Starting phenix.real_space_refine on Tue Feb 20 07:27:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/02_2024/6oay_20005_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/02_2024/6oay_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_20005/02_2024/6oay_20005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/02_2024/6oay_20005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/02_2024/6oay_20005_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oay_20005/02_2024/6oay_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.88, per 1000 atoms: 0.51 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: 9.77 Conformation dependent library (CDL) restraints added in 4.9 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: 5.47 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: 8.00 Time building geometry restraints manager: 10.55 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: 16378 34.18 - 68.36: 629 68.36 - 102.55: 42 102.55 - 136.73: 4 136.73 - 170.91: 2 Dihedral angle restraints: 17055 sinusoidal: 7243 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 17052 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: 0.990 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: 0.020 Extract box with map and model: 4.990 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 67.300 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.970 ------------------------------------------------------------------------------- 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 : 17.599 170.908 10723 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 % Allowed : 13.64 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 543 HIS 0.017 0.002 HIS C 641 PHE 0.031 0.003 PHE D 337 TYR 0.025 0.003 TYR D 671 ARG 0.011 0.001 ARG D 789 *********************** 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 : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 TYR cc_start: 0.8331 (m-80) cc_final: 0.7936 (m-80) REVERT: C 283 MET cc_start: 0.8014 (ppp) cc_final: 0.7693 (ppp) REVERT: C 322 TYR cc_start: 0.6439 (t80) cc_final: 0.4151 (t80) REVERT: C 396 GLU cc_start: 0.7860 (pt0) cc_final: 0.7604 (tt0) REVERT: C 636 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8295 (mt-10) REVERT: C 657 GLU cc_start: 0.7384 (pm20) cc_final: 0.7081 (pm20) REVERT: C 669 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7396 (mtp85) REVERT: C 710 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8116 (mtt180) REVERT: C 728 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7355 (ttt-90) REVERT: C 734 TYR cc_start: 0.1722 (OUTLIER) cc_final: 0.1363 (t80) REVERT: C 750 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7616 (mmm160) REVERT: C 826 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7390 (mt-10) REVERT: F 258 ARG cc_start: 0.5149 (mmm160) cc_final: 0.4685 (tpp-160) REVERT: F 309 HIS cc_start: 0.5364 (t-170) cc_final: 0.4883 (m90) REVERT: F 337 PHE cc_start: 0.6825 (m-80) cc_final: 0.6020 (t80) REVERT: F 395 ASP cc_start: 0.5085 (m-30) cc_final: 0.4791 (m-30) REVERT: E 181 ILE cc_start: 0.7883 (tp) cc_final: 0.7397 (mm) REVERT: E 207 GLU cc_start: 0.7904 (tt0) cc_final: 0.7052 (mp0) REVERT: E 335 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8372 (mtmm) REVERT: E 359 LEU cc_start: 0.8713 (mm) cc_final: 0.8399 (mm) REVERT: E 584 ILE cc_start: 0.8586 (pt) cc_final: 0.8173 (mp) REVERT: E 661 TYR cc_start: 0.8520 (t80) cc_final: 0.7968 (t80) REVERT: E 756 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7072 (mtt180) REVERT: D 180 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8826 (t) REVERT: D 780 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8422 (mtmm) REVERT: D 792 GLU cc_start: 0.7168 (tt0) cc_final: 0.6832 (pt0) REVERT: B 252 ARG cc_start: 0.5412 (ttt90) cc_final: 0.4477 (ttp80) REVERT: B 641 HIS cc_start: 0.6481 (t-90) cc_final: 0.6059 (p90) REVERT: B 664 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6451 (mt-10) REVERT: B 705 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7179 (mtm-85) REVERT: B 750 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7036 (ttm170) REVERT: A 319 TYR cc_start: 0.5767 (t80) cc_final: 0.5386 (t80) REVERT: A 343 VAL cc_start: 0.6196 (t) cc_final: 0.5993 (t) REVERT: A 353 LEU cc_start: 0.7910 (tp) cc_final: 0.7662 (tt) REVERT: A 542 ARG cc_start: 0.5643 (mtp-110) cc_final: 0.5322 (mtt-85) REVERT: A 629 MET cc_start: 0.4792 (mmt) cc_final: 0.4426 (tpp) REVERT: A 710 ARG cc_start: 0.6903 (ttp80) cc_final: 0.6216 (tpt170) REVERT: A 802 LEU cc_start: -0.0280 (OUTLIER) cc_final: -0.0605 (pp) outliers start: 39 outliers final: 13 residues processed: 569 average time/residue: 0.4899 time to fit residues: 404.5014 Evaluate side-chains 419 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 403 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 734 TYR Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 856 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU 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: 1.9990 chunk 142 optimal weight: 0.9990 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: 1.0786 ------------------------------------------------------------------------------- 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 703 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 ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27672 Z= 0.244 Angle : 0.691 7.878 37399 Z= 0.353 Chirality : 0.047 0.211 4240 Planarity : 0.006 0.070 4870 Dihedral : 11.562 176.188 3982 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.53 % Favored : 92.35 % Rotamer: Outliers : 2.83 % Allowed : 18.07 % Favored : 79.10 % 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: -4.63 (0.12), residues: 3348 helix: -3.87 (0.09), residues: 1347 sheet: -2.71 (0.25), residues: 313 loop : -2.37 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 543 HIS 0.006 0.001 HIS B 641 PHE 0.024 0.002 PHE E 637 TYR 0.017 0.002 TYR B 322 ARG 0.011 0.000 ARG C 305 *********************** 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 543 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 462 time to evaluate : 3.141 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: C 170 GLU cc_start: 0.7818 (tt0) cc_final: 0.7557 (tt0) REVERT: C 251 TYR cc_start: 0.8113 (m-80) cc_final: 0.7901 (m-80) REVERT: C 279 GLU cc_start: 0.8120 (mp0) cc_final: 0.7476 (mt-10) REVERT: C 283 MET cc_start: 0.8058 (ppp) cc_final: 0.7653 (ppp) REVERT: C 322 TYR cc_start: 0.6361 (t80) cc_final: 0.4161 (t80) REVERT: C 669 ARG cc_start: 0.7796 (tpt170) cc_final: 0.7504 (mtp-110) REVERT: C 708 ASP cc_start: 0.7798 (t0) cc_final: 0.7439 (t0) REVERT: C 710 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7937 (mtt-85) REVERT: C 728 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6927 (ttt-90) REVERT: C 826 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7290 (mt-10) REVERT: F 199 LYS cc_start: 0.6025 (ptmt) cc_final: 0.5449 (pttm) REVERT: F 200 ASN cc_start: 0.6042 (p0) cc_final: 0.5561 (p0) REVERT: F 242 MET cc_start: 0.2584 (OUTLIER) cc_final: 0.2204 (mtt) REVERT: F 337 PHE cc_start: 0.6742 (m-80) cc_final: 0.5951 (t80) REVERT: F 355 GLU cc_start: 0.5630 (mp0) cc_final: 0.5386 (mp0) REVERT: F 687 PHE cc_start: 0.2040 (m-10) cc_final: 0.1764 (m-80) REVERT: E 207 GLU cc_start: 0.7841 (tt0) cc_final: 0.6833 (mp0) REVERT: E 320 ARG cc_start: 0.7311 (ttp-110) cc_final: 0.6974 (ttp80) REVERT: E 355 GLU cc_start: 0.7660 (mp0) cc_final: 0.7289 (mp0) REVERT: E 359 LEU cc_start: 0.8763 (mm) cc_final: 0.8445 (mm) REVERT: E 560 LEU cc_start: 0.7722 (mm) cc_final: 0.7414 (mm) REVERT: E 584 ILE cc_start: 0.8657 (pt) cc_final: 0.8270 (mp) REVERT: E 690 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8718 (tt) REVERT: E 756 ARG cc_start: 0.7361 (mmt180) cc_final: 0.7047 (mtt180) REVERT: E 794 HIS cc_start: 0.7866 (m90) cc_final: 0.7499 (m170) REVERT: D 180 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8762 (t) REVERT: D 344 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7044 (mm-30) REVERT: D 681 LYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2257 (mmpt) REVERT: D 750 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7251 (mtm110) REVERT: D 792 GLU cc_start: 0.7178 (tt0) cc_final: 0.6959 (pt0) REVERT: B 238 LEU cc_start: 0.9247 (mp) cc_final: 0.9035 (mt) REVERT: B 241 ASP cc_start: 0.7881 (p0) cc_final: 0.7669 (p0) REVERT: B 252 ARG cc_start: 0.5495 (ttt90) cc_final: 0.4793 (ttp80) REVERT: B 591 LEU cc_start: 0.6224 (mm) cc_final: 0.5881 (mm) REVERT: B 641 HIS cc_start: 0.6838 (t-90) cc_final: 0.6064 (p-80) REVERT: B 681 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7795 (mmtp) REVERT: B 705 ARG cc_start: 0.7658 (mtm180) cc_final: 0.6953 (mtm-85) REVERT: A 225 ASN cc_start: 0.6778 (m110) cc_final: 0.6111 (t0) REVERT: A 326 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5835 (m-30) REVERT: A 588 ARG cc_start: 0.5896 (mmt180) cc_final: 0.5305 (mtt180) REVERT: A 710 ARG cc_start: 0.6949 (ttp80) cc_final: 0.6336 (tpt170) REVERT: A 802 LEU cc_start: -0.0266 (OUTLIER) cc_final: -0.0617 (pp) outliers start: 81 outliers final: 38 residues processed: 519 average time/residue: 0.4445 time to fit residues: 347.3034 Evaluate side-chains 436 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 392 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 333 optimal weight: 0.0970 chunk 274 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 247 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 823 GLN F 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 778 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 297 ASN A 573 GLN A 711 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27672 Z= 0.204 Angle : 0.633 9.725 37399 Z= 0.319 Chirality : 0.045 0.221 4240 Planarity : 0.005 0.069 4870 Dihedral : 10.944 178.192 3975 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 3.49 % Allowed : 19.78 % Favored : 76.73 % 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: -3.94 (0.13), residues: 3348 helix: -3.19 (0.11), residues: 1345 sheet: -2.43 (0.27), residues: 307 loop : -2.07 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 543 HIS 0.010 0.001 HIS B 360 PHE 0.041 0.001 PHE B 753 TYR 0.018 0.001 TYR B 656 ARG 0.015 0.000 ARG C 705 *********************** 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 541 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 441 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 GLU cc_start: 0.7791 (tt0) cc_final: 0.7537 (tt0) REVERT: C 279 GLU cc_start: 0.8085 (mp0) cc_final: 0.7400 (mt-10) REVERT: C 321 GLN cc_start: 0.8128 (mt0) cc_final: 0.7746 (tm-30) REVERT: C 322 TYR cc_start: 0.6286 (t80) cc_final: 0.4041 (t80) REVERT: C 353 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8705 (mp) REVERT: C 657 GLU cc_start: 0.7355 (pm20) cc_final: 0.6960 (pm20) REVERT: C 658 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 669 ARG cc_start: 0.7783 (tpt170) cc_final: 0.7504 (mtp-110) REVERT: C 708 ASP cc_start: 0.7763 (t0) cc_final: 0.7459 (t0) REVERT: C 710 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8151 (mtt-85) REVERT: C 728 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6931 (ttt-90) REVERT: C 826 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7297 (mt-10) REVERT: F 200 ASN cc_start: 0.5890 (p0) cc_final: 0.5504 (p0) REVERT: F 242 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2302 (mtt) REVERT: F 337 PHE cc_start: 0.6765 (m-80) cc_final: 0.5969 (t80) REVERT: F 556 ARG cc_start: 0.2126 (tpp-160) cc_final: 0.1471 (tpm170) REVERT: F 634 MET cc_start: 0.7824 (mmm) cc_final: 0.7218 (mmm) REVERT: F 687 PHE cc_start: 0.2204 (m-10) cc_final: 0.1959 (m-80) REVERT: F 819 ARG cc_start: 0.6620 (tpt90) cc_final: 0.6141 (mmm-85) REVERT: E 181 ILE cc_start: 0.8067 (tp) cc_final: 0.7470 (mm) REVERT: E 207 GLU cc_start: 0.7929 (tt0) cc_final: 0.6968 (mp0) REVERT: E 320 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7135 (ttp80) REVERT: E 560 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7593 (mm) REVERT: E 584 ILE cc_start: 0.8533 (pt) cc_final: 0.8191 (mp) REVERT: E 690 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8805 (tt) REVERT: E 700 THR cc_start: 0.8642 (t) cc_final: 0.8429 (p) REVERT: E 705 ARG cc_start: 0.7547 (ptp-170) cc_final: 0.7253 (ptp90) REVERT: E 756 ARG cc_start: 0.7373 (mmt180) cc_final: 0.7095 (mtt180) REVERT: E 794 HIS cc_start: 0.7813 (m90) cc_final: 0.7500 (m-70) REVERT: D 344 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6988 (mm-30) REVERT: D 681 LYS cc_start: 0.2389 (OUTLIER) cc_final: 0.1707 (mmtt) REVERT: B 252 ARG cc_start: 0.5442 (ttt180) cc_final: 0.4758 (ttp-170) REVERT: B 591 LEU cc_start: 0.6220 (mm) cc_final: 0.5839 (mm) REVERT: B 629 MET cc_start: 0.8470 (ttp) cc_final: 0.8187 (ttp) REVERT: B 641 HIS cc_start: 0.6808 (t-90) cc_final: 0.5992 (p-80) REVERT: B 661 TYR cc_start: 0.7788 (t80) cc_final: 0.7565 (t80) REVERT: B 669 ARG cc_start: 0.7873 (ttt90) cc_final: 0.7616 (ttp80) REVERT: B 675 LEU cc_start: 0.8828 (tp) cc_final: 0.8620 (tt) REVERT: B 681 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7803 (mmtp) REVERT: A 225 ASN cc_start: 0.6698 (m110) cc_final: 0.6180 (t0) REVERT: A 242 MET cc_start: 0.5282 (tpp) cc_final: 0.4436 (tmm) REVERT: A 557 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 588 ARG cc_start: 0.6012 (mmt180) cc_final: 0.5346 (mtt180) REVERT: A 710 ARG cc_start: 0.6967 (ttp80) cc_final: 0.6347 (tpt170) REVERT: A 802 LEU cc_start: -0.0252 (OUTLIER) cc_final: -0.0647 (pp) outliers start: 100 outliers final: 48 residues processed: 513 average time/residue: 0.4274 time to fit residues: 334.3185 Evaluate side-chains 443 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 389 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU 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: 2.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 293 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 776 GLN ** 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 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS D 281 HIS D 309 HIS D 334 GLN D 620 ASN D 703 GLN D 778 GLN ** D 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27672 Z= 0.356 Angle : 0.690 9.464 37399 Z= 0.344 Chirality : 0.048 0.203 4240 Planarity : 0.005 0.069 4870 Dihedral : 10.915 177.008 3972 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 4.40 % Allowed : 21.35 % Favored : 74.25 % 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: -3.65 (0.13), residues: 3348 helix: -2.85 (0.11), residues: 1351 sheet: -2.41 (0.26), residues: 322 loop : -1.95 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 543 HIS 0.010 0.001 HIS B 360 PHE 0.035 0.002 PHE B 753 TYR 0.019 0.002 TYR B 656 ARG 0.011 0.000 ARG C 705 *********************** 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 538 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 412 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 GLU cc_start: 0.7913 (tt0) cc_final: 0.7612 (tt0) REVERT: C 201 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.7736 (p0) REVERT: C 279 GLU cc_start: 0.8140 (mp0) cc_final: 0.7505 (mt-10) REVERT: C 321 GLN cc_start: 0.8136 (mt0) cc_final: 0.7753 (tm-30) REVERT: C 322 TYR cc_start: 0.6370 (t80) cc_final: 0.4317 (t80) REVERT: C 657 GLU cc_start: 0.7389 (pm20) cc_final: 0.7072 (pm20) REVERT: C 669 ARG cc_start: 0.7911 (tpt170) cc_final: 0.7552 (mtp-110) REVERT: C 708 ASP cc_start: 0.7774 (t0) cc_final: 0.7420 (t0) REVERT: C 710 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8118 (mtt-85) REVERT: C 728 ARG cc_start: 0.7940 (mtt180) cc_final: 0.6912 (ttt-90) REVERT: C 826 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7324 (mt-10) REVERT: F 199 LYS cc_start: 0.5910 (ptmt) cc_final: 0.5296 (pttm) REVERT: F 200 ASN cc_start: 0.5952 (p0) cc_final: 0.5625 (p0) REVERT: F 235 ARG cc_start: 0.6128 (mtt180) cc_final: 0.5916 (mtp180) REVERT: F 242 MET cc_start: 0.2700 (OUTLIER) cc_final: 0.2398 (mtt) REVERT: F 337 PHE cc_start: 0.6584 (m-80) cc_final: 0.5774 (t80) REVERT: F 556 ARG cc_start: 0.2336 (tpp-160) cc_final: 0.1449 (tpm170) REVERT: F 562 MET cc_start: 0.2353 (ttt) cc_final: 0.1891 (ttp) REVERT: F 687 PHE cc_start: 0.2292 (m-10) cc_final: 0.2052 (m-80) REVERT: F 819 ARG cc_start: 0.6577 (tpt90) cc_final: 0.6064 (mmm-85) REVERT: E 181 ILE cc_start: 0.8198 (tp) cc_final: 0.7609 (mm) REVERT: E 207 GLU cc_start: 0.7942 (tt0) cc_final: 0.6861 (mp0) REVERT: E 322 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6802 (t80) REVERT: E 559 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8636 (tt) REVERT: E 560 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7751 (mm) REVERT: E 584 ILE cc_start: 0.8599 (pt) cc_final: 0.8211 (mp) REVERT: E 690 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8868 (tt) REVERT: E 700 THR cc_start: 0.8675 (t) cc_final: 0.8448 (p) REVERT: E 756 ARG cc_start: 0.7417 (mmt180) cc_final: 0.7119 (mtt180) REVERT: E 794 HIS cc_start: 0.7794 (m90) cc_final: 0.7410 (m90) REVERT: D 681 LYS cc_start: 0.2642 (OUTLIER) cc_final: 0.1895 (mmtt) REVERT: B 252 ARG cc_start: 0.5468 (ttt180) cc_final: 0.4647 (ttp-110) REVERT: B 316 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 591 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5878 (mm) REVERT: B 638 MET cc_start: 0.7656 (mmm) cc_final: 0.7434 (mpp) REVERT: B 641 HIS cc_start: 0.6580 (t-90) cc_final: 0.6048 (p90) REVERT: B 661 TYR cc_start: 0.7872 (t80) cc_final: 0.7531 (t80) REVERT: B 675 LEU cc_start: 0.8866 (tp) cc_final: 0.8623 (tt) REVERT: B 681 LYS cc_start: 0.8334 (mmtp) cc_final: 0.8037 (mmtp) REVERT: B 705 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7074 (mtm-85) REVERT: A 225 ASN cc_start: 0.6681 (m110) cc_final: 0.6206 (t0) REVERT: A 326 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5845 (m-30) REVERT: A 588 ARG cc_start: 0.6027 (mmt180) cc_final: 0.5379 (mtt180) REVERT: A 710 ARG cc_start: 0.6895 (ttp80) cc_final: 0.6396 (tpt170) REVERT: A 802 LEU cc_start: -0.0184 (OUTLIER) cc_final: -0.0596 (pp) outliers start: 126 outliers final: 80 residues processed: 499 average time/residue: 0.4270 time to fit residues: 326.1446 Evaluate side-chains 482 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 391 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 637 PHE Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 279 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 824 GLN ** F 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS D 849 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 824 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27672 Z= 0.249 Angle : 0.638 13.547 37399 Z= 0.318 Chirality : 0.046 0.202 4240 Planarity : 0.004 0.068 4870 Dihedral : 10.599 177.045 3972 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.38 % Favored : 92.50 % Rotamer: Outliers : 4.22 % Allowed : 22.40 % Favored : 73.38 % 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: -3.32 (0.13), residues: 3348 helix: -2.53 (0.12), residues: 1361 sheet: -2.41 (0.27), residues: 308 loop : -1.77 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 543 HIS 0.008 0.001 HIS B 360 PHE 0.032 0.001 PHE B 753 TYR 0.024 0.001 TYR B 656 ARG 0.007 0.000 ARG D 852 *********************** 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 532 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 411 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 170 GLU cc_start: 0.7821 (tt0) cc_final: 0.7526 (tt0) REVERT: C 201 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.7989 (p0) REVERT: C 279 GLU cc_start: 0.8039 (mp0) cc_final: 0.7411 (mt-10) REVERT: C 321 GLN cc_start: 0.8148 (mt0) cc_final: 0.7741 (tm-30) REVERT: C 322 TYR cc_start: 0.6275 (t80) cc_final: 0.4133 (t80) REVERT: C 550 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5996 (ttt180) REVERT: C 669 ARG cc_start: 0.7918 (tpt170) cc_final: 0.7554 (mtp-110) REVERT: C 708 ASP cc_start: 0.7712 (t0) cc_final: 0.7378 (t0) REVERT: C 710 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8065 (mtt-85) REVERT: C 826 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7279 (mt-10) REVERT: F 199 LYS cc_start: 0.5798 (ptmt) cc_final: 0.5200 (pttm) REVERT: F 200 ASN cc_start: 0.5964 (p0) cc_final: 0.5623 (p0) REVERT: F 242 MET cc_start: 0.2713 (OUTLIER) cc_final: 0.2428 (mtt) REVERT: F 337 PHE cc_start: 0.6627 (m-80) cc_final: 0.5761 (t80) REVERT: F 556 ARG cc_start: 0.2422 (tpp-160) cc_final: 0.1450 (tpm170) REVERT: F 562 MET cc_start: 0.2306 (ttt) cc_final: 0.1871 (ttp) REVERT: F 634 MET cc_start: 0.7885 (mmm) cc_final: 0.7537 (mmm) REVERT: F 687 PHE cc_start: 0.2379 (m-10) cc_final: 0.2140 (m-80) REVERT: F 819 ARG cc_start: 0.6705 (tpt90) cc_final: 0.6076 (mmm-85) REVERT: E 181 ILE cc_start: 0.8237 (tp) cc_final: 0.7587 (mm) REVERT: E 193 VAL cc_start: 0.8598 (p) cc_final: 0.8328 (t) REVERT: E 207 GLU cc_start: 0.7965 (tt0) cc_final: 0.6997 (mp0) REVERT: E 322 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6795 (t80) REVERT: E 559 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8582 (tp) REVERT: E 560 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7735 (mm) REVERT: E 584 ILE cc_start: 0.8562 (pt) cc_final: 0.8148 (mp) REVERT: E 656 TYR cc_start: 0.7523 (t80) cc_final: 0.7171 (t80) REVERT: E 690 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8839 (tt) REVERT: E 756 ARG cc_start: 0.7375 (mmt180) cc_final: 0.7067 (mtt180) REVERT: E 794 HIS cc_start: 0.7815 (m90) cc_final: 0.7433 (m90) REVERT: D 344 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7036 (mm-30) REVERT: D 681 LYS cc_start: 0.2434 (OUTLIER) cc_final: 0.1821 (mmtt) REVERT: B 212 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7481 (mtmm) REVERT: B 252 ARG cc_start: 0.5454 (ttt180) cc_final: 0.4744 (ttp-170) REVERT: B 591 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5837 (mm) REVERT: B 629 MET cc_start: 0.8468 (ttp) cc_final: 0.8166 (ttp) REVERT: B 641 HIS cc_start: 0.6553 (t-90) cc_final: 0.6027 (p90) REVERT: B 661 TYR cc_start: 0.7822 (t80) cc_final: 0.7549 (t80) REVERT: B 675 LEU cc_start: 0.8859 (tp) cc_final: 0.8639 (tt) REVERT: B 681 LYS cc_start: 0.8363 (mmtp) cc_final: 0.8014 (mmtp) REVERT: B 705 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7088 (mtm-85) REVERT: B 798 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.5195 (pt0) REVERT: A 242 MET cc_start: 0.5410 (mmp) cc_final: 0.4403 (mmm) REVERT: A 326 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5892 (m-30) REVERT: A 551 MET cc_start: 0.3593 (OUTLIER) cc_final: 0.3202 (mtp) REVERT: A 557 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6026 (tt0) REVERT: A 588 ARG cc_start: 0.5903 (mmt180) cc_final: 0.5271 (mtt180) REVERT: A 710 ARG cc_start: 0.6824 (ttp80) cc_final: 0.6318 (tpt170) REVERT: A 802 LEU cc_start: -0.0073 (OUTLIER) cc_final: -0.0496 (pp) outliers start: 121 outliers final: 74 residues processed: 496 average time/residue: 0.4455 time to fit residues: 335.8004 Evaluate side-chains 478 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 391 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 322 TYR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 776 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 HIS B 692 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 711 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.133 27672 Z= 0.638 Angle : 0.854 12.434 37399 Z= 0.421 Chirality : 0.055 0.292 4240 Planarity : 0.006 0.067 4870 Dihedral : 11.225 178.098 3970 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.77 % Favored : 90.02 % Rotamer: Outliers : 5.34 % Allowed : 22.51 % Favored : 72.16 % 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: -3.56 (0.13), residues: 3348 helix: -2.74 (0.11), residues: 1386 sheet: -2.53 (0.27), residues: 282 loop : -1.90 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 543 HIS 0.014 0.002 HIS B 360 PHE 0.030 0.003 PHE B 753 TYR 0.028 0.003 TYR B 322 ARG 0.007 0.001 ARG C 815 *********************** 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 537 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 384 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ILE cc_start: 0.3801 (OUTLIER) cc_final: 0.3595 (pt) REVERT: C 201 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8134 (p0) REVERT: C 321 GLN cc_start: 0.8221 (mt0) cc_final: 0.7800 (tm-30) REVERT: C 322 TYR cc_start: 0.6477 (t80) cc_final: 0.4418 (t80) REVERT: C 669 ARG cc_start: 0.8001 (tpt170) cc_final: 0.7631 (mtp-110) REVERT: C 710 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8179 (mtt-85) REVERT: C 826 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7332 (mt-10) REVERT: F 200 ASN cc_start: 0.5805 (p0) cc_final: 0.5434 (p0) REVERT: F 242 MET cc_start: 0.2964 (OUTLIER) cc_final: 0.2707 (mtt) REVERT: F 528 ARG cc_start: 0.6097 (mmt-90) cc_final: 0.5332 (mmm-85) REVERT: F 556 ARG cc_start: 0.2414 (tpp-160) cc_final: 0.1559 (tpm170) REVERT: F 634 MET cc_start: 0.7795 (mmm) cc_final: 0.6540 (mmm) REVERT: F 638 MET cc_start: -0.0935 (mmp) cc_final: -0.1504 (mmp) REVERT: F 687 PHE cc_start: 0.2531 (m-10) cc_final: 0.2275 (m-80) REVERT: F 797 ASP cc_start: 0.6348 (p0) cc_final: 0.6042 (p0) REVERT: E 207 GLU cc_start: 0.8066 (tt0) cc_final: 0.6942 (mp0) REVERT: E 260 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7985 (mmmm) REVERT: E 560 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7736 (mm) REVERT: E 661 TYR cc_start: 0.8379 (t80) cc_final: 0.8109 (t80) REVERT: E 690 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8884 (tt) REVERT: E 756 ARG cc_start: 0.7381 (mmt180) cc_final: 0.7019 (mtt180) REVERT: E 794 HIS cc_start: 0.7858 (m90) cc_final: 0.7417 (m170) REVERT: D 681 LYS cc_start: 0.2419 (OUTLIER) cc_final: 0.1881 (mmtt) REVERT: B 212 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7525 (mtmm) REVERT: B 252 ARG cc_start: 0.5367 (ttt180) cc_final: 0.4406 (ttp-110) REVERT: B 316 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8316 (tp) REVERT: B 641 HIS cc_start: 0.6691 (t-90) cc_final: 0.6385 (p-80) REVERT: B 681 LYS cc_start: 0.8426 (mmtp) cc_final: 0.8125 (mmtp) REVERT: B 705 ARG cc_start: 0.7796 (mtm180) cc_final: 0.6844 (mtm-85) REVERT: B 750 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7361 (ttm-80) REVERT: B 798 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5298 (pt0) REVERT: A 242 MET cc_start: 0.5452 (mmp) cc_final: 0.4413 (mmm) REVERT: A 326 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5851 (m-30) REVERT: A 588 ARG cc_start: 0.5951 (mmt180) cc_final: 0.5359 (mtt180) REVERT: A 710 ARG cc_start: 0.6794 (ttp80) cc_final: 0.6318 (tpt170) outliers start: 153 outliers final: 99 residues processed: 492 average time/residue: 0.4414 time to fit residues: 329.9283 Evaluate side-chains 477 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 369 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 800 LEU Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN 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: 0.8980 chunk 186 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 776 GLN ** 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 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 711 ASN A 806 ASN A 824 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27672 Z= 0.221 Angle : 0.654 14.279 37399 Z= 0.325 Chirality : 0.045 0.207 4240 Planarity : 0.005 0.067 4870 Dihedral : 10.675 179.651 3970 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.29 % Favored : 92.59 % Rotamer: Outliers : 3.87 % Allowed : 24.39 % Favored : 71.74 % 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: -3.17 (0.14), residues: 3348 helix: -2.34 (0.12), residues: 1372 sheet: -2.45 (0.28), residues: 284 loop : -1.72 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 543 HIS 0.008 0.001 HIS B 360 PHE 0.029 0.001 PHE B 753 TYR 0.026 0.001 TYR B 656 ARG 0.012 0.000 ARG D 750 *********************** 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 518 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 407 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 GLN cc_start: 0.8193 (mt0) cc_final: 0.7765 (tm-30) REVERT: C 322 TYR cc_start: 0.6293 (t80) cc_final: 0.4124 (t80) REVERT: C 570 VAL cc_start: 0.8933 (t) cc_final: 0.8695 (p) REVERT: C 669 ARG cc_start: 0.7943 (tpt170) cc_final: 0.7631 (mtp-110) REVERT: C 708 ASP cc_start: 0.7714 (t0) cc_final: 0.7365 (t0) REVERT: C 710 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8198 (mtt-85) REVERT: C 826 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7309 (mt-10) REVERT: F 199 LYS cc_start: 0.6095 (ptmt) cc_final: 0.5517 (pttm) REVERT: F 200 ASN cc_start: 0.5723 (p0) cc_final: 0.5370 (p0) REVERT: F 337 PHE cc_start: 0.7323 (m-80) cc_final: 0.5739 (t80) REVERT: F 528 ARG cc_start: 0.5967 (mmt-90) cc_final: 0.5313 (mmm-85) REVERT: F 556 ARG cc_start: 0.2444 (tpp-160) cc_final: 0.1449 (tpm170) REVERT: F 562 MET cc_start: 0.2216 (ttt) cc_final: 0.1664 (ttp) REVERT: F 616 LYS cc_start: 0.7195 (tttt) cc_final: 0.6915 (tttt) REVERT: F 634 MET cc_start: 0.7906 (mmm) cc_final: 0.7506 (mmm) REVERT: F 638 MET cc_start: -0.1760 (mmp) cc_final: -0.2377 (mmp) REVERT: F 687 PHE cc_start: 0.2368 (m-10) cc_final: 0.2155 (m-80) REVERT: F 797 ASP cc_start: 0.6267 (p0) cc_final: 0.5965 (p0) REVERT: E 207 GLU cc_start: 0.7886 (tt0) cc_final: 0.6855 (mp0) REVERT: E 560 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7672 (mm) REVERT: E 584 ILE cc_start: 0.8518 (pt) cc_final: 0.8172 (mp) REVERT: E 690 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8873 (tt) REVERT: E 756 ARG cc_start: 0.7402 (mmt180) cc_final: 0.7006 (mtt180) REVERT: E 794 HIS cc_start: 0.7801 (m90) cc_final: 0.7420 (m170) REVERT: D 166 ILE cc_start: 0.2260 (OUTLIER) cc_final: 0.1814 (mp) REVERT: D 344 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 681 LYS cc_start: 0.2206 (OUTLIER) cc_final: 0.1852 (mmtt) REVERT: B 212 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7506 (mtmm) REVERT: B 252 ARG cc_start: 0.5492 (ttt180) cc_final: 0.4775 (ttp-170) REVERT: B 585 ARG cc_start: 0.6564 (mtp180) cc_final: 0.6262 (mtp180) REVERT: B 638 MET cc_start: 0.7541 (mmm) cc_final: 0.7317 (mpp) REVERT: B 641 HIS cc_start: 0.6554 (t-90) cc_final: 0.6061 (p90) REVERT: B 681 LYS cc_start: 0.8397 (mmtp) cc_final: 0.8055 (mmtp) REVERT: B 705 ARG cc_start: 0.7760 (mtm180) cc_final: 0.6893 (mtm-85) REVERT: A 181 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6173 (tt) REVERT: A 242 MET cc_start: 0.5364 (mmp) cc_final: 0.4372 (mmm) REVERT: A 326 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.6072 (m-30) REVERT: A 557 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6254 (tt0) REVERT: A 588 ARG cc_start: 0.5800 (mmt180) cc_final: 0.5285 (mtt180) REVERT: A 710 ARG cc_start: 0.6827 (ttp80) cc_final: 0.6271 (tpt170) outliers start: 111 outliers final: 84 residues processed: 486 average time/residue: 0.4351 time to fit residues: 318.6289 Evaluate side-chains 479 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 389 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 256 optimal weight: 0.0670 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS E 776 GLN B 297 ASN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 824 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27672 Z= 0.214 Angle : 0.634 13.499 37399 Z= 0.314 Chirality : 0.045 0.241 4240 Planarity : 0.004 0.066 4870 Dihedral : 10.432 179.967 3970 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.35 % Favored : 92.53 % Rotamer: Outliers : 3.77 % Allowed : 24.84 % Favored : 71.39 % 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: -2.96 (0.14), residues: 3348 helix: -2.13 (0.13), residues: 1376 sheet: -2.40 (0.28), residues: 291 loop : -1.63 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 543 HIS 0.007 0.001 HIS B 360 PHE 0.028 0.001 PHE B 753 TYR 0.025 0.001 TYR B 656 ARG 0.010 0.000 ARG D 750 *********************** 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 521 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 413 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 321 GLN cc_start: 0.8194 (mt0) cc_final: 0.7741 (tm-30) REVERT: C 322 TYR cc_start: 0.6271 (t80) cc_final: 0.4122 (t80) REVERT: C 570 VAL cc_start: 0.8893 (t) cc_final: 0.8612 (p) REVERT: C 669 ARG cc_start: 0.7915 (tpt170) cc_final: 0.7520 (mtp-110) REVERT: C 708 ASP cc_start: 0.7666 (t0) cc_final: 0.7294 (t0) REVERT: C 710 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8041 (mtt-85) REVERT: C 826 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7243 (mt-10) REVERT: F 199 LYS cc_start: 0.6092 (ptmt) cc_final: 0.5513 (pttm) REVERT: F 200 ASN cc_start: 0.5709 (p0) cc_final: 0.5322 (p0) REVERT: F 238 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.4034 (tt) REVERT: F 309 HIS cc_start: 0.4409 (m90) cc_final: 0.4171 (m90) REVERT: F 337 PHE cc_start: 0.7286 (m-80) cc_final: 0.5741 (t80) REVERT: F 528 ARG cc_start: 0.5964 (mmt-90) cc_final: 0.5309 (mmm-85) REVERT: F 556 ARG cc_start: 0.2430 (tpp-160) cc_final: 0.1655 (tpm170) REVERT: F 562 MET cc_start: 0.2190 (ttt) cc_final: 0.1665 (ttp) REVERT: F 616 LYS cc_start: 0.7158 (tttt) cc_final: 0.6892 (tttt) REVERT: F 634 MET cc_start: 0.7847 (mmm) cc_final: 0.6657 (mmm) REVERT: E 207 GLU cc_start: 0.7957 (tt0) cc_final: 0.7006 (mp0) REVERT: E 252 ARG cc_start: 0.8016 (mpp-170) cc_final: 0.7690 (mtm-85) REVERT: E 560 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7601 (mm) REVERT: E 584 ILE cc_start: 0.8502 (pt) cc_final: 0.8159 (mp) REVERT: E 690 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8859 (tt) REVERT: E 756 ARG cc_start: 0.7365 (mmt180) cc_final: 0.6993 (mtt180) REVERT: E 794 HIS cc_start: 0.7787 (m90) cc_final: 0.7232 (m90) REVERT: D 166 ILE cc_start: 0.2490 (OUTLIER) cc_final: 0.2031 (mp) REVERT: D 344 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7056 (mm-30) REVERT: D 762 VAL cc_start: 0.7467 (t) cc_final: 0.7194 (m) REVERT: B 212 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7528 (mtmm) REVERT: B 252 ARG cc_start: 0.5467 (ttt180) cc_final: 0.4809 (ttp-170) REVERT: B 629 MET cc_start: 0.8496 (ttp) cc_final: 0.8182 (ttp) REVERT: B 638 MET cc_start: 0.7566 (mmm) cc_final: 0.7349 (mpp) REVERT: B 641 HIS cc_start: 0.6563 (t-90) cc_final: 0.6041 (p90) REVERT: B 681 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8071 (mmtp) REVERT: B 705 ARG cc_start: 0.7775 (mtm180) cc_final: 0.6889 (mtm-85) REVERT: B 798 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5240 (pt0) REVERT: A 242 MET cc_start: 0.5459 (mmp) cc_final: 0.4440 (mmm) REVERT: A 326 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.6095 (m-30) REVERT: A 557 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6338 (tt0) REVERT: A 588 ARG cc_start: 0.5769 (mmt180) cc_final: 0.5411 (mtt180) REVERT: A 710 ARG cc_start: 0.6838 (ttp80) cc_final: 0.6276 (tpt170) outliers start: 108 outliers final: 86 residues processed: 490 average time/residue: 0.4325 time to fit residues: 322.4761 Evaluate side-chains 475 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 383 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 334 GLN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 533 ASP Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 285 optimal weight: 0.3980 chunk 304 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 239 optimal weight: 0.0770 chunk 93 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 overall best weight: 1.6944 ------------------------------------------------------------------------------- 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 776 GLN ** 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 824 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 770 HIS ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27672 Z= 0.287 Angle : 0.661 13.238 37399 Z= 0.326 Chirality : 0.047 0.253 4240 Planarity : 0.005 0.066 4870 Dihedral : 10.395 179.415 3964 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.65 % Favored : 92.20 % Rotamer: Outliers : 3.91 % Allowed : 24.84 % Favored : 71.25 % 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: -2.90 (0.14), residues: 3348 helix: -2.09 (0.13), residues: 1379 sheet: -2.38 (0.28), residues: 293 loop : -1.58 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 543 HIS 0.007 0.001 HIS B 360 PHE 0.025 0.001 PHE B 753 TYR 0.036 0.001 TYR E 656 ARG 0.015 0.000 ARG D 750 *********************** 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 503 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 391 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 GLN cc_start: 0.8213 (mt0) cc_final: 0.7754 (tm-30) REVERT: C 322 TYR cc_start: 0.6319 (t80) cc_final: 0.4169 (t80) REVERT: C 570 VAL cc_start: 0.8929 (t) cc_final: 0.8656 (p) REVERT: C 669 ARG cc_start: 0.7923 (tpt170) cc_final: 0.7513 (mtp-110) REVERT: C 708 ASP cc_start: 0.7674 (t0) cc_final: 0.7296 (t0) REVERT: C 710 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8050 (mtt-85) REVERT: C 826 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7253 (mt-10) REVERT: F 199 LYS cc_start: 0.6098 (ptmt) cc_final: 0.5517 (pttm) REVERT: F 200 ASN cc_start: 0.5811 (p0) cc_final: 0.5466 (p0) REVERT: F 337 PHE cc_start: 0.7297 (m-80) cc_final: 0.5785 (t80) REVERT: F 528 ARG cc_start: 0.6220 (mmt-90) cc_final: 0.5439 (tpm170) REVERT: F 556 ARG cc_start: 0.2422 (tpp-160) cc_final: 0.1430 (tpm170) REVERT: F 562 MET cc_start: 0.2138 (ttt) cc_final: 0.1640 (ttp) REVERT: F 616 LYS cc_start: 0.7161 (tttt) cc_final: 0.6887 (tttt) REVERT: E 207 GLU cc_start: 0.7892 (tt0) cc_final: 0.6912 (mp0) REVERT: E 252 ARG cc_start: 0.7984 (mpp-170) cc_final: 0.7703 (mtm-85) REVERT: E 560 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7586 (mm) REVERT: E 584 ILE cc_start: 0.8516 (pt) cc_final: 0.8169 (mp) REVERT: E 690 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8859 (tt) REVERT: E 756 ARG cc_start: 0.7381 (mmt180) cc_final: 0.7074 (mtt180) REVERT: E 794 HIS cc_start: 0.7662 (m90) cc_final: 0.7201 (m170) REVERT: D 166 ILE cc_start: 0.2445 (OUTLIER) cc_final: 0.1973 (mp) REVERT: D 344 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 681 LYS cc_start: 0.2765 (OUTLIER) cc_final: 0.2328 (mmtt) REVERT: D 789 ARG cc_start: 0.8225 (mmm160) cc_final: 0.8024 (mmt180) REVERT: B 212 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7627 (mtmm) REVERT: B 252 ARG cc_start: 0.5473 (ttt180) cc_final: 0.4785 (ttp-170) REVERT: B 585 ARG cc_start: 0.6635 (mtp180) cc_final: 0.5815 (mmp-170) REVERT: B 629 MET cc_start: 0.8474 (ttp) cc_final: 0.8163 (ttp) REVERT: B 641 HIS cc_start: 0.6605 (t-90) cc_final: 0.6056 (p90) REVERT: B 681 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8084 (mmtp) REVERT: B 705 ARG cc_start: 0.7780 (mtm180) cc_final: 0.6917 (mtm-85) REVERT: B 798 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5284 (pt0) REVERT: A 242 MET cc_start: 0.5462 (mmp) cc_final: 0.4448 (mmm) REVERT: A 557 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6380 (tt0) REVERT: A 588 ARG cc_start: 0.5904 (mmt180) cc_final: 0.5415 (mtt180) REVERT: A 710 ARG cc_start: 0.6767 (ttp80) cc_final: 0.6261 (tpt170) outliers start: 112 outliers final: 89 residues processed: 477 average time/residue: 0.4352 time to fit residues: 317.8062 Evaluate side-chains 478 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 384 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 322 TYR Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 824 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 776 GLN ** 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 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27672 Z= 0.203 Angle : 0.633 12.852 37399 Z= 0.313 Chirality : 0.045 0.258 4240 Planarity : 0.004 0.066 4870 Dihedral : 10.118 177.408 3962 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 3.24 % Allowed : 25.30 % Favored : 71.46 % 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: -2.74 (0.14), residues: 3348 helix: -1.91 (0.13), residues: 1374 sheet: -2.32 (0.28), residues: 291 loop : -1.53 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 543 HIS 0.006 0.001 HIS B 360 PHE 0.027 0.001 PHE B 753 TYR 0.030 0.001 TYR E 656 ARG 0.015 0.000 ARG D 750 ********************** 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 494 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 401 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 GLN cc_start: 0.8177 (mt0) cc_final: 0.7705 (tm-30) REVERT: C 322 TYR cc_start: 0.6247 (t80) cc_final: 0.4050 (t80) REVERT: C 570 VAL cc_start: 0.8892 (t) cc_final: 0.8625 (p) REVERT: C 669 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7505 (mtp-110) REVERT: C 710 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8138 (mtt-85) REVERT: C 826 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7229 (mt-10) REVERT: F 199 LYS cc_start: 0.6074 (ptmt) cc_final: 0.5488 (pttm) REVERT: F 200 ASN cc_start: 0.5809 (p0) cc_final: 0.5482 (p0) REVERT: F 337 PHE cc_start: 0.7291 (m-80) cc_final: 0.5813 (t80) REVERT: F 528 ARG cc_start: 0.6194 (mmt-90) cc_final: 0.5456 (mmm-85) REVERT: F 556 ARG cc_start: 0.2596 (tpp-160) cc_final: 0.1394 (tpm170) REVERT: F 562 MET cc_start: 0.2213 (ttt) cc_final: 0.1698 (ttp) REVERT: F 616 LYS cc_start: 0.7146 (tttt) cc_final: 0.6891 (tttt) REVERT: F 819 ARG cc_start: 0.6607 (tpt90) cc_final: 0.6024 (mmm-85) REVERT: E 181 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7590 (mm) REVERT: E 207 GLU cc_start: 0.7914 (tt0) cc_final: 0.6908 (mp0) REVERT: E 252 ARG cc_start: 0.7945 (mpp-170) cc_final: 0.7712 (mtm-85) REVERT: E 560 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7543 (mm) REVERT: E 584 ILE cc_start: 0.8499 (pt) cc_final: 0.8132 (mp) REVERT: E 690 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8841 (tt) REVERT: E 794 HIS cc_start: 0.7594 (m90) cc_final: 0.7269 (m90) REVERT: D 166 ILE cc_start: 0.2146 (OUTLIER) cc_final: 0.1683 (mp) REVERT: D 344 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 681 LYS cc_start: 0.2732 (OUTLIER) cc_final: 0.2203 (mmtt) REVERT: D 742 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7877 (tp) REVERT: D 762 VAL cc_start: 0.7319 (t) cc_final: 0.7063 (m) REVERT: B 166 ILE cc_start: 0.8732 (mp) cc_final: 0.8461 (tt) REVERT: B 212 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7601 (mtmm) REVERT: B 252 ARG cc_start: 0.5451 (ttt180) cc_final: 0.4819 (ttp-170) REVERT: B 585 ARG cc_start: 0.6677 (mtp180) cc_final: 0.5930 (mmp-170) REVERT: B 641 HIS cc_start: 0.6592 (t-90) cc_final: 0.6049 (p90) REVERT: B 656 TYR cc_start: 0.8224 (t80) cc_final: 0.8015 (t80) REVERT: B 681 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8089 (mmtp) REVERT: B 705 ARG cc_start: 0.7758 (mtm180) cc_final: 0.6892 (mtm-85) REVERT: B 798 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.5221 (pt0) REVERT: A 242 MET cc_start: 0.5411 (mmp) cc_final: 0.4423 (mmm) REVERT: A 557 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6520 (tt0) REVERT: A 588 ARG cc_start: 0.5886 (mmt180) cc_final: 0.5288 (mtt180) REVERT: A 710 ARG cc_start: 0.6780 (ttp80) cc_final: 0.6276 (tpt170) outliers start: 93 outliers final: 80 residues processed: 471 average time/residue: 0.4460 time to fit residues: 317.6582 Evaluate side-chains 473 residues out of total 2866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 386 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 383 ASP Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 626 ASP Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 707 VAL Chi-restraints excluded: chain F residue 712 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain F residue 764 HIS Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 822 GLN Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 334 GLN Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 754 ILE Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 625 SER Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain D residue 701 ASP Chi-restraints excluded: chain D residue 737 MET Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 798 GLU Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 777 ILE 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: 1.9990 chunk 286 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 247 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 776 GLN ** 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 824 GLN E 334 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.210454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162397 restraints weight = 32859.085| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.31 r_work: 0.3478 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27672 Z= 0.241 Angle : 0.639 12.142 37399 Z= 0.316 Chirality : 0.046 0.263 4240 Planarity : 0.004 0.066 4870 Dihedral : 10.083 176.505 3962 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.41 % Favored : 92.44 % Rotamer: Outliers : 3.63 % Allowed : 24.98 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.14), residues: 3348 helix: -1.88 (0.13), residues: 1383 sheet: -2.36 (0.28), residues: 291 loop : -1.51 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 543 HIS 0.006 0.001 HIS B 360 PHE 0.025 0.001 PHE B 753 TYR 0.032 0.001 TYR E 656 ARG 0.013 0.000 ARG D 750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.94 seconds wall clock time: 122 minutes 5.00 seconds (7325.00 seconds total)