Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 19 14:34:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/08_2023/6oay_20005_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.010 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 29 5.49 5 S 97 5.16 5 C 17025 2.51 5 N 4946 2.21 5 O 5164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C GLU 553": "OE1" <-> "OE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 657": "OE1" <-> "OE2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C ASP 723": "OD1" <-> "OD2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C GLU 787": "OE1" <-> "OE2" Residue "C GLU 788": "OE1" <-> "OE2" Residue "C GLU 798": "OE1" <-> "OE2" Residue "C GLU 805": "OE1" <-> "OE2" Residue "C GLU 826": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 395": "OD1" <-> "OD2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F GLU 535": "OE1" <-> "OE2" Residue "F ASP 578": "OD1" <-> "OD2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 626": "OD1" <-> "OD2" Residue "F GLU 627": "OE1" <-> "OE2" Residue "F GLU 636": "OE1" <-> "OE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 733": "OD1" <-> "OD2" Residue "F PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 815": "NH1" <-> "NH2" Residue "F GLU 826": "OE1" <-> "OE2" Residue "F GLU 850": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 326": "OD1" <-> "OD2" Residue "E PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E ASP 395": "OD1" <-> "OD2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E ASP 533": "OD1" <-> "OD2" Residue "E GLU 535": "OE1" <-> "OE2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "E GLU 557": "OE1" <-> "OE2" Residue "E GLU 575": "OE1" <-> "OE2" Residue "E GLU 627": "OE1" <-> "OE2" Residue "E GLU 658": "OE1" <-> "OE2" Residue "E TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 680": "OE1" <-> "OE2" Residue "E ASP 696": "OD1" <-> "OD2" Residue "E PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 739": "OE1" <-> "OE2" Residue "E PHE 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 758": "OD1" <-> "OD2" Residue "E GLU 787": "OE1" <-> "OE2" Residue "E TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 826": "OE1" <-> "OE2" Residue "E ASP 851": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ASP 395": "OD1" <-> "OD2" Residue "D GLU 535": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D GLU 575": "OE1" <-> "OE2" Residue "D GLU 627": "OE1" <-> "OE2" Residue "D PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D ASP 701": "OD1" <-> "OD2" Residue "D ASP 708": "OD1" <-> "OD2" Residue "D GLU 731": "OE1" <-> "OE2" Residue "D ASP 733": "OD1" <-> "OD2" Residue "D TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 739": "OE1" <-> "OE2" Residue "D PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 788": "OE1" <-> "OE2" Residue "D TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 797": "OD1" <-> "OD2" Residue "D ARG 815": "NH1" <-> "NH2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 627": "OE1" <-> "OE2" Residue "B ASP 633": "OD1" <-> "OD2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 758": "OD1" <-> "OD2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 785": "NH1" <-> "NH2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 797": "OD1" <-> "OD2" Residue "B GLU 805": "OE1" <-> "OE2" Residue "B TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 851": "OD1" <-> "OD2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ASP 677": "OD1" <-> "OD2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 696": "OD1" <-> "OD2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A GLU 792": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 27261 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "F" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4426 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 20, 'TRANS': 537} Chain breaks: 3 Chain: "E" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "D" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "B" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4510 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 22, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4340 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 2 Chain: "P" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.60, per 1000 atoms: 0.50 Number of scatterers: 27261 At special positions: 0 Unit cell: (141.384, 144.48, 116.616, 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 97 16.00 P 29 15.00 O 5164 8.00 N 4946 7.00 C 17025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 4.0 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 25 sheets defined 33.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 187 through 193 Processing helix chain 'C' and resid 213 through 224 removed outlier: 4.210A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.078A pdb=" N ASP C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.556A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 No H-bonds generated for 'chain 'C' and resid 318 through 321' Processing helix chain 'C' and resid 327 through 330 No H-bonds generated for 'chain 'C' and resid 327 through 330' Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.505A pdb=" N ALA C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.700A pdb=" N ALA C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 405 removed outlier: 3.635A pdb=" N ASP C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.582A pdb=" N VAL C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 577 through 588 removed outlier: 3.775A pdb=" N ALA C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 640 through 644 removed outlier: 3.652A pdb=" N VAL C 643 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 644 " --> pdb=" O HIS C 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 640 through 644' Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 751 through 754 No H-bonds generated for 'chain 'C' and resid 751 through 754' Processing helix chain 'C' and resid 768 through 784 removed outlier: 3.972A pdb=" N SER C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 782 " --> pdb=" O GLN C 778 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 784 " --> pdb=" O LYS C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 828 through 830 No H-bonds generated for 'chain 'C' and resid 828 through 830' Processing helix chain 'F' and resid 168 through 172 Processing helix chain 'F' and resid 184 through 194 removed outlier: 3.599A pdb=" N ILE F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 removed outlier: 4.664A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG F 222 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 removed outlier: 4.964A pdb=" N VAL F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.680A pdb=" N ARG F 320 " --> pdb=" O LEU F 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 316 through 320' Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 343 through 351 removed outlier: 3.865A pdb=" N LEU F 350 " --> pdb=" O THR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 374 No H-bonds generated for 'chain 'F' and resid 371 through 374' Processing helix chain 'F' and resid 386 through 392 removed outlier: 4.340A pdb=" N ILE F 391 " --> pdb=" O PRO F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 403 removed outlier: 3.850A pdb=" N SER F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 544 removed outlier: 3.778A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 558 No H-bonds generated for 'chain 'F' and resid 555 through 558' Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 751 through 753 No H-bonds generated for 'chain 'F' and resid 751 through 753' Processing helix chain 'F' and resid 771 through 774 No H-bonds generated for 'chain 'F' and resid 771 through 774' Processing helix chain 'F' and resid 780 through 783 No H-bonds generated for 'chain 'F' and resid 780 through 783' Processing helix chain 'F' and resid 814 through 820 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 184 through 192 Processing helix chain 'E' and resid 212 through 224 removed outlier: 4.180A pdb=" N VAL E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 297 through 304 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 343 through 361 removed outlier: 3.637A pdb=" N ALA E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 374 removed outlier: 3.500A pdb=" N VAL E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 379 No H-bonds generated for 'chain 'E' and resid 376 through 379' Processing helix chain 'E' and resid 388 through 405 removed outlier: 3.643A pdb=" N LEU E 393 " --> pdb=" O LYS E 389 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 396 " --> pdb=" O ASP E 392 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 543 removed outlier: 3.725A pdb=" N GLU E 538 " --> pdb=" O ALA E 534 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 539 " --> pdb=" O GLU E 535 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 583 through 586 No H-bonds generated for 'chain 'E' and resid 583 through 586' Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.517A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 623 Processing helix chain 'E' and resid 642 through 647 removed outlier: 4.097A pdb=" N VAL E 647 " --> pdb=" O SER E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 684 through 694 removed outlier: 3.639A pdb=" N ILE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLN E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL E 693 " --> pdb=" O ILE E 689 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 694 " --> pdb=" O LEU E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 726 No H-bonds generated for 'chain 'E' and resid 723 through 726' Processing helix chain 'E' and resid 753 through 756 No H-bonds generated for 'chain 'E' and resid 753 through 756' Processing helix chain 'E' and resid 768 through 787 removed outlier: 4.026A pdb=" N SER E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN E 776 " --> pdb=" O ALA E 772 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 777 " --> pdb=" O SER E 773 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 781 " --> pdb=" O ILE E 777 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'E' and resid 815 through 824 removed outlier: 3.550A pdb=" N GLN E 822 " --> pdb=" O LYS E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 834 removed outlier: 3.756A pdb=" N GLN E 831 " --> pdb=" O ASN E 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 213 through 223 removed outlier: 4.337A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.029A pdb=" N ASP D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.720A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 304' Processing helix chain 'D' and resid 318 through 321 No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.683A pdb=" N ALA D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 360 removed outlier: 3.711A pdb=" N LEU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.814A pdb=" N VAL D 371 " --> pdb=" O PRO D 368 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA D 372 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 390 through 406 Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.574A pdb=" N ALA D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 removed outlier: 3.542A pdb=" N LEU D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 574 through 588 removed outlier: 3.982A pdb=" N ALA D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 622 removed outlier: 3.965A pdb=" N CYS D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 616 " --> pdb=" O THR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 641 through 645 removed outlier: 3.726A pdb=" N ARG D 645 " --> pdb=" O SER D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 684 through 693 removed outlier: 4.196A pdb=" N ILE D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 691 " --> pdb=" O PHE D 687 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 693 " --> pdb=" O ILE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 725 No H-bonds generated for 'chain 'D' and resid 722 through 725' Processing helix chain 'D' and resid 737 through 744 removed outlier: 4.181A pdb=" N VAL D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 754 No H-bonds generated for 'chain 'D' and resid 751 through 754' Processing helix chain 'D' and resid 768 through 778 removed outlier: 3.530A pdb=" N SER D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 777 " --> pdb=" O SER D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 removed outlier: 3.525A pdb=" N LYS D 784 " --> pdb=" O LYS D 780 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D 785 " --> pdb=" O ARG D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 806 Processing helix chain 'D' and resid 815 through 824 removed outlier: 3.685A pdb=" N GLN D 822 " --> pdb=" O LYS D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 833 removed outlier: 3.800A pdb=" N GLN D 832 " --> pdb=" O PRO D 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 171 No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.692A pdb=" N GLN B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.504A pdb=" N ASP B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 318 through 321 No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.575A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.553A pdb=" N SER B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.525A pdb=" N LEU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 removed outlier: 4.139A pdb=" N GLU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 574 through 588 removed outlier: 3.650A pdb=" N ASP B 578 " --> pdb=" O ASN B 574 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 582 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 583 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 641 through 645 removed outlier: 3.550A pdb=" N SER B 644 " --> pdb=" O HIS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 687 through 694 removed outlier: 4.368A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 769 through 780 removed outlier: 3.733A pdb=" N ALA B 775 " --> pdb=" O ILE B 771 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 777 " --> pdb=" O SER B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 removed outlier: 3.885A pdb=" N SER B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 Proline residue: B 816 - end of helix removed outlier: 3.838A pdb=" N ARG B 819 " --> pdb=" O PRO B 816 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 821 " --> pdb=" O LYS B 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.775A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 267' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 343 through 351 removed outlier: 4.016A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.682A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 533 through 544 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.836A pdb=" N ILE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.668A pdb=" N ALA A 617 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 619 " --> pdb=" O CYS A 615 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 692 through 695 No H-bonds generated for 'chain 'A' and resid 692 through 695' Processing helix chain 'A' and resid 736 through 739 No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 751 through 756 removed outlier: 4.062A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 756' Processing helix chain 'A' and resid 769 through 774 removed outlier: 3.780A pdb=" N SER A 773 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 817 through 820 Processing sheet with id= A, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.460A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 236 through 238 Processing sheet with id= C, first strand: chain 'C' and resid 759 through 762 removed outlier: 6.381A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 698 through 700 Processing sheet with id= E, first strand: chain 'C' and resid 793 through 795 removed outlier: 6.071A pdb=" N ILE C 844 " --> pdb=" O HIS C 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 334 through 338 removed outlier: 7.285A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY F 206 " --> pdb=" O GLY F 312 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR F 314 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 202 through 205 removed outlier: 6.576A pdb=" N GLN E 334 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE E 205 " --> pdb=" O GLN E 334 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL E 336 " --> pdb=" O ILE E 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 236 through 239 removed outlier: 6.503A pdb=" N HIS E 309 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 277 " --> pdb=" O HIS E 309 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL E 311 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 759 through 762 removed outlier: 6.103A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 698 through 700 Processing sheet with id= K, first strand: chain 'E' and resid 792 through 795 removed outlier: 3.645A pdb=" N VAL E 856 " --> pdb=" O ARG E 845 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 852 " --> pdb=" O ASN E 849 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 237 through 239 removed outlier: 6.416A pdb=" N ILE D 274 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS D 309 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 277 " --> pdb=" O HIS D 309 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 759 through 763 removed outlier: 3.547A pdb=" N THR D 717 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 698 through 700 Processing sheet with id= O, first strand: chain 'D' and resid 792 through 795 Processing sheet with id= P, first strand: chain 'B' and resid 202 through 206 removed outlier: 6.502A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.706A pdb=" N ILE B 274 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 240 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE B 276 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 313 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 713 through 718 removed outlier: 6.114A pdb=" N GLY B 599 " --> pdb=" O VAL B 714 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET B 716 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE B 601 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER B 718 " --> pdb=" O PHE B 601 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE B 603 " --> pdb=" O SER B 718 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU B 759 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 604 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 761 " --> pdb=" O LEU B 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 631 through 633 removed outlier: 5.791A pdb=" N LEU B 675 " --> pdb=" O ILE B 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'B' and resid 698 through 700 Processing sheet with id= U, first strand: chain 'B' and resid 793 through 795 removed outlier: 7.390A pdb=" N ILE B 844 " --> pdb=" O HIS B 794 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.564A pdb=" N GLN A 334 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 203 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 601 through 604 removed outlier: 7.011A pdb=" N GLU A 759 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU A 604 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 761 " --> pdb=" O LEU A 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'A' and resid 674 through 676 Processing sheet with id= Y, first strand: chain 'A' and resid 698 through 700 469 hydrogen bonds defined for protein. 1359 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: 8.83 Time building geometry restraints manager: 11.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 9575 1.35 - 1.50: 7650 1.50 - 1.65: 10272 1.65 - 1.80: 134 1.80 - 1.95: 41 Bond restraints: 27672 Sorted by residual: bond pdb=" CA GLY D 743 " pdb=" C GLY D 743 " ideal model delta sigma weight residual 1.514 1.449 0.065 1.41e-02 5.03e+03 2.12e+01 bond pdb=" CG1 ILE D 571 " pdb=" CD1 ILE D 571 " ideal model delta sigma weight residual 1.513 1.383 0.130 3.90e-02 6.57e+02 1.10e+01 bond pdb=" C ARG C 815 " pdb=" N PRO C 816 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.526 1.472 0.054 1.70e-02 3.46e+03 1.02e+01 bond pdb=" CB ARG C 196 " pdb=" CG ARG C 196 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.87e+00 ... (remaining 27667 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.46: 475 104.46 - 112.34: 13339 112.34 - 120.23: 12907 120.23 - 128.11: 10491 128.11 - 135.99: 187 Bond angle restraints: 37399 Sorted by residual: angle pdb=" N GLN B 321 " pdb=" CA GLN B 321 " pdb=" C GLN B 321 " ideal model delta sigma weight residual 111.36 100.66 10.70 1.09e+00 8.42e-01 9.64e+01 angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 111.88 104.54 7.34 1.06e+00 8.90e-01 4.79e+01 angle pdb=" N GLU C 324 " pdb=" CA GLU C 324 " pdb=" C GLU C 324 " ideal model delta sigma weight residual 114.16 104.62 9.54 1.48e+00 4.57e-01 4.16e+01 angle pdb=" C TYR C 734 " pdb=" CA TYR C 734 " pdb=" CB TYR C 734 " ideal model delta sigma weight residual 116.54 110.29 6.25 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C VAL D 336 " pdb=" N PHE D 337 " pdb=" CA PHE D 337 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 ... (remaining 37394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 16352 34.18 - 68.36: 579 68.36 - 102.55: 41 102.55 - 136.73: 4 136.73 - 170.91: 2 Dihedral angle restraints: 16978 sinusoidal: 7166 harmonic: 9812 Sorted by residual: dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 110.91 -170.91 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual 300.00 177.66 122.33 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O2A ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PA ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 60.83 -120.83 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 16975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3905 0.115 - 0.229: 300 0.229 - 0.344: 31 0.344 - 0.458: 2 0.458 - 0.573: 2 Chirality restraints: 4240 Sorted by residual: chirality pdb=" CB ILE C 323 " pdb=" CA ILE C 323 " pdb=" CG1 ILE C 323 " pdb=" CG2 ILE C 323 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" CB VAL C 228 " pdb=" CA VAL C 228 " pdb=" CG1 VAL C 228 " pdb=" CG2 VAL C 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CB VAL C 531 " pdb=" CA VAL C 531 " pdb=" CG1 VAL C 531 " pdb=" CG2 VAL C 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4237 not shown) Planarity restraints: 4870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 367 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO B 368 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 367 " -0.059 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO E 368 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 367 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO D 368 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 368 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 368 " -0.046 5.00e-02 4.00e+02 ... (remaining 4867 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 186 2.43 - 3.05: 15518 3.05 - 3.67: 42657 3.67 - 4.28: 65639 4.28 - 4.90: 106309 Nonbonded interactions: 230309 Sorted by model distance: nonbonded pdb=" O MET E 638 " pdb=" O GLU E 639 " model vdw 1.815 3.040 nonbonded pdb=" O ASP D 696 " pdb=" OD1 ASP D 696 " model vdw 2.092 3.040 nonbonded pdb=" O HIS D 747 " pdb=" OD1 ASN D 748 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR B 322 " pdb=" CB LEU B 329 " model vdw 2.196 3.440 nonbonded pdb=" CG MET E 638 " pdb=" OD2 ASP D 685 " model vdw 2.205 3.440 ... (remaining 230304 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 161 through 648 or resid 661 through 835)) selection = (chain 'B' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'C' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'D' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'E' and (resid 161 through 648 or resid 661 through 835)) selection = (chain 'F' and resid 161 through 835) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.930 Check model and map are aligned: 1.950 Set scattering table: 0.000 Process input model: 66.770 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.140 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.012 0.135 27672 Z= 0.798 Angle : 1.193 12.930 37399 Z= 0.651 Chirality : 0.070 0.573 4240 Planarity : 0.008 0.089 4870 Dihedral : 17.272 170.908 10646 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.89 % Favored : 89.61 % Rotamer Outliers : 1.36 % 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: -5.50 (0.11), residues: 3348 helix: -4.73 (0.06), residues: 1322 sheet: -3.00 (0.24), residues: 314 loop : -2.82 (0.13), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 536 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 569 average time/residue: 0.5129 time to fit residues: 426.9948 Evaluate side-chains 416 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 403 time to evaluate : 4.913 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3454 time to fit residues: 12.2769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 307 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN C 269 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 ASN C 688 ASN C 703 GLN C 776 GLN C 824 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 HIS F 711 ASN ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN F 824 GLN E 321 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN E 770 HIS D 192 GLN D 264 ASN D 334 GLN D 747 HIS D 778 GLN D 822 GLN D 823 GLN D 831 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 334 GLN ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 764 HIS B 857 GLN A 174 GLN A 573 GLN A 726 GLN A 770 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 27672 Z= 0.286 Angle : 0.710 8.036 37399 Z= 0.364 Chirality : 0.047 0.214 4240 Planarity : 0.006 0.070 4870 Dihedral : 9.934 176.644 3879 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.64 (0.12), residues: 3348 helix: -3.88 (0.09), residues: 1349 sheet: -2.73 (0.25), residues: 314 loop : -2.36 (0.14), residues: 1685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 456 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 37 residues processed: 508 average time/residue: 0.4416 time to fit residues: 338.8204 Evaluate side-chains 419 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 382 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2390 time to fit residues: 21.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 0.0070 chunk 256 optimal weight: 8.9990 chunk 209 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 247 optimal weight: 0.5980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 GLN ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN E 770 HIS D 703 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 297 ASN A 573 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 27672 Z= 0.280 Angle : 0.683 13.455 37399 Z= 0.340 Chirality : 0.047 0.231 4240 Planarity : 0.005 0.069 4870 Dihedral : 9.515 178.222 3879 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.98 (0.13), residues: 3348 helix: -3.23 (0.11), residues: 1335 sheet: -2.57 (0.26), residues: 313 loop : -2.05 (0.14), residues: 1700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 438 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 29 residues processed: 499 average time/residue: 0.4778 time to fit residues: 366.1102 Evaluate side-chains 417 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 388 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2694 time to fit residues: 19.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 88 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 HIS ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS D 281 HIS D 703 GLN ** D 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27672 Z= 0.190 Angle : 0.626 10.202 37399 Z= 0.312 Chirality : 0.045 0.203 4240 Planarity : 0.005 0.068 4870 Dihedral : 9.089 176.822 3879 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.81 % Favored : 93.07 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.49 (0.13), residues: 3348 helix: -2.69 (0.12), residues: 1341 sheet: -2.40 (0.27), residues: 319 loop : -1.87 (0.15), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 432 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 31 residues processed: 488 average time/residue: 0.4446 time to fit residues: 331.7033 Evaluate side-chains 430 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 399 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2579 time to fit residues: 19.4647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 243 optimal weight: 0.6980 chunk 135 optimal weight: 0.2980 chunk 279 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS D 309 HIS D 849 ASN B 620 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 27672 Z= 0.300 Angle : 0.660 8.173 37399 Z= 0.328 Chirality : 0.047 0.201 4240 Planarity : 0.005 0.068 4870 Dihedral : 9.032 176.590 3879 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.47 % Favored : 92.41 % Rotamer Outliers : 2.09 % 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: -3.28 (0.13), residues: 3348 helix: -2.47 (0.12), residues: 1348 sheet: -2.41 (0.27), residues: 308 loop : -1.78 (0.15), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 412 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 31 residues processed: 451 average time/residue: 0.4396 time to fit residues: 302.9248 Evaluate side-chains 416 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 385 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2568 time to fit residues: 19.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 192 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 327 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS B 582 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 27672 Z= 0.174 Angle : 0.602 7.741 37399 Z= 0.300 Chirality : 0.044 0.204 4240 Planarity : 0.004 0.066 4870 Dihedral : 8.701 177.918 3879 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.94 (0.14), residues: 3348 helix: -2.15 (0.13), residues: 1360 sheet: -2.24 (0.27), residues: 308 loop : -1.61 (0.15), residues: 1680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 434 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 24 residues processed: 470 average time/residue: 0.4494 time to fit residues: 321.6574 Evaluate side-chains 412 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 388 time to evaluate : 3.125 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3021 time to fit residues: 16.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 7.9990 chunk 36 optimal weight: 0.0040 chunk 186 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 204 optimal weight: 0.0970 chunk 199 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS D 794 HIS ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 27672 Z= 0.161 Angle : 0.594 8.085 37399 Z= 0.295 Chirality : 0.044 0.231 4240 Planarity : 0.004 0.065 4870 Dihedral : 8.512 178.296 3879 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer Outliers : 1.12 % 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: -2.73 (0.14), residues: 3348 helix: -1.96 (0.13), residues: 1381 sheet: -2.13 (0.28), residues: 308 loop : -1.49 (0.16), residues: 1659 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 427 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 14 residues processed: 447 average time/residue: 0.4587 time to fit residues: 311.8284 Evaluate side-chains 411 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 397 time to evaluate : 2.996 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2560 time to fit residues: 10.7665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 0.0020 chunk 98 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 27672 Z= 0.199 Angle : 0.607 7.917 37399 Z= 0.301 Chirality : 0.045 0.240 4240 Planarity : 0.004 0.064 4870 Dihedral : 8.489 179.664 3879 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer Outliers : 1.19 % 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: -2.64 (0.14), residues: 3348 helix: -1.89 (0.13), residues: 1384 sheet: -2.08 (0.29), residues: 283 loop : -1.46 (0.16), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 410 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 429 average time/residue: 0.4689 time to fit residues: 305.3501 Evaluate side-chains 414 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 397 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3402 time to fit residues: 14.4720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 7.9990 chunk 313 optimal weight: 0.0370 chunk 285 optimal weight: 0.4980 chunk 304 optimal weight: 8.9990 chunk 312 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 239 optimal weight: 0.0000 chunk 93 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 HIS ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 27672 Z= 0.161 Angle : 0.597 10.530 37399 Z= 0.296 Chirality : 0.045 0.252 4240 Planarity : 0.004 0.063 4870 Dihedral : 8.348 178.727 3879 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.24 % Favored : 93.61 % Rotamer Outliers : 0.59 % 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: -2.47 (0.14), residues: 3348 helix: -1.71 (0.13), residues: 1374 sheet: -2.04 (0.29), residues: 300 loop : -1.38 (0.16), residues: 1674 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 409 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 418 average time/residue: 0.4466 time to fit residues: 282.3172 Evaluate side-chains 411 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 402 time to evaluate : 3.399 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2657 time to fit residues: 9.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.0000 chunk 199 optimal weight: 0.3980 chunk 321 optimal weight: 0.3980 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 223 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 310 optimal weight: 0.9990 chunk 268 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN ** F 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 27672 Z= 0.154 Angle : 0.593 9.482 37399 Z= 0.293 Chirality : 0.045 0.265 4240 Planarity : 0.004 0.065 4870 Dihedral : 8.235 177.486 3879 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.39 % Favored : 93.46 % Rotamer Outliers : 0.35 % 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: -2.31 (0.14), residues: 3348 helix: -1.56 (0.14), residues: 1360 sheet: -2.05 (0.29), residues: 285 loop : -1.31 (0.16), residues: 1703 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 413 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 422 average time/residue: 0.4777 time to fit residues: 303.5593 Evaluate side-chains 396 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 392 time to evaluate : 2.987 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2394 time to fit residues: 5.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.5980 chunk 213 optimal weight: 0.0070 chunk 286 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 247 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 269 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 276 optimal weight: 0.0000 chunk 34 optimal weight: 0.0980 overall best weight: 0.0228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 778 GLN ** F 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.217396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168410 restraints weight = 33041.338| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.34 r_work: 0.3586 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 27672 Z= 0.138 Angle : 0.589 9.369 37399 Z= 0.292 Chirality : 0.044 0.267 4240 Planarity : 0.004 0.063 4870 Dihedral : 8.024 176.121 3879 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Rotamer Outliers : 0.52 % 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: -2.12 (0.14), residues: 3348 helix: -1.36 (0.14), residues: 1346 sheet: -1.93 (0.28), residues: 315 loop : -1.24 (0.16), residues: 1687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.68 seconds wall clock time: 126 minutes 3.93 seconds (7563.93 seconds total)