.2739 (pmm) cc_final: 0.2423 (pmm) REVERT: C 68 LEU cc_start: 0.1287 (OUTLIER) cc_final: 0.0654 (mp) REVERT: C 364 MET cc_start: 0.3627 (mtt) cc_final: 0.0960 (ttp) REVERT: D 380 VAL cc_start: 0.2895 (OUTLIER) cc_final: 0.2668 (m) REVERT: D 422 GLN cc_start: -0.1149 (OUTLIER) cc_final: -0.1467 (mt0) REVERT: E 320 MET cc_start: -0.0021 (tpt) cc_final: -0.0700 (tpt) REVERT: E 401 TYR cc_start: 0.3698 (t80) cc_final: 0.2715 (t80) REVERT: F 41 GLN cc_start: 0.4956 (tp40) cc_final: 0.3918 (tp40) REVERT: F 320 MET cc_start: 0.0712 (ptt) cc_final: -0.0724 (mtt) REVERT: F 328 THR cc_start: 0.1266 (OUTLIER) cc_final: 0.0703 (t) outliers start: 37 outliers final: 16 residues processed: 169 average time/residue: 0.2428 time to fit residues: 63.0260 Evaluate side-chains 137 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1513 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14975 Z= 0.196 Angle : 0.700 10.999 20232 Z= 0.336 Chirality : 0.044 0.201 2395 Planarity : 0.005 0.072 2578 Dihedral : 9.814 157.786 2113 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.22 % Allowed : 17.89 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.16), residues: 1875 helix: -2.78 (0.14), residues: 897 sheet: -1.83 (0.35), residues: 185 loop : -2.04 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.005 0.001 HIS C 20 PHE 0.017 0.002 PHE A 312 TYR 0.010 0.002 TYR E 446 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.1614 (OUTLIER) cc_final: 0.0152 (tpt) REVERT: B 364 MET cc_start: -0.0247 (ttp) cc_final: -0.0779 (ptp) REVERT: C 113 MET cc_start: 0.2756 (ttt) cc_final: 0.2209 (ttt) REVERT: C 364 MET cc_start: 0.3341 (mtt) cc_final: 0.0472 (ttp) REVERT: D 380 VAL cc_start: 0.2897 (m) cc_final: 0.2666 (m) REVERT: D 401 TYR cc_start: 0.5071 (m-80) cc_final: 0.4814 (m-80) REVERT: E 320 MET cc_start: -0.0101 (tpt) cc_final: -0.0635 (tpt) REVERT: F 41 GLN cc_start: 0.4896 (tp40) cc_final: 0.4508 (mm-40) REVERT: F 90 MET cc_start: 0.1572 (tmm) cc_final: 0.0920 (tmm) REVERT: F 113 MET cc_start: -0.0237 (ptp) cc_final: -0.0858 (ptt) REVERT: F 320 MET cc_start: 0.0674 (ptt) cc_final: -0.0830 (mtt) REVERT: F 404 GLN cc_start: -0.0084 (OUTLIER) cc_final: -0.4251 (tm-30) outliers start: 35 outliers final: 14 residues processed: 147 average time/residue: 0.2521 time to fit residues: 56.6909 Evaluate side-chains 124 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1639 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14975 Z= 0.191 Angle : 0.694 12.111 20232 Z= 0.331 Chirality : 0.044 0.280 2395 Planarity : 0.004 0.059 2578 Dihedral : 9.464 141.318 2113 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.66 % Allowed : 19.54 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.17), residues: 1875 helix: -2.34 (0.15), residues: 898 sheet: -1.68 (0.35), residues: 189 loop : -1.91 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 283 HIS 0.006 0.001 HIS E 245 PHE 0.018 0.002 PHE C 300 TYR 0.012 0.001 TYR E 446 ARG 0.008 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 ASP cc_start: 0.1164 (OUTLIER) cc_final: -0.0531 (p0) REVERT: B 83 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6769 (tt) REVERT: B 113 MET cc_start: 0.1752 (OUTLIER) cc_final: 0.0285 (tpt) REVERT: B 364 MET cc_start: -0.0226 (ttp) cc_final: -0.0635 (ptp) REVERT: C 364 MET cc_start: 0.3435 (mtt) cc_final: 0.0734 (ttp) REVERT: D 62 MET cc_start: 0.4141 (tpp) cc_final: 0.3762 (mmp) REVERT: D 346 ILE cc_start: 0.1676 (OUTLIER) cc_final: 0.1323 (mt) REVERT: D 380 VAL cc_start: 0.3363 (OUTLIER) cc_final: 0.3140 (m) REVERT: E 88 MET cc_start: 0.4696 (tpp) cc_final: 0.4413 (tpt) REVERT: E 320 MET cc_start: -0.0073 (tpt) cc_final: -0.0514 (tpt) REVERT: F 41 GLN cc_start: 0.4941 (tp40) cc_final: 0.3872 (tm-30) REVERT: F 65 GLU cc_start: -0.2310 (OUTLIER) cc_final: -0.3618 (mm-30) REVERT: F 113 MET cc_start: -0.0464 (ptp) cc_final: -0.1360 (ptt) REVERT: F 320 MET cc_start: 0.0242 (ptt) cc_final: -0.1017 (mtt) outliers start: 42 outliers final: 23 residues processed: 145 average time/residue: 0.2369 time to fit residues: 53.2129 Evaluate side-chains 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 125 optimal weight: 0.0470 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 0.3980 chunk 45 optimal weight: 0.0070 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS D 49 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1750 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14975 Z= 0.184 Angle : 0.680 10.742 20232 Z= 0.322 Chirality : 0.043 0.227 2395 Planarity : 0.004 0.056 2578 Dihedral : 8.960 115.695 2113 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.92 % Allowed : 20.49 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.18), residues: 1875 helix: -1.88 (0.15), residues: 906 sheet: -1.50 (0.39), residues: 171 loop : -1.79 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.009 0.001 HIS C 305 PHE 0.017 0.002 PHE C 300 TYR 0.012 0.001 TYR D 362 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.3090 (tmm) cc_final: 0.2249 (tmm) REVERT: A 439 ASP cc_start: 0.1183 (OUTLIER) cc_final: -0.0483 (p0) REVERT: B 113 MET cc_start: 0.1804 (OUTLIER) cc_final: 0.0232 (tpt) REVERT: B 364 MET cc_start: -0.0229 (ttp) cc_final: -0.0698 (ptp) REVERT: C 102 TYR cc_start: 0.3233 (m-80) cc_final: 0.0775 (m-80) REVERT: C 116 PHE cc_start: -0.2422 (OUTLIER) cc_final: -0.2991 (m-80) REVERT: C 364 MET cc_start: 0.2974 (mtt) cc_final: 0.0450 (ttp) REVERT: D 62 MET cc_start: 0.4495 (tpp) cc_final: 0.4256 (mmp) REVERT: D 346 ILE cc_start: 0.1283 (OUTLIER) cc_final: 0.0949 (mt) REVERT: D 380 VAL cc_start: 0.3841 (OUTLIER) cc_final: 0.3624 (m) REVERT: E 88 MET cc_start: 0.4753 (tpp) cc_final: 0.4457 (tpt) REVERT: E 320 MET cc_start: 0.0176 (tpt) cc_final: -0.0124 (tpt) REVERT: E 326 MET cc_start: 0.2289 (OUTLIER) cc_final: 0.2084 (ptt) REVERT: F 65 GLU cc_start: -0.2238 (OUTLIER) cc_final: -0.3769 (mm-30) REVERT: F 113 MET cc_start: -0.0548 (ptp) cc_final: -0.1621 (ptt) REVERT: F 320 MET cc_start: 0.0504 (ptt) cc_final: -0.0759 (mtt) REVERT: F 325 ILE cc_start: 0.3030 (OUTLIER) cc_final: 0.2283 (mm) REVERT: F 382 MET cc_start: -0.1291 (mtm) cc_final: -0.1679 (mtm) outliers start: 46 outliers final: 23 residues processed: 159 average time/residue: 0.2453 time to fit residues: 59.6968 Evaluate side-chains 144 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.0270 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1776 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14975 Z= 0.160 Angle : 0.647 10.718 20232 Z= 0.303 Chirality : 0.043 0.187 2395 Planarity : 0.004 0.054 2578 Dihedral : 8.721 110.895 2113 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.86 % Allowed : 21.45 % Favored : 75.70 % 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: -2.40 (0.18), residues: 1875 helix: -1.47 (0.16), residues: 897 sheet: -1.52 (0.38), residues: 179 loop : -1.57 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.004 0.001 HIS E 245 PHE 0.017 0.001 PHE C 300 TYR 0.010 0.001 TYR D 362 ARG 0.005 0.000 ARG E 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2228 (pmm) cc_final: -0.0241 (ttm) REVERT: A 371 MET cc_start: 0.3561 (tmm) cc_final: 0.2164 (tmm) REVERT: A 372 LYS cc_start: 0.0921 (OUTLIER) cc_final: 0.0717 (mtmm) REVERT: A 375 ILE cc_start: -0.1006 (OUTLIER) cc_final: -0.1263 (mt) REVERT: A 439 ASP cc_start: 0.1161 (OUTLIER) cc_final: -0.0528 (p0) REVERT: B 113 MET cc_start: 0.1851 (OUTLIER) cc_final: 0.0256 (tpt) REVERT: B 342 GLU cc_start: 0.4294 (OUTLIER) cc_final: 0.2773 (mm-30) REVERT: B 364 MET cc_start: -0.0030 (ttp) cc_final: -0.0778 (ptp) REVERT: B 386 ILE cc_start: -0.1635 (OUTLIER) cc_final: -0.1974 (tt) REVERT: C 96 MET cc_start: 0.4175 (mpp) cc_final: 0.3709 (mpp) REVERT: C 102 TYR cc_start: 0.3590 (m-80) cc_final: 0.3086 (m-80) REVERT: C 116 PHE cc_start: -0.2287 (OUTLIER) cc_final: -0.2853 (m-80) REVERT: C 364 MET cc_start: 0.2864 (mtt) cc_final: 0.0432 (ttp) REVERT: C 403 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2593 (tp) REVERT: D 62 MET cc_start: 0.4707 (tpp) cc_final: 0.4454 (mmp) REVERT: D 380 VAL cc_start: 0.3918 (OUTLIER) cc_final: 0.3715 (m) REVERT: E 88 MET cc_start: 0.4776 (tpp) cc_final: 0.4489 (tpt) REVERT: E 336 ARG cc_start: 0.3112 (OUTLIER) cc_final: 0.2757 (mtm-85) REVERT: F 65 GLU cc_start: -0.2624 (OUTLIER) cc_final: -0.3961 (mm-30) REVERT: F 90 MET cc_start: 0.2358 (tmm) cc_final: 0.1828 (tmm) REVERT: F 320 MET cc_start: 0.0098 (ptt) cc_final: -0.1066 (mtt) REVERT: F 325 ILE cc_start: 0.3057 (OUTLIER) cc_final: 0.2269 (mm) REVERT: F 328 THR cc_start: 0.1120 (OUTLIER) cc_final: 0.0714 (t) REVERT: F 382 MET cc_start: -0.1424 (mtm) cc_final: -0.1791 (mtm) outliers start: 45 outliers final: 20 residues processed: 162 average time/residue: 0.2529 time to fit residues: 61.7654 Evaluate side-chains 152 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 92 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1697 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14975 Z= 0.137 Angle : 0.614 8.709 20232 Z= 0.288 Chirality : 0.042 0.189 2395 Planarity : 0.003 0.047 2578 Dihedral : 8.476 112.817 2113 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.60 % Allowed : 21.83 % Favored : 75.57 % 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: -2.04 (0.19), residues: 1875 helix: -1.21 (0.17), residues: 907 sheet: -1.27 (0.39), residues: 171 loop : -1.38 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.006 0.001 HIS C 305 PHE 0.017 0.001 PHE C 300 TYR 0.012 0.001 TYR D 362 ARG 0.005 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1419 (mmp) cc_final: 0.0335 (mmp) REVERT: A 364 MET cc_start: 0.1974 (pmm) cc_final: -0.0376 (ttm) REVERT: A 371 MET cc_start: 0.3066 (tmm) cc_final: 0.1755 (tmm) REVERT: A 439 ASP cc_start: 0.1006 (OUTLIER) cc_final: -0.0656 (p0) REVERT: B 113 MET cc_start: 0.1917 (OUTLIER) cc_final: 0.1472 (mmp) REVERT: B 342 GLU cc_start: 0.4073 (OUTLIER) cc_final: 0.2672 (mm-30) REVERT: B 364 MET cc_start: -0.0076 (ttp) cc_final: -0.0753 (ptt) REVERT: C 96 MET cc_start: 0.4387 (mpp) cc_final: 0.3903 (mpp) REVERT: C 102 TYR cc_start: 0.3775 (m-80) cc_final: 0.3054 (m-80) REVERT: C 116 PHE cc_start: -0.1841 (OUTLIER) cc_final: -0.2431 (m-80) REVERT: C 306 MET cc_start: 0.2547 (pmm) cc_final: -0.0601 (ttt) REVERT: C 364 MET cc_start: 0.2242 (mtt) cc_final: 0.0380 (ttp) REVERT: C 403 LEU cc_start: 0.2531 (OUTLIER) cc_final: 0.2247 (tp) REVERT: E 88 MET cc_start: 0.4783 (tpp) cc_final: 0.4488 (tpt) REVERT: E 326 MET cc_start: 0.1962 (OUTLIER) cc_final: 0.1719 (ptt) REVERT: E 336 ARG cc_start: 0.2862 (OUTLIER) cc_final: 0.2554 (mtm-85) REVERT: E 392 ARG cc_start: 0.3773 (tpt170) cc_final: 0.1720 (mtm110) REVERT: F 65 GLU cc_start: -0.2688 (OUTLIER) cc_final: -0.4699 (mt-10) REVERT: F 113 MET cc_start: -0.0871 (ptp) cc_final: -0.3871 (mtp) REVERT: F 320 MET cc_start: 0.0089 (ptt) cc_final: -0.1103 (mtt) REVERT: F 325 ILE cc_start: 0.2909 (OUTLIER) cc_final: 0.2031 (mm) REVERT: F 328 THR cc_start: 0.1056 (OUTLIER) cc_final: 0.0691 (t) REVERT: F 382 MET cc_start: -0.1240 (mtm) cc_final: -0.1632 (mtm) REVERT: F 404 GLN cc_start: 0.0565 (OUTLIER) cc_final: -0.3349 (tm-30) outliers start: 41 outliers final: 18 residues processed: 150 average time/residue: 0.2475 time to fit residues: 56.4935 Evaluate side-chains 145 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 0.0980 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1819 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14975 Z= 0.158 Angle : 0.633 9.036 20232 Z= 0.298 Chirality : 0.043 0.174 2395 Planarity : 0.004 0.049 2578 Dihedral : 8.376 116.274 2113 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.28 % Allowed : 21.95 % Favored : 75.76 % 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: -1.90 (0.19), residues: 1875 helix: -1.10 (0.17), residues: 916 sheet: -1.24 (0.39), residues: 176 loop : -1.28 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS C 348 PHE 0.016 0.001 PHE C 300 TYR 0.009 0.001 TYR D 362 ARG 0.009 0.000 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2183 (pmm) cc_final: -0.0040 (ttm) REVERT: A 372 LYS cc_start: 0.0784 (OUTLIER) cc_final: 0.0443 (mtmm) REVERT: A 439 ASP cc_start: 0.1146 (OUTLIER) cc_final: -0.0567 (p0) REVERT: B 113 MET cc_start: 0.1963 (OUTLIER) cc_final: 0.1451 (mmp) REVERT: B 342 GLU cc_start: 0.4335 (OUTLIER) cc_final: 0.2576 (mm-30) REVERT: B 364 MET cc_start: 0.0191 (ttp) cc_final: -0.0569 (ptt) REVERT: B 386 ILE cc_start: -0.1465 (OUTLIER) cc_final: -0.1827 (tt) REVERT: C 96 MET cc_start: 0.4024 (mpp) cc_final: 0.3770 (mpp) REVERT: C 102 TYR cc_start: 0.4249 (m-80) cc_final: 0.3428 (m-80) REVERT: C 306 MET cc_start: 0.2659 (pmm) cc_final: -0.0373 (ttt) REVERT: C 364 MET cc_start: 0.2350 (mtt) cc_final: 0.0567 (ttp) REVERT: C 403 LEU cc_start: 0.2870 (OUTLIER) cc_final: 0.2563 (tp) REVERT: E 88 MET cc_start: 0.4838 (tpp) cc_final: 0.4554 (tpt) REVERT: E 90 MET cc_start: 0.2324 (mtt) cc_final: 0.1715 (ptp) REVERT: E 330 ARG cc_start: 0.3628 (mmm160) cc_final: 0.3315 (mmm160) REVERT: E 336 ARG cc_start: 0.3197 (OUTLIER) cc_final: 0.2746 (mtm-85) REVERT: F 65 GLU cc_start: -0.2852 (OUTLIER) cc_final: -0.4606 (mm-30) REVERT: F 320 MET cc_start: 0.0208 (ptt) cc_final: -0.1169 (mtt) REVERT: F 382 MET cc_start: -0.1425 (mtm) cc_final: -0.1827 (mtm) REVERT: F 404 GLN cc_start: 0.0828 (OUTLIER) cc_final: -0.2968 (tm-30) outliers start: 36 outliers final: 22 residues processed: 148 average time/residue: 0.2698 time to fit residues: 59.4607 Evaluate side-chains 144 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1973 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14975 Z= 0.185 Angle : 0.684 10.688 20232 Z= 0.324 Chirality : 0.044 0.250 2395 Planarity : 0.004 0.054 2578 Dihedral : 8.540 118.345 2113 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.41 % Allowed : 22.34 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.04 (0.19), residues: 1875 helix: -1.11 (0.17), residues: 925 sheet: -1.54 (0.37), residues: 176 loop : -1.42 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 283 HIS 0.006 0.001 HIS C 348 PHE 0.015 0.002 PHE A 312 TYR 0.013 0.002 TYR F 401 ARG 0.004 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2251 (pmm) cc_final: 0.0667 (ttm) REVERT: A 439 ASP cc_start: 0.1238 (OUTLIER) cc_final: -0.0554 (p0) REVERT: B 113 MET cc_start: 0.1774 (OUTLIER) cc_final: 0.1251 (mmp) REVERT: B 342 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.3211 (mm-30) REVERT: B 364 MET cc_start: 0.0364 (ttp) cc_final: -0.0362 (ptp) REVERT: B 386 ILE cc_start: -0.1623 (OUTLIER) cc_final: -0.1995 (tt) REVERT: C 96 MET cc_start: 0.3917 (mpp) cc_final: 0.3631 (mpp) REVERT: C 102 TYR cc_start: 0.5060 (m-80) cc_final: 0.4247 (m-80) REVERT: C 306 MET cc_start: 0.2439 (pmm) cc_final: -0.0134 (ttt) REVERT: C 364 MET cc_start: 0.2467 (mtt) cc_final: 0.0417 (ttp) REVERT: C 403 LEU cc_start: 0.2794 (OUTLIER) cc_final: 0.2495 (tp) REVERT: E 88 MET cc_start: 0.4837 (tpp) cc_final: 0.4578 (tpt) REVERT: E 90 MET cc_start: 0.2312 (mtt) cc_final: 0.1142 (ptp) REVERT: E 320 MET cc_start: 0.0967 (tpt) cc_final: -0.0285 (tpt) REVERT: E 336 ARG cc_start: 0.3200 (OUTLIER) cc_final: 0.2698 (mtm-85) REVERT: F 65 GLU cc_start: -0.3078 (OUTLIER) cc_final: -0.4338 (mm-30) REVERT: F 320 MET cc_start: 0.0491 (ptt) cc_final: -0.1389 (mtt) REVERT: F 382 MET cc_start: -0.1308 (mtm) cc_final: -0.1695 (mtm) REVERT: F 404 GLN cc_start: 0.1112 (OUTLIER) cc_final: -0.2417 (tm-30) outliers start: 38 outliers final: 23 residues processed: 143 average time/residue: 0.2693 time to fit residues: 58.1307 Evaluate side-chains 141 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.6980 chunk 84 optimal weight: 0.0370 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 172 optimal weight: 0.2980 chunk 149 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1851 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14975 Z= 0.136 Angle : 0.624 10.033 20232 Z= 0.293 Chirality : 0.043 0.327 2395 Planarity : 0.003 0.048 2578 Dihedral : 8.271 119.136 2113 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.78 % Allowed : 23.22 % Favored : 75.00 % 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: -1.70 (0.19), residues: 1875 helix: -0.84 (0.17), residues: 928 sheet: -1.26 (0.38), residues: 170 loop : -1.28 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 283 HIS 0.005 0.001 HIS C 348 PHE 0.018 0.001 PHE C 300 TYR 0.008 0.001 TYR D 362 ARG 0.007 0.000 ARG E 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3750 Ramachandran restraints generated. 1875 Oldfield, 0 Emsley, 1875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.1883 (pmm) cc_final: 0.0544 (ttm) REVERT: A 439 ASP cc_start: 0.0939 (OUTLIER) cc_final: -0.0919 (p0) REVERT: B 364 MET cc_start: 0.0170 (ttp) cc_final: -0.0481 (ptt) REVERT: B 386 ILE cc_start: -0.1794 (OUTLIER) cc_final: -0.2170 (tt) REVERT: C 96 MET cc_start: 0.4037 (mpp) cc_final: 0.3791 (mmm) REVERT: C 102 TYR cc_start: 0.4783 (m-80) cc_final: 0.3919 (m-80) REVERT: C 306 MET cc_start: 0.2500 (pmm) cc_final: 0.0185 (ttt) REVERT: C 364 MET cc_start: 0.2391 (mtt) cc_final: 0.0439 (ttp) REVERT: C 403 LEU cc_start: 0.2479 (OUTLIER) cc_final: 0.2150 (tp) REVERT: D 380 VAL cc_start: 0.3943 (m) cc_final: 0.3704 (m) REVERT: E 88 MET cc_start: 0.4761 (tpp) cc_final: 0.4531 (tpt) REVERT: E 90 MET cc_start: 0.2060 (mtt) cc_final: 0.1479 (ptp) REVERT: E 336 ARG cc_start: 0.3631 (OUTLIER) cc_final: 0.2959 (mtm-85) REVERT: F 65 GLU cc_start: -0.3278 (OUTLIER) cc_final: -0.4429 (mm-30) REVERT: F 90 MET cc_start: 0.1906 (tmm) cc_final: 0.0273 (tpt) REVERT: F 113 MET cc_start: -0.0249 (ptp) cc_final: -0.3415 (mtp) REVERT: F 320 MET cc_start: 0.0429 (ptt) cc_final: -0.1417 (mtt) REVERT: F 382 MET cc_start: -0.1328 (mtm) cc_final: -0.1774 (mtm) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 0.2601 time to fit residues: 55.0441 Evaluate side-chains 139 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 336 ARG Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 34 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.247630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223439 restraints weight = 21095.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.228028 restraints weight = 13443.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.231215 restraints weight = 9473.643| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1849 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14975 Z= 0.164 Angle : 0.654 10.501 20232 Z= 0.307 Chirality : 0.043 0.381 2395 Planarity : 0.004 0.050 2578 Dihedral : 8.230 119.459 2113 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.90 % Allowed : 23.48 % Favored : 74.62 % 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: -1.65 (0.19), residues: 1875 helix: -0.80 (0.17), residues: 919 sheet: -1.35 (0.38), residues: 162 loop : -1.22 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 283 HIS 0.005 0.001 HIS C 348 PHE 0.015 0.001 PHE C 300 TYR 0.019 0.001 TYR B 314 ARG 0.008 0.001 ARG E 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.27 seconds wall clock time: 47 minutes 14.02 seconds (2834.02 seconds total)