Starting phenix.real_space_refine on Mon Apr 8 23:41:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/04_2024/6qi8_4552_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/04_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_4552/04_2024/6qi8_4552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/04_2024/6qi8_4552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/04_2024/6qi8_4552_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qi8_4552/04_2024/6qi8_4552_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.89, 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: 5.63 Conformation dependent library (CDL) restraints added in 2.7 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... running ksdssp... Secondary structure from input PDB file: 98 helices and 16 sheets defined 43.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 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 76 through 85 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) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 108 through 116 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 243 through 246 No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.638A pdb=" N LYS A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 309 through 316 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 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 368 through 381 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) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.958A pdb=" N HIS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.772A pdb=" N GLN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.595A pdb=" N LEU A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.554A pdb=" N GLU A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 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 43 through 57 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 78 through 86 removed outlier: 3.849A pdb=" N ALA B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 108 through 116 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 246 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) 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 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 309 through 317 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) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 371 through 380 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 388 through 394 removed outlier: 3.710A pdb=" N HIS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.535A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.617A pdb=" N GLN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'B' and resid 427 through 436 removed outlier: 4.207A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.604A pdb=" N ASP B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 18 removed outlier: 3.547A pdb=" N HIS C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 44 through 57 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 76 through 82 removed outlier: 3.754A pdb=" N ALA C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.740A pdb=" N VAL C 111 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 114 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 116 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 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) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 274 through 277 No H-bonds generated for 'chain 'C' and resid 274 through 277' Processing helix chain 'C' and resid 280 through 289 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 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 317 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 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.693A pdb=" N ASP C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 368 through 382 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 388 through 400 removed outlier: 3.769A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.794A pdb=" N ILE C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.535A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 449 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 50 through 64 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 85 through 92 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 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 115 through 123 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 248 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.615A pdb=" N GLN D 275 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE D 276 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 277 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 281 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU D 282 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP D 283 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 284 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 317 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) removed outlier: 4.167A pdb=" N GLU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.702A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG D 353 " --> pdb=" O ASP D 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 353' Processing helix chain 'D' and resid 364 through 377 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 384 through 396 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 405 through 408 No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 432 removed outlier: 4.824A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 452 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) Processing helix chain 'E' and resid 50 through 65 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 84 through 92 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 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 244 through 252 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) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 271 through 283 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 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 306 through 312 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) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.739A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 353' Processing helix chain 'E' and resid 364 through 377 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) Processing helix chain 'E' and resid 386 through 394 removed outlier: 3.537A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 415 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 423 through 432 removed outlier: 3.613A pdb=" N TYR E 430 " --> pdb=" O ILE E 426 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 451 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) Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 50 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 83 through 93 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) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 245 through 249 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 263 Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.540A pdb=" N ALA F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 306 through 317 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) removed outlier: 3.913A pdb=" N GLU F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.878A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 366 through 376 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 384 through 396 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 405 through 415 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 424 through 432 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 441 through 451 removed outlier: 3.560A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 358 through 363 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: 7.418A pdb=" N THR A 363 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA A 69 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 329 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY A 70 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER A 331 " --> pdb=" O GLY A 70 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 93 through 97 removed outlier: 7.264A pdb=" N VAL A 298 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N MET A 96 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE A 300 " --> pdb=" O MET A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 363 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: 7.328A pdb=" N THR B 363 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 69 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 94 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 300 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= F, first strand: chain 'C' and resid 65 through 70 Processing sheet with id= G, first strand: chain 'C' and resid 94 through 97 removed outlier: 6.733A pdb=" N ILE C 326 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 301 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= I, first strand: chain 'D' and resid 354 through 358 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) removed outlier: 3.844A pdb=" N THR D 328 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 102 through 104 removed outlier: 6.531A pdb=" N PHE D 297 " --> pdb=" O ILE D 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= L, first strand: chain 'E' and resid 354 through 358 removed outlier: 6.779A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 101 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 127 through 130 Processing sheet with id= N, first strand: chain 'E' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.834A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 328 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 332 through 334 333 hydrogen bonds defined for protein. 963 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: 3.81 Time building geometry restraints manager: 6.10 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: 114 2.58 - 3.16: 10795 3.16 - 3.74: 21269 3.74 - 4.32: 29684 4.32 - 4.90: 48379 Nonbonded interactions: 110241 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 110236 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: 0.860 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: 4.290 Check model and map are aligned: 0.260 Set scattering table: 0.120 Process input model: 40.160 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.870 ------------------------------------------------------------------------------- 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 : 1.636 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: 0.2881 time to fit residues: 69.5714 Evaluate side-chains 111 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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: 0.7980 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 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** 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 E 369 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1612 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 14975 Z= 0.431 Angle : 1.040 11.759 20232 Z= 0.517 Chirality : 0.055 0.500 2395 Planarity : 0.008 0.091 2578 Dihedral : 10.945 174.937 2113 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 2.54 % Allowed : 15.42 % Favored : 82.04 % 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: -4.76 (0.15), residues: 1875 helix: -3.98 (0.10), residues: 862 sheet: -2.09 (0.36), residues: 192 loop : -2.27 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 283 HIS 0.016 0.004 HIS F 302 PHE 0.028 0.004 PHE D 100 TYR 0.029 0.004 TYR A 405 ARG 0.018 0.001 ARG F 14 *********************** 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 171 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1743 (tpp) cc_final: 0.1541 (mmp) REVERT: A 439 ASP cc_start: 0.1290 (OUTLIER) cc_final: -0.0706 (p0) REVERT: B 61 MET cc_start: 0.1313 (tpp) cc_final: 0.0999 (tpt) REVERT: B 332 ASN cc_start: 0.5285 (OUTLIER) cc_final: 0.4992 (m110) REVERT: B 359 MET cc_start: 0.2522 (pmm) cc_final: 0.2051 (pmm) REVERT: C 113 MET cc_start: 0.2045 (tpt) cc_final: 0.1284 (ttt) REVERT: C 364 MET cc_start: 0.3716 (mtt) cc_final: 0.0843 (ttp) REVERT: D 88 MET cc_start: 0.0067 (mtp) cc_final: -0.1038 (mtp) REVERT: D 330 ARG cc_start: 0.4456 (mtp85) cc_final: 0.1675 (mtp85) REVERT: D 380 VAL cc_start: 0.2773 (m) cc_final: 0.2567 (m) REVERT: D 422 GLN cc_start: -0.0784 (OUTLIER) cc_final: -0.1247 (mt0) REVERT: E 320 MET cc_start: -0.0006 (tpt) cc_final: -0.0688 (tpt) REVERT: E 336 ARG cc_start: 0.1484 (ttt90) cc_final: 0.1282 (ttm-80) REVERT: F 41 GLN cc_start: 0.4864 (tp40) cc_final: 0.3907 (tp40) REVERT: F 320 MET cc_start: 0.0750 (ptt) cc_final: -0.0696 (mtt) REVERT: F 328 THR cc_start: 0.1119 (OUTLIER) cc_final: 0.0533 (t) outliers start: 40 outliers final: 18 residues processed: 167 average time/residue: 0.2660 time to fit residues: 67.8455 Evaluate side-chains 134 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 LEU 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 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: 9.9990 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 137 optimal weight: 0.0040 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 369 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1316 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14975 Z= 0.143 Angle : 0.627 9.480 20232 Z= 0.300 Chirality : 0.043 0.189 2395 Planarity : 0.004 0.054 2578 Dihedral : 9.586 157.752 2113 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.71 % Allowed : 18.21 % Favored : 80.08 % 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: -3.64 (0.17), residues: 1875 helix: -2.96 (0.14), residues: 861 sheet: -1.46 (0.37), residues: 187 loop : -1.83 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.005 0.001 HIS B 429 PHE 0.018 0.001 PHE D 297 TYR 0.009 0.001 TYR E 340 ARG 0.004 0.000 ARG F 284 *********************** 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 143 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.3389 (tmm) cc_final: 0.2142 (tmm) REVERT: B 61 MET cc_start: 0.0381 (tpp) cc_final: -0.0513 (tpt) REVERT: B 96 MET cc_start: 0.3323 (ptt) cc_final: 0.3098 (ptt) REVERT: B 364 MET cc_start: -0.0370 (ttp) cc_final: -0.0856 (ptp) REVERT: C 76 LYS cc_start: 0.0996 (ptpt) cc_final: 0.0709 (ptpp) REVERT: C 113 MET cc_start: 0.1535 (tpt) cc_final: 0.0763 (ttt) REVERT: D 330 ARG cc_start: 0.4334 (mtp85) cc_final: 0.1870 (mtp85) REVERT: E 320 MET cc_start: -0.0055 (tpt) cc_final: -0.0525 (tpt) REVERT: F 41 GLN cc_start: 0.4612 (tp40) cc_final: 0.3559 (tp40) REVERT: F 90 MET cc_start: 0.1848 (tmm) cc_final: 0.1260 (tmm) REVERT: F 113 MET cc_start: 0.0272 (ptp) cc_final: -0.0132 (ptt) REVERT: F 320 MET cc_start: 0.0762 (ptt) cc_final: -0.0783 (mtt) REVERT: F 382 MET cc_start: -0.1276 (mtm) cc_final: -0.1736 (mtm) REVERT: F 404 GLN cc_start: -0.0415 (OUTLIER) cc_final: -0.4395 (tm-30) outliers start: 27 outliers final: 8 residues processed: 140 average time/residue: 0.2643 time to fit residues: 55.8914 Evaluate side-chains 115 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 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 E residue 16 VAL Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.0060 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- 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** B 18 HIS B 241 HIS ** 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1368 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14975 Z= 0.134 Angle : 0.620 11.388 20232 Z= 0.287 Chirality : 0.042 0.172 2395 Planarity : 0.003 0.048 2578 Dihedral : 9.054 141.229 2113 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.78 % Allowed : 19.10 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.18), residues: 1875 helix: -2.35 (0.15), residues: 872 sheet: -1.29 (0.36), residues: 197 loop : -1.49 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 283 HIS 0.003 0.001 HIS B 429 PHE 0.022 0.001 PHE C 300 TYR 0.007 0.001 TYR E 446 ARG 0.010 0.000 ARG E 18 *********************** 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 137 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.3361 (tmm) cc_final: 0.2007 (tmm) REVERT: B 61 MET cc_start: 0.0802 (tpp) cc_final: 0.0557 (tpt) REVERT: B 96 MET cc_start: 0.3576 (ptt) cc_final: 0.3262 (ptt) REVERT: B 113 MET cc_start: 0.1740 (OUTLIER) cc_final: 0.0244 (tpt) REVERT: B 364 MET cc_start: -0.0327 (ttp) cc_final: -0.0810 (ptp) REVERT: C 96 MET cc_start: 0.3975 (mmm) cc_final: 0.3720 (mpp) REVERT: C 113 MET cc_start: 0.1760 (tpt) cc_final: 0.0887 (ttt) REVERT: C 364 MET cc_start: 0.3422 (mtt) cc_final: 0.0800 (ttp) REVERT: D 62 MET cc_start: 0.4296 (tpp) cc_final: 0.3926 (mmp) REVERT: E 320 MET cc_start: -0.0008 (tpt) cc_final: -0.0441 (tpt) REVERT: F 41 GLN cc_start: 0.4568 (tp40) cc_final: 0.3398 (tp40) REVERT: F 65 GLU cc_start: -0.2299 (OUTLIER) cc_final: -0.3135 (mm-30) REVERT: F 90 MET cc_start: 0.1643 (tmm) cc_final: 0.1038 (tmm) REVERT: F 113 MET cc_start: -0.0119 (ptp) cc_final: -0.0486 (ptt) REVERT: F 320 MET cc_start: 0.0365 (ptt) cc_final: -0.1086 (mtt) REVERT: F 382 MET cc_start: -0.1265 (mtm) cc_final: -0.1822 (mtm) outliers start: 28 outliers final: 14 residues processed: 132 average time/residue: 0.2726 time to fit residues: 54.2443 Evaluate side-chains 118 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 113 MET 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 323 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 403 ILE 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: 0.6980 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 163 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 380 GLN C 241 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 329 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1645 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14975 Z= 0.186 Angle : 0.672 10.897 20232 Z= 0.316 Chirality : 0.044 0.352 2395 Planarity : 0.004 0.048 2578 Dihedral : 8.833 118.739 2113 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.47 % Allowed : 19.54 % Favored : 77.98 % 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: -2.68 (0.18), residues: 1875 helix: -1.93 (0.16), residues: 853 sheet: -1.13 (0.36), residues: 195 loop : -1.59 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.010 0.001 HIS B 305 PHE 0.017 0.002 PHE A 329 TYR 0.012 0.001 TYR E 446 ARG 0.005 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 155 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.3244 (tmm) cc_final: 0.1643 (tmm) REVERT: B 61 MET cc_start: 0.0880 (tpp) cc_final: 0.0642 (tpt) REVERT: B 113 MET cc_start: 0.2011 (OUTLIER) cc_final: 0.0583 (tpt) REVERT: B 364 MET cc_start: -0.0213 (ttp) cc_final: -0.0659 (ptt) REVERT: C 113 MET cc_start: 0.1652 (tpt) cc_final: 0.0651 (ttt) REVERT: C 364 MET cc_start: 0.3403 (mtt) cc_final: 0.0742 (ttp) REVERT: C 371 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.3132 (ttt) REVERT: D 62 MET cc_start: 0.4432 (tpp) cc_final: 0.4167 (mmp) REVERT: D 346 ILE cc_start: 0.1559 (OUTLIER) cc_final: 0.1146 (mt) REVERT: E 320 MET cc_start: 0.0020 (tpt) cc_final: -0.0249 (tpt) REVERT: E 326 MET cc_start: 0.1977 (OUTLIER) cc_final: 0.1777 (ptt) REVERT: F 41 GLN cc_start: 0.4779 (tp40) cc_final: 0.3743 (tm-30) REVERT: F 65 GLU cc_start: -0.2485 (OUTLIER) cc_final: -0.3328 (mm-30) REVERT: F 113 MET cc_start: -0.0798 (ptp) cc_final: -0.1363 (ptt) REVERT: F 320 MET cc_start: 0.0217 (ptt) cc_final: -0.1268 (mtt) REVERT: F 382 MET cc_start: -0.1070 (mtm) cc_final: -0.1589 (mtm) outliers start: 39 outliers final: 21 residues processed: 149 average time/residue: 0.2636 time to fit residues: 59.0864 Evaluate side-chains 132 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 303 GLU 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 323 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 295 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 393 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 370 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 Chi-restraints excluded: chain F residue 403 ILE 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: 1.9990 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1678 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14975 Z= 0.151 Angle : 0.631 9.476 20232 Z= 0.295 Chirality : 0.043 0.233 2395 Planarity : 0.003 0.045 2578 Dihedral : 8.663 114.342 2113 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.84 % Allowed : 21.19 % Favored : 76.97 % 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: -2.34 (0.18), residues: 1875 helix: -1.56 (0.16), residues: 852 sheet: -1.02 (0.39), residues: 181 loop : -1.52 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 283 HIS 0.006 0.001 HIS C 305 PHE 0.019 0.001 PHE C 300 TYR 0.012 0.001 TYR F 340 ARG 0.005 0.000 ARG C 357 *********************** 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 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.1237 (mmp) cc_final: 0.1030 (mmp) REVERT: A 364 MET cc_start: 0.2028 (pmm) cc_final: -0.0216 (ttm) REVERT: A 371 MET cc_start: 0.3127 (tmm) cc_final: 0.1531 (tmm) REVERT: B 113 MET cc_start: 0.1954 (OUTLIER) cc_final: 0.0486 (tpt) REVERT: B 364 MET cc_start: -0.0057 (ttp) cc_final: -0.0587 (ptt) REVERT: C 102 TYR cc_start: 0.2760 (m-80) cc_final: 0.0269 (m-80) REVERT: C 113 MET cc_start: 0.1693 (tpt) cc_final: 0.0554 (ttt) REVERT: C 364 MET cc_start: 0.3558 (mtt) cc_final: 0.0940 (ttp) REVERT: D 62 MET cc_start: 0.4651 (tpp) cc_final: 0.4406 (mmp) REVERT: D 346 ILE cc_start: 0.1573 (OUTLIER) cc_final: 0.1201 (mt) REVERT: E 326 MET cc_start: 0.1826 (OUTLIER) cc_final: 0.1542 (ptt) REVERT: F 41 GLN cc_start: 0.4853 (tp40) cc_final: 0.3826 (tm-30) REVERT: F 62 MET cc_start: 0.2589 (mtm) cc_final: 0.2344 (mtm) REVERT: F 65 GLU cc_start: -0.2304 (OUTLIER) cc_final: -0.3355 (mm-30) REVERT: F 320 MET cc_start: 0.0308 (ptt) cc_final: -0.1090 (mtt) REVERT: F 382 MET cc_start: -0.1137 (mtm) cc_final: -0.1650 (mtm) REVERT: F 404 GLN cc_start: 0.0191 (OUTLIER) cc_final: -0.4261 (tm-30) outliers start: 29 outliers final: 13 residues processed: 132 average time/residue: 0.2733 time to fit residues: 54.2745 Evaluate side-chains 126 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 MET 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 332 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 326 MET 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 245 HIS Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 404 GLN 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: 0.8980 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 181 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 332 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1859 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14975 Z= 0.180 Angle : 0.675 9.968 20232 Z= 0.317 Chirality : 0.043 0.228 2395 Planarity : 0.004 0.053 2578 Dihedral : 8.656 112.441 2113 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.09 % Allowed : 22.27 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.16 (0.18), residues: 1875 helix: -1.31 (0.17), residues: 840 sheet: -0.90 (0.40), residues: 174 loop : -1.55 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 283 HIS 0.004 0.001 HIS D 302 PHE 0.017 0.002 PHE C 300 TYR 0.010 0.001 TYR F 401 ARG 0.009 0.001 ARG E 330 *********************** 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 147 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.2165 (pmm) cc_final: 0.0524 (ttm) REVERT: B 364 MET cc_start: 0.0548 (ttp) cc_final: -0.0552 (ptt) REVERT: C 96 MET cc_start: 0.4160 (mpp) cc_final: 0.3633 (mpp) REVERT: C 102 TYR cc_start: 0.3615 (m-80) cc_final: 0.0974 (m-80) REVERT: C 113 MET cc_start: 0.2280 (tpt) cc_final: 0.0919 (ttt) REVERT: C 364 MET cc_start: 0.3427 (mtt) cc_final: 0.1008 (ttp) REVERT: D 346 ILE cc_start: 0.1786 (OUTLIER) cc_final: 0.1446 (mt) REVERT: E 320 MET cc_start: 0.1196 (tpt) cc_final: -0.0071 (tpt) REVERT: F 41 GLN cc_start: 0.4600 (tp40) cc_final: 0.3464 (tm-30) REVERT: F 62 MET cc_start: 0.2713 (mtm) cc_final: 0.2422 (mtm) REVERT: F 320 MET cc_start: 0.0331 (ptt) cc_final: -0.1398 (mtt) REVERT: F 382 MET cc_start: -0.1256 (mtm) cc_final: -0.1813 (mtm) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.2370 time to fit residues: 51.2036 Evaluate side-chains 134 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 295 VAL 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 323 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 326 MET 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 E residue 16 VAL Chi-restraints excluded: chain E residue 245 HIS Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3572 > 50: distance: 65 - 70: 30.301 distance: 70 - 71: 34.582 distance: 71 - 72: 55.992 distance: 72 - 73: 55.299 distance: 72 - 78: 38.781 distance: 74 - 75: 23.803 distance: 75 - 76: 26.502 distance: 75 - 77: 31.546 distance: 78 - 79: 4.538 distance: 79 - 80: 40.627 distance: 79 - 82: 47.710 distance: 80 - 81: 15.153 distance: 80 - 89: 42.456 distance: 83 - 85: 44.905 distance: 84 - 86: 51.317 distance: 85 - 87: 44.913 distance: 86 - 88: 14.235 distance: 87 - 88: 56.696 distance: 89 - 90: 12.087 distance: 91 - 92: 19.329 distance: 91 - 96: 45.125 distance: 93 - 95: 5.538 distance: 96 - 97: 21.850 distance: 97 - 98: 41.844 distance: 97 - 100: 54.667 distance: 98 - 99: 15.182 distance: 98 - 104: 38.232 distance: 100 - 101: 47.634 distance: 101 - 102: 4.541 distance: 101 - 103: 24.113 distance: 104 - 105: 42.291 distance: 105 - 106: 55.687 distance: 105 - 108: 38.737 distance: 106 - 107: 57.641 distance: 106 - 113: 69.040 distance: 108 - 109: 41.912 distance: 109 - 110: 48.081 distance: 110 - 111: 68.626 distance: 110 - 112: 36.153 distance: 113 - 114: 31.573 distance: 114 - 115: 50.191 distance: 114 - 117: 33.130 distance: 115 - 116: 55.847 distance: 115 - 120: 41.260 distance: 117 - 119: 39.796 distance: 120 - 121: 39.283 distance: 121 - 122: 68.363 distance: 121 - 124: 39.835 distance: 122 - 123: 62.453 distance: 122 - 130: 56.413 distance: 124 - 125: 26.239 distance: 125 - 126: 14.045 distance: 125 - 127: 26.271 distance: 126 - 128: 40.949 distance: 127 - 129: 23.754 distance: 128 - 129: 30.043 distance: 131 - 134: 51.628 distance: 132 - 133: 56.703 distance: 132 - 138: 17.863 distance: 134 - 135: 37.320 distance: 135 - 136: 39.404 distance: 136 - 137: 32.939 distance: 138 - 139: 20.744 distance: 139 - 140: 40.629 distance: 139 - 142: 57.974 distance: 140 - 141: 40.600 distance: 140 - 146: 56.864 distance: 142 - 143: 39.187 distance: 143 - 144: 44.695 distance: 143 - 145: 21.011 distance: 146 - 147: 39.326 distance: 147 - 148: 40.837 distance: 148 - 149: 42.845 distance: 148 - 154: 33.914 distance: 150 - 151: 19.865 distance: 151 - 152: 21.336 distance: 151 - 153: 18.648